BLASTP 2.2.25+


Reference:
Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database
search programs", Nucleic Acids Res. 25:3389-3402.



Reference for composition-based statistics:
Alejandro A. Schäffer, L. Aravind, Thomas L. Madden, Sergei
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST
protein database searches with composition-based statistics and
other refinements", Nucleic Acids Res. 29:2994-3005.



Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF
excluding environmental samples from WGS projects
           15,229,318 sequences; 5,219,829,388 total letters



Query= Rv1020

Length=1234
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

gi|15608160|ref|NP_215536.1|  transcription-repair coupling facto...  2465    0.0  
gi|289442441|ref|ZP_06432185.1|  transcription-repair coupling fa...  2464    0.0  
gi|339631081|ref|YP_004722723.1|  transcription-repair coupling f...  2463    0.0  
gi|254550004|ref|ZP_05140451.1|  transcription-repair coupling fa...  2462    0.0  
gi|289761156|ref|ZP_06520534.1|  transcription-repair coupling fa...  2462    0.0  
gi|298524516|ref|ZP_07011925.1|  transcription-repair coupling fa...  2462    0.0  
gi|340626031|ref|YP_004744483.1|  putative transcription-repair c...  2462    0.0  
gi|289573660|ref|ZP_06453887.1|  transcription-repair coupling fa...  2461    0.0  
gi|240169894|ref|ZP_04748553.1|  transcription-repair coupling fa...  2131    0.0  
gi|336461334|gb|EGO40205.1|  transcription-repair coupling factor...  2117    0.0  
gi|41407085|ref|NP_959921.1|  hypothetical protein MAP0987 [Mycob...  2106    0.0  
gi|342861623|ref|ZP_08718269.1|  transcription-repair coupling fa...  2093    0.0  
gi|254774025|ref|ZP_05215541.1|  hypothetical protein MaviaA2_050...  2088    0.0  
gi|183984436|ref|YP_001852727.1|  transcription-repair coupling f...  2088    0.0  
gi|118619716|ref|YP_908048.1|  transcription-repair coupling fact...  2078    0.0  
gi|254819273|ref|ZP_05224274.1|  hypothetical protein MintA_05066...  2071    0.0  
gi|221229524|ref|YP_002502940.1|  putative transcription-repair c...  2035    0.0  
gi|15827046|ref|NP_301309.1|  transcription-repair coupling facto...  2034    0.0  
gi|296169893|ref|ZP_06851505.1|  transcription-repair coupling fa...  2031    0.0  
gi|126437189|ref|YP_001072880.1|  transcription-repair coupling f...  1946    0.0  
gi|108801209|ref|YP_641406.1|  transcription-repair coupling fact...  1943    0.0  
gi|120405727|ref|YP_955556.1|  transcription-repair coupling fact...  1912    0.0  
gi|118471657|ref|YP_889663.1|  transcription-repair coupling fact...  1892    0.0  
gi|333989623|ref|YP_004522237.1|  transcription-repair coupling f...  1884    0.0  
gi|315442986|ref|YP_004075865.1|  transcription-repair coupling f...  1866    0.0  
gi|145222538|ref|YP_001133216.1|  transcription-repair coupling f...  1864    0.0  
gi|169628250|ref|YP_001701899.1|  transcription-repair coupling f...  1740    0.0  
gi|226365233|ref|YP_002783016.1|  transcription-repair coupling f...  1658    0.0  
gi|111022724|ref|YP_705696.1|  transcription repair coupling fact...  1654    0.0  
gi|325676609|ref|ZP_08156287.1|  transcription-repair coupling fa...  1640    0.0  
gi|312138702|ref|YP_004006038.1|  transcription repair coupling f...  1639    0.0  
gi|229494982|ref|ZP_04388731.1|  transcription-repair coupling fa...  1628    0.0  
gi|226307788|ref|YP_002767748.1|  transcription-repair coupling f...  1626    0.0  
gi|54026849|ref|YP_121091.1|  putative transcription-repair coupl...  1617    0.0  
gi|296140872|ref|YP_003648115.1|  transcription-repair coupling f...  1588    0.0  
gi|289555197|ref|ZP_06444407.1|  LOW QUALITY PROTEIN: transcripti...  1572    0.0  
gi|289757102|ref|ZP_06516480.1|  LOW QUALITY PROTEIN: transcripti...  1541    0.0  
gi|343926966|ref|ZP_08766456.1|  transcription-repair coupling fa...  1535    0.0  
gi|262201520|ref|YP_003272728.1|  transcription-repair coupling f...  1518    0.0  
gi|333921138|ref|YP_004494719.1|  transcription-repair coupling f...  1506    0.0  
gi|326385186|ref|ZP_08206853.1|  transcription-repair coupling fa...  1493    0.0  
gi|134097431|ref|YP_001103092.1|  transcription-repair coupling f...  1429    0.0  
gi|256374814|ref|YP_003098474.1|  transcription-repair coupling f...  1419    0.0  
gi|319949680|ref|ZP_08023714.1|  transcription-repair coupling fa...  1415    0.0  
gi|302530260|ref|ZP_07282602.1|  transcription-repair coupling fa...  1405    0.0  
gi|300790028|ref|YP_003770319.1|  transcription-repair coupling f...  1390    0.0  
gi|340531704|gb|AEK46909.1|  transcription-repair coupling factor...  1389    0.0  
gi|257057197|ref|YP_003135029.1|  transcription-repair coupling f...  1377    0.0  
gi|25027590|ref|NP_737644.1|  putative transcription-repair coupl...  1377    0.0  
gi|259507006|ref|ZP_05749906.1|  transcription-repair coupling fa...  1375    0.0  


>gi|15608160|ref|NP_215536.1| transcription-repair coupling factor Mfd (TRCF) [Mycobacterium 
tuberculosis H37Rv]
 gi|15840448|ref|NP_335485.1| transcription-repair coupling factor [Mycobacterium tuberculosis 
CDC1551]
 gi|31792211|ref|NP_854704.1| transcription-repair coupling factor Mfd (TRCF) [Mycobacterium 
bovis AF2122/97]
 56 more sequence titles
 Length=1234

 Score = 2465 bits (6389),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1234/1234 (100%), Positives = 1234/1234 (100%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|289442441|ref|ZP_06432185.1| transcription-repair coupling factor mfd [Mycobacterium tuberculosis 
T46]
 gi|289753081|ref|ZP_06512459.1| transcription-repair coupling factor Mfd [Mycobacterium tuberculosis 
EAS054]
 gi|289415360|gb|EFD12600.1| transcription-repair coupling factor mfd [Mycobacterium tuberculosis 
T46]
 gi|289693668|gb|EFD61097.1| transcription-repair coupling factor Mfd [Mycobacterium tuberculosis 
EAS054]
Length=1234

 Score = 2464 bits (6385),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1233/1234 (99%), Positives = 1233/1234 (99%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGD VALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDTVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|339631081|ref|YP_004722723.1| transcription-repair coupling factor MFD [Mycobacterium africanum 
GM041182]
 gi|339330437|emb|CCC26102.1| putative transcription-repair coupling factor MFD (TRCF) [Mycobacterium 
africanum GM041182]
Length=1234

 Score = 2463 bits (6383),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1233/1234 (99%), Positives = 1233/1234 (99%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPA ESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAVESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|254550004|ref|ZP_05140451.1| transcription-repair coupling factor mfd [Mycobacterium tuberculosis 
'98-R604 INH-RIF-EM']
Length=1234

 Score = 2462 bits (6382),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1233/1234 (99%), Positives = 1234/1234 (100%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA+QHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAEQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|289761156|ref|ZP_06520534.1| transcription-repair coupling factor mfd [Mycobacterium tuberculosis 
GM 1503]
 gi|289708662|gb|EFD72678.1| transcription-repair coupling factor mfd [Mycobacterium tuberculosis 
GM 1503]
Length=1234

 Score = 2462 bits (6382),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1233/1234 (99%), Positives = 1233/1234 (99%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAA LIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAAHLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|298524516|ref|ZP_07011925.1| transcription-repair coupling factor [Mycobacterium tuberculosis 
94_M4241A]
 gi|298494310|gb|EFI29604.1| transcription-repair coupling factor [Mycobacterium tuberculosis 
94_M4241A]
Length=1234

 Score = 2462 bits (6381),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1233/1234 (99%), Positives = 1233/1234 (99%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGA RIRDVELVQMVADLIT
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGARRIRDVELVQMVADLIT  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|340626031|ref|YP_004744483.1| putative transcription-repair coupling factor MFD (TRCF) [Mycobacterium 
canettii CIPT 140010059]
 gi|340004221|emb|CCC43361.1| putative transcription-repair coupling factor MFD (TRCF) [Mycobacterium 
canettii CIPT 140010059]
Length=1234

 Score = 2462 bits (6380),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1231/1234 (99%), Positives = 1234/1234 (100%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDARLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEA+LPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEALLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLI+
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIS  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|289573660|ref|ZP_06453887.1| transcription-repair coupling factor mfd [Mycobacterium tuberculosis 
K85]
 gi|289538091|gb|EFD42669.1| transcription-repair coupling factor mfd [Mycobacterium tuberculosis 
K85]
Length=1234

 Score = 2461 bits (6378),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1232/1234 (99%), Positives = 1233/1234 (99%), Gaps = 0/1234 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG
Sbjct  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH
Sbjct  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD
Sbjct  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF
Sbjct  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG
Sbjct  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL
Sbjct  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGFVELDQ RAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA
Sbjct  361   GGSGFVELDQARAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP
Sbjct  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN
Sbjct  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV
Sbjct  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER
Sbjct  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET
Sbjct  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF
Sbjct  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV
Sbjct  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELV+MVADLIT
Sbjct  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVEMVADLIT  1200

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234
             ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP
Sbjct  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP  1234


>gi|240169894|ref|ZP_04748553.1| transcription-repair coupling factor Mfd (TrcF) [Mycobacterium 
kansasii ATCC 12478]
Length=1238

 Score = 2131 bits (5522),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1074/1244 (87%), Positives = 1147/1244 (93%), Gaps = 19/1244 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG A  DTPIAGLVELAL+APTFQQL+ RA  RPD+LTL+ PASARL VASALAR G
Sbjct  1     MTAPGAASPDTPIAGLVELALAAPTFQQLIARASDRPDDLTLVGPASARLFVASALARLG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDL AEL+GV G AVA+ PSWETLPHERLSPGVDTVG RL+ LRRLA+
Sbjct  61    PLLVVTATGREADDLTAELQGVLGGAVAVFPSWETLPHERLSPGVDTVGARLLVLRRLAY  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGP L VVVT+VRSLLQPMTPQLG  EPL L+VG E  FDGV+ARLVELAYTRVD
Sbjct  121   PDDARLGPSLRVVVTAVRSLLQPMTPQLGRQEPLALSVGQEIDFDGVIARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILD+FAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEI++ TLVA 
Sbjct  181   MVGRRGEFAVRGGILDVFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIEVDTLVAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLW--S  298
             ACRELLL++DVR RAA+LAA+HPAAE+ VTGS SDMLAKLAEGI VDGMEA+LPVL    
Sbjct  241   ACRELLLTDDVRVRAAELAAQHPAAENAVTGSVSDMLAKLAEGIPVDGMEALLPVLHPAQ  300

Query  299   DG----HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTA-ENQA  353
             DG    H LLTDQLP+GTPVL+CDPEK+RTRAADLI+TGREFLEASWSVAALG+  ENQA
Sbjct  301   DGANGAHTLLTDQLPEGTPVLLCDPEKIRTRAADLIKTGREFLEASWSVAALGSGPENQA  360

Query  354   PVDVEQLGGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDE  413
             PVDVEQLGGSGF ELD+V  AA  +GHPWWTLSQLS E+ +ELDVR +PSARGHQRDID 
Sbjct  361   PVDVEQLGGSGFAELDEVHTAATGSGHPWWTLSQLSGEAVLELDVRPSPSARGHQRDIDG  420

Query  414   IFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPL  473
             IFAMLRAH++TGGYA +VAPGTGTAHR+VERL+ESD PA MLDPG  PK G+VGV +GPL
Sbjct  421   IFAMLRAHVSTGGYAVMVAPGTGTAHRMVERLTESDIPAAMLDPGATPKLGLVGVFKGPL  480

Query  474   RDGVIIPG----ANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQH  529
              DG+++PG    A+LVV+TE+DLTGSRV+AAEGKRLAAKRRN VDPLALTAGDLVVHDQH
Sbjct  481   HDGIVVPGVVPGADLVVVTESDLTGSRVTAAEGKRLAAKRRNTVDPLALTAGDLVVHDQH  540

Query  530   GIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPA  589
             GIGRFVEMVERTVGGARREYLVLEYAS+KRGG   +TDKLYVPMDSLDQLSRYVGGQAPA
Sbjct  541   GIGRFVEMVERTVGGARREYLVLEYASSKRGG-QNSTDKLYVPMDSLDQLSRYVGGQAPA  599

Query  590   LSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTE  649
             LSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQAS GHAF+PDTPWQAE+EDAFGFTE
Sbjct  600   LSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASSGHAFAPDTPWQAEMEDAFGFTE  659

Query  650   TVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLL  709
             TVDQLTAI+EVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLL
Sbjct  660   TVDQLTAIQEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLL  719

Query  710   ADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWK  769
             ADQHLQTF +RMSGFPVT+KGLSRFTDAAESR VIDGLADGSVDIVIGTHRLLQTGVRWK
Sbjct  720   ADQHLQTFAQRMSGFPVTVKGLSRFTDAAESRTVIDGLADGSVDIVIGTHRLLQTGVRWK  779

Query  770   DLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE  829
             DLGLVVVDEEQRFGVEHKEHIKS+RTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE
Sbjct  780   DLGLVVVDEEQRFGVEHKEHIKSMRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE  839

Query  830   ERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVA  889
             ERYPVLTYVGPHDDKQ+AAALRRELLRDGQAFYVHNRVSSID AAA VRELVPEARVVVA
Sbjct  840   ERYPVLTYVGPHDDKQVAAALRRELLRDGQAFYVHNRVSSIDRAAAHVRELVPEARVVVA  899

Query  890   HGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRG  949
             HGQMPE+LLE TVQ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRG
Sbjct  900   HGQMPEELLERTVQGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRG  959

Query  950   RVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGI  1009
             RVGRSRERGYAYFLYPPQ PLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLG+
Sbjct  960   RVGRSRERGYAYFLYPPQAPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGV  1019

Query  1010  EQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPD  1069
             EQSGHVAGVGFDLYVRLVGEA+E    AYRAAADG+TV TAEEPKD+RIDLPVDAHLPPD
Sbjct  1020  EQSGHVAGVGFDLYVRLVGEAVE----AYRAAADGKTVTTAEEPKDLRIDLPVDAHLPPD  1075

Query  1070  YIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGI  1129
             YI SDRLRLE YRRLAAASSD EVAAVV+EL DRYG LPEPARRL AVARLRLLCR SGI
Sbjct  1076  YIGSDRLRLEAYRRLAAASSDNEVAAVVEELNDRYGPLPEPARRLVAVARLRLLCRDSGI  1135

Query  1130  TDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDV  1189
             T+V+A SAATVRL+P+TLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGG+GAPRIRDV
Sbjct  1136  TEVSAPSAATVRLAPMTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGIGAPRIRDV  1195

Query  1190  ELVQMVADLITALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQ  1233
             ELVQMVADL+TALAG P++ IGIT+ S  G+D   R  + KER+
Sbjct  1196  ELVQMVADLVTALAGIPQKDIGITSSS--GDDA-DRPVSSKERR  1236


>gi|336461334|gb|EGO40205.1| transcription-repair coupling factor Mfd [Mycobacterium avium 
subsp. paratuberculosis S397]
Length=1219

 Score = 2117 bits (5486),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1056/1226 (87%), Positives = 1133/1226 (93%), Gaps = 9/1226 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG A  +TPIAGLVELAL+APTFQQL+  A   P +L+L+ PAS RL VASALAR G
Sbjct  1     MTAPGAARPETPIAGLVELALTAPTFQQLIDTAAASPADLSLVGPASTRLFVASALARLG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDL AELRGV GDAVA+ PSWETLPHERLSPGVDTVG RL  LRRLAH
Sbjct  61    PLLVVTATGREADDLTAELRGVVGDAVAVFPSWETLPHERLSPGVDTVGARLTVLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPL VVVT+VRSLLQPMTPQLG++EP+TL+VG E  F+ V+ARLVELAY+RVD
Sbjct  121   PDDARLGPPLQVVVTAVRSLLQPMTPQLGLVEPVTLSVGQEIEFEHVIARLVELAYSRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILD+F PTAEHPVRVEFWGDE++EMRMFSVADQRSIPEI + T++A 
Sbjct  181   MVGRRGEFAVRGGILDVFPPTAEHPVRVEFWGDEVSEMRMFSVADQRSIPEIAVDTVIAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELLL+EDVRARAA+LAA+HPA+E  +TGS SDMLAK+A+GIAVDGMEA+LPVL    
Sbjct  241   PCRELLLTEDVRARAAELAAQHPASEPAITGSVSDMLAKIADGIAVDGMEALLPVLRPGK  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
               LLTDQL D TPVL+CDPEK+RTRAADLI+TGREFLEASWSVAALGT ENQAP+DVEQL
Sbjct  301   QVLLTDQLADRTPVLLCDPEKIRTRAADLIKTGREFLEASWSVAALGTLENQAPIDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGF ELD+VRAAA R GHPWWTLSQLSDESA+ELDVRAAPSARGHQ DID IFAMLRA
Sbjct  361   GGSGFAELDEVRAAAVRGGHPWWTLSQLSDESAVELDVRAAPSARGHQHDIDGIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H++TGG+AA+VAPGTGTAHRVVERL+E DTPA ML+ G AP+ GVVGVL+GPL DG++IP
Sbjct  421   HVSTGGHAAVVAPGTGTAHRVVERLAECDTPAAMLESGAAPRAGVVGVLKGPLHDGIVIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRV+A EGKRLAAKRRN VDPLALTAGDLVVHDQHGIGRFVEM ER
Sbjct  481   GANLVVITETDLTGSRVAAVEGKRLAAKRRNTVDPLALTAGDLVVHDQHGIGRFVEMTER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYAS+KRGGG   +DKLYVPMDSLDQLSRYVGGQAPALS+LGGSDWAN
Sbjct  541   TVGGARREYLVLEYASSKRGGG---SDKLYVPMDSLDQLSRYVGGQAPALSKLGGSDWAN  597

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAE+EDAFG+TETVDQLTAI EV
Sbjct  598   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAEMEDAFGYTETVDQLTAITEV  657

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K+DMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +R
Sbjct  658   KSDMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTDR  717

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTDAAESRAVI+GLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  718   MAGFPVTVKGLSRFTDAAESRAVIEGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  777

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  778   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  837

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQ+AAALRRELLRDGQAFYVHNRVSSID AAARVRELVPEARVVVAHGQMPE+ LE 
Sbjct  838   HDDKQVAAALRRELLRDGQAFYVHNRVSSIDRAAARVRELVPEARVVVAHGQMPEERLER  897

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  898   TVQGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  957

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPP  PLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLG+EQSGHVAGVGF
Sbjct  958   YFLYPPHAPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGVEQSGHVAGVGF  1017

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADGQTV TAEEPKDVRIDLPVDAHLPPDYIASDRLRLE 
Sbjct  1018  DLYVRLVGEAVE----AYRAAADGQTVTTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEA  1073

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAA SD E+ AVV+EL DRYGALPEPA RL AVARLRLLCR +GIT+V+A SAATV
Sbjct  1074  YRRLAAAGSDDEIDAVVEELVDRYGALPEPALRLVAVARLRLLCRAAGITEVSAPSAATV  1133

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSP+TLPDSAQVRLKRMYP A YRATT+TVQVPIPRAGG+GAPR+RDVELVQMVA+L+T
Sbjct  1134  RLSPITLPDSAQVRLKRMYPAASYRATTSTVQVPIPRAGGVGAPRLRDVELVQMVANLVT  1193

Query  1201  ALAGKPRQHIGITNP--SPPGEDGRG  1224
             AL GKP+  +G   P  +   E+GRG
Sbjct  1194  ALQGKPQTDVGTGTPVAAMASEEGRG  1219


>gi|41407085|ref|NP_959921.1| hypothetical protein MAP0987 [Mycobacterium avium subsp. paratuberculosis 
K-10]
 gi|41395436|gb|AAS03304.1| Mfd [Mycobacterium avium subsp. paratuberculosis K-10]
Length=1221

 Score = 2106 bits (5457),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1055/1228 (86%), Positives = 1133/1228 (93%), Gaps = 11/1228 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG A  +TPIAGLVELAL+APTFQQL+  A   P +L+L+ PAS RL VASALAR G
Sbjct  1     MTAPGAARPETPIAGLVELALTAPTFQQLIDTAAASPADLSLVGPASTRLFVASALARLG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDL AELRGV GDAVA+ PSWETLPHERLSPGVDTVG RL  LRRLAH
Sbjct  61    PLLVVTATGREADDLTAELRGVVGDAVAVFPSWETLPHERLSPGVDTVGARLTVLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPL VVVT+VRSLLQPMTPQLG++EP+TL+VG E  F+ V+ARLVELAY+RVD
Sbjct  121   PDDARLGPPLQVVVTAVRSLLQPMTPQLGLVEPVTLSVGQEIEFEHVIARLVELAYSRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILD+F PTAEHPVRVEFWGDE++EMRMFSVADQRSIPEI + T+++ 
Sbjct  181   MVGRRGEFAVRGGILDVFPPTAEHPVRVEFWGDEVSEMRMFSVADQRSIPEIAVDTVISV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELLL+EDVRARAA+LAA+HPA+E  +TGS SDMLAK+A+GIAVDGMEA+LPVL    
Sbjct  241   PCRELLLTEDVRARAAELAAQHPASEPAITGSVSDMLAKIADGIAVDGMEALLPVLRPGK  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
               LLTDQL D TPVL+CDPEK+RTRAADLI+TGREFLEASWSVAALGT ENQAP+DVEQL
Sbjct  301   QVLLTDQLADRTPVLLCDPEKIRTRAADLIKTGREFLEASWSVAALGTLENQAPIDVEQL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGF ELD+VRAAA R GHPWWTLSQLSDESA+ELDVRAAPSARGHQ DID IFAMLRA
Sbjct  361   GGSGFAELDEVRAAAVRGGHPWWTLSQLSDESAVELDVRAAPSARGHQHDIDGIFAMLRA  420

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H++TGG+AA+VAPGTGTAHRVVERL+E DTPA ML+ G AP+ GVVGVL+GPL DG++IP
Sbjct  421   HVSTGGHAAVVAPGTGTAHRVVERLAECDTPAAMLESGAAPRAGVVGVLKGPLHDGIVIP  480

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVVITETDLTGSRV+A EGKRLAAKRRN VDPLALTAGDLVVHDQHGIGRFVEM ER
Sbjct  481   GANLVVITETDLTGSRVAAVEGKRLAAKRRNTVDPLALTAGDLVVHDQHGIGRFVEMTER  540

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYAS+KRGGG   +DKLYVPMDSLDQLSRYVGGQAPALS+LGGSDWAN
Sbjct  541   TVGGARREYLVLEYASSKRGGG---SDKLYVPMDSLDQLSRYVGGQAPALSKLGGSDWAN  597

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAE+EDAFG+TETVDQLTAI EV
Sbjct  598   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAEMEDAFGYTETVDQLTAITEV  657

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K+DMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +R
Sbjct  658   KSDMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTDR  717

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTDAAESRAVI+GLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  718   MAGFPVTVKGLSRFTDAAESRAVIEGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  777

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  778   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  837

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEAR--VVVAHGQMPEDLL  898
             HDDKQ+AAALRRELLRDGQAFYVHNRVSSID AAARVRELVPEAR  VVVAHGQMPE+ L
Sbjct  838   HDDKQVAAALRRELLRDGQAFYVHNRVSSIDRAAARVRELVPEARVVVVVAHGQMPEERL  897

Query  899   ETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERG  958
             E TVQ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERG
Sbjct  898   ERTVQGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERG  957

Query  959   YAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGV  1018
             YAYFLYPP  PLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLG+EQSGHVAGV
Sbjct  958   YAYFLYPPHAPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGVEQSGHVAGV  1017

Query  1019  GFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRL  1078
             GFDLYVRLVGEA+E    AYRAAADGQTV TAEEPKDVRIDLPVDAHLPPDYIASDRLRL
Sbjct  1018  GFDLYVRLVGEAVE----AYRAAADGQTVTTAEEPKDVRIDLPVDAHLPPDYIASDRLRL  1073

Query  1079  EGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAA  1138
             E YRRLAAA SD E+ AVV+EL DRYGALPEPA RL AVARLRLLCR +GIT+V+A SAA
Sbjct  1074  EAYRRLAAAGSDDEIDAVVEELVDRYGALPEPALRLVAVARLRLLCRAAGITEVSAPSAA  1133

Query  1139  TVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADL  1198
             TVRLSP+TLPDSAQVRLKRMYP A YRATT+TVQVPIPRAGG+GAPR+RDVELVQMVA+L
Sbjct  1134  TVRLSPITLPDSAQVRLKRMYPAASYRATTSTVQVPIPRAGGVGAPRLRDVELVQMVANL  1193

Query  1199  ITALAGKPRQHIGITNP--SPPGEDGRG  1224
             +TAL GKP+  +G   P  +   E+GRG
Sbjct  1194  VTALQGKPQTDVGTGTPVAAMASEEGRG  1221


>gi|342861623|ref|ZP_08718269.1| transcription-repair coupling factor [Mycobacterium colombiense 
CECT 3035]
 gi|342130757|gb|EGT84053.1| transcription-repair coupling factor [Mycobacterium colombiense 
CECT 3035]
Length=1221

 Score = 2093 bits (5422),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1038/1214 (86%), Positives = 1118/1214 (93%), Gaps = 10/1214 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG A  +TPIAGLVELAL+APTFQQL+  A   P EL L+ PASARL VASALAR G
Sbjct  5     MTAPGAARPETPIAGLVELALTAPTFQQLIDSASASPAELHLVGPASARLFVASALARLG  64

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDL AELRGVFGD+VA+ PSWETLPHERLSPGVDTVG RL  LRRLAH
Sbjct  65    PLLVVTATGREADDLTAELRGVFGDSVAVFPSWETLPHERLSPGVDTVGARLTVLRRLAH  124

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDD++LGPPL VVVT+VRSLLQPMTPQLG++EP+TL VG E  F+GV+ RL ELAYTRVD
Sbjct  125   PDDSRLGPPLQVVVTAVRSLLQPMTPQLGLVEPVTLNVGTEIEFEGVITRLAELAYTRVD  184

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILD+F PTAEHPVRVEFWGDE++EMRMFSVADQRSIPEI++ TL+A 
Sbjct  185   MVGRRGEFAVRGGILDVFPPTAEHPVRVEFWGDEVSEMRMFSVADQRSIPEIEVDTLIAV  244

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELLL+++VR RAA+LAARH + E  +TGS SDMLAK+ EGI+VDGMEA+LPVL    
Sbjct  245   PCRELLLTDEVRERAAELAARHRSTEPAITGSVSDMLAKIGEGISVDGMEALLPVLRPGE  304

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             H LLTDQL + TPVL+CDPEKVRTRAADLI+TG EFLEASWSVAALGT    APVDV Q 
Sbjct  305   HVLLTDQLAERTPVLLCDPEKVRTRAADLIKTGSEFLEASWSVAALGT---DAPVDVAQF  361

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGF ELD+VRAAAAR GHPWWTLSQLSDESA+ELD+R+APSARGHQ DID IFAMLRA
Sbjct  362   GGSGFAELDEVRAAAARAGHPWWTLSQLSDESAVELDIRSAPSARGHQHDIDGIFAMLRA  421

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H++TGGYA +VAPGTGTAHRVVERL+E DTPA ML+ G APK GVVGVL+GPL DGVIIP
Sbjct  422   HVSTGGYAVVVAPGTGTAHRVVERLAECDTPAAMLESGAAPKAGVVGVLKGPLHDGVIIP  481

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GA LVVITETDLTGSRV+A EGKRLAAKRRN VDPLAL+AGDLVVHDQHGIGRFVEMVER
Sbjct  482   GATLVVITETDLTGSRVTAVEGKRLAAKRRNTVDPLALSAGDLVVHDQHGIGRFVEMVER  541

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYAS+KRGGG   +DKLYVPMDSLDQLSRYVGGQAPALS+LGGSDW N
Sbjct  542   TVGGARREYLVLEYASSKRGGG---SDKLYVPMDSLDQLSRYVGGQAPALSKLGGSDWTN  598

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIAGELVSLYAKRQASPGHAF PDTPWQAE+EDAFG+TETVDQLTAI EV
Sbjct  599   TKTKARRAVREIAGELVSLYAKRQASPGHAFGPDTPWQAEMEDAFGYTETVDQLTAITEV  658

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K+DMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +R
Sbjct  659   KSDMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFSDR  718

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTD  ES+AV++GLA+GSVD+VIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  719   MTGFPVTVKGLSRFTDPTESKAVVEGLAEGSVDVVIGTHRLLQTGVRWKDLGLVVVDEEQ  778

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  779   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  838

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQ+AAALRRELLRDGQ FYVHNRVSSID AAAR+RELVPEARVVVAHGQMPE+ LE 
Sbjct  839   HDDKQVAAALRRELLRDGQVFYVHNRVSSIDRAAARIRELVPEARVVVAHGQMPEERLER  898

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  899   TVQGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  958

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPP  PLTETAYDRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG+EQSGHVAGVGF
Sbjct  959   YFLYPPHSPLTETAYDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGVEQSGHVAGVGF  1018

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADGQTV TAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG
Sbjct  1019  DLYVRLVGEAVE----AYRAAADGQTVTTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1074

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAA+SD E+ AVV+EL DRYGALPEPA RL AVARLRLLCR +GIT+V+AASA+TV
Sbjct  1075  YRRLAAAASDGEIDAVVEELIDRYGALPEPALRLVAVARLRLLCRAAGITEVSAASASTV  1134

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RLSP+TLPDSAQVRLKRMYP A YRATT+TVQVPIPRAGG+GAPR+RDVELVQMVA+L+T
Sbjct  1135  RLSPMTLPDSAQVRLKRMYPAASYRATTSTVQVPIPRAGGVGAPRLRDVELVQMVANLVT  1194

Query  1201  ALAGKPRQHIGITN  1214
             AL GKP+Q I IT+
Sbjct  1195  ALQGKPQQEIDITS  1208


>gi|254774025|ref|ZP_05215541.1| hypothetical protein MaviaA2_05024 [Mycobacterium avium subsp. 
avium ATCC 25291]
Length=1201

 Score = 2088 bits (5410),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1040/1208 (87%), Positives = 1118/1208 (93%), Gaps = 9/1208 (0%)

Query  19    LALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTATGREADDLAAE  78
             +AL+APTFQQL+  A   P +L+L+ PASARL VASALAR GPLLVVTATGREADDL AE
Sbjct  1     MALTAPTFQQLIDTAAASPADLSLVGPASARLFVASALARLGPLLVVTATGREADDLTAE  60

Query  79    LRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPPLGVVVTSVR  138
             LRGV GDAVA+ PSWETLPHERLSPGVDTVG RL  LRRLAHPDDA+LGPPL VVVT+VR
Sbjct  61    LRGVVGDAVAVFPSWETLPHERLSPGVDTVGARLTVLRRLAHPDDARLGPPLQVVVTAVR  120

Query  139   SLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIF  198
             SLLQPMTPQLG++EP+TL+VG E  F+ V+ARLVELAY+RVDMVGRRGEFAVRGGILD+F
Sbjct  121   SLLQPMTPQLGLVEPVTLSVGQEIEFEHVIARLVELAYSRVDMVGRRGEFAVRGGILDVF  180

Query  199   APTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSEDVRARAAQL  258
              PTAEHPVRVEFWGDE++EMRMFSVADQRSIPEI + T++A  CRELLL+EDVRARAA+L
Sbjct  181   PPTAEHPVRVEFWGDEVSEMRMFSVADQRSIPEIAVDTVIAVPCRELLLTEDVRARAAEL  240

Query  259   AARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGTPVLVCD  318
             AA+HPA+E  +TGS SDMLAK+A+GIAVDGMEA+LPVL      LLTDQL + TPVL+CD
Sbjct  241   AAQHPASEPAITGSVSDMLAKIADGIAVDGMEALLPVLRPGKQVLLTDQLAERTPVLLCD  300

Query  319   PEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLGGSGFVELDQVRAAAART  378
             PEK+RTRAADLI+TGREFLEASWSVAALGT ENQAP+DVEQLGGSGF ELD+VRAAA R 
Sbjct  301   PEKIRTRAADLIKTGREFLEASWSVAALGTLENQAPIDVEQLGGSGFAELDEVRAAAVRG  360

Query  379   GHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRAHIATGGYAALVAPGTGTA  438
             GHPWWTLSQLSDESA+ELDVRAAPSARGHQ DID IFAMLRAH++TGG+AA+VAPGTGTA
Sbjct  361   GHPWWTLSQLSDESAVELDVRAAPSARGHQHDIDGIFAMLRAHVSTGGHAAVVAPGTGTA  420

Query  439   HRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDLTGSRVS  498
             HRVVERL+E DTPA ML+ G AP+ GVVGVL+GPL DG++IPGANLVVITETDLTGSRV+
Sbjct  421   HRVVERLAECDTPAAMLESGAAPRAGVVGVLKGPLHDGIVIPGANLVVITETDLTGSRVA  480

Query  499   AAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAK  558
             A EGKRLAAKRRN VDPLALTAGDLVVHDQHGIGRFVEM ERT GGARREYLVLEYAS+K
Sbjct  481   AVEGKRLAAKRRNTVDPLALTAGDLVVHDQHGIGRFVEMTERTGGGARREYLVLEYASSK  540

Query  559   RGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVS  618
             RGGG   +DKLYVPMDSLDQLSRYVGGQAPALS+LGGSDWANTKTKARRAVREIAGELVS
Sbjct  541   RGGG---SDKLYVPMDSLDQLSRYVGGQAPALSKLGGSDWANTKTKARRAVREIAGELVS  597

Query  619   LYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDV  678
             LYAKRQASPGHAFSPDTPWQAE+EDAFG+TETVDQLTAI EVK+DMEKPIPMDRVICGDV
Sbjct  598   LYAKRQASPGHAFSPDTPWQAEMEDAFGYTETVDQLTAITEVKSDMEKPIPMDRVICGDV  657

Query  679   GYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAA  738
             GYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +RM+GFPVT+KGLSRFTDAA
Sbjct  658   GYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTDRMAGFPVTVKGLSRFTDAA  717

Query  739   ESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVD  798
             ESRAVI+GLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVD
Sbjct  718   ESRAVIEGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVD  777

Query  799   VLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDG  858
             VLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQ+AAALRRELLRDG
Sbjct  778   VLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQVAAALRRELLRDG  837

Query  859   QAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTI  918
             QAFYVHNRVSSID AAARVRELVPEARVVVAHGQMPE+ LE TVQ FWNRE+DILVCTTI
Sbjct  838   QAFYVHNRVSSIDRAAARVRELVPEARVVVAHGQMPEERLERTVQGFWNREYDILVCTTI  897

Query  919   VETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRL  978
             VETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPP  PLTETAYDRL
Sbjct  898   VETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPHAPLTETAYDRL  957

Query  979   ATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAY  1038
             ATIAQNNELGAGMAVALKDLEIRGAGNVLG+EQSGHVAGVGFDLYVRLVGEA+E    AY
Sbjct  958   ATIAQNNELGAGMAVALKDLEIRGAGNVLGVEQSGHVAGVGFDLYVRLVGEAVE----AY  1013

Query  1039  RAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVD  1098
             RAAADGQTV TAEEPKDVRIDLPVDAHLPPDYIASDRLRLE YRRLAAA SD E+ AVV+
Sbjct  1014  RAAADGQTVTTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEAYRRLAAAGSDDEIDAVVE  1073

Query  1099  ELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKRM  1158
             EL DRYGALPEPA RL AVARLRLLCR +GIT+V+A SAATVRLSP+TLPDSAQVRLKRM
Sbjct  1074  ELVDRYGALPEPALRLVAVARLRLLCRAAGITEVSAPSAATVRLSPITLPDSAQVRLKRM  1133

Query  1159  YPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITNP--S  1216
             YP A YRATT+TVQVPIPRAGG+GAPR+RDVELVQMVA+L+TAL GKP+  +G   P  +
Sbjct  1134  YPAASYRATTSTVQVPIPRAGGVGAPRLRDVELVQMVANLVTALQGKPQTDVGTGAPVAA  1193

Query  1217  PPGEDGRG  1224
                E+GRG
Sbjct  1194  MASEEGRG  1201


>gi|183984436|ref|YP_001852727.1| transcription-repair coupling factor Mfd (TrcF) [Mycobacterium 
marinum M]
 gi|183177762|gb|ACC42872.1| transcription-repair coupling factor Mfd (TrcF) [Mycobacterium 
marinum M]
Length=1222

 Score = 2088 bits (5410),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1059/1233 (86%), Positives = 1135/1233 (93%), Gaps = 13/1233 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG A  DTPIAGLV+LAL+APTFQQL+ RA  RPDELTL+ PASAR  VASALA+QG
Sbjct  1     MTAPGAASPDTPIAGLVDLALTAPTFQQLIARASDRPDELTLVGPASARSFVASALAQQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADD+ AELRGVFG+AVAL PSWETLPHERLSPGVDTVG RL+ LRRLAH
Sbjct  61    PLLVVTATGREADDVTAELRGVFGEAVALFPSWETLPHERLSPGVDTVGARLLLLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             P+D +LGPPL VVVT+VRSLLQPMTPQLG  EP++L+VG E  FD V+ARLVELAYTRVD
Sbjct  121   PEDTRLGPPLRVVVTAVRSLLQPMTPQLGRQEPVSLSVGQEIGFDEVIARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILD+FAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEI++ TLVA 
Sbjct  181   MVGRRGEFAVRGGILDLFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIEVSTLVAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLL+EDVRARAA LAA+HPA+E+TVTGS  DMLAKLAEGI  DGMEA+LPVL  D 
Sbjct  241   ACRELLLTEDVRARAAALAAQHPASENTVTGSVIDMLAKLAEGIPTDGMEALLPVLRPDD  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQL +GTPVLVCDPEKVRTRAADLI+TGREFLEASWSVAA+GT    APVDVE L
Sbjct  301   HALLTDQLAEGTPVLVCDPEKVRTRAADLIKTGREFLEASWSVAAMGT---DAPVDVEAL  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGF EL+QV+ AA+ +GHPWWTLSQLS+ESA EL+VRAAPSARGHQ+DID+IFAMLRA
Sbjct  358   GGSGFAELEQVQTAASSSGHPWWTLSQLSEESATELEVRAAPSARGHQKDIDDIFAMLRA  417

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H++TGGYA +V PGTGTAHR+VERL+ESD PA ML+PG APK GVVGVL+GPLRDGVI+P
Sbjct  418   HVSTGGYAVMVEPGTGTAHRMVERLAESDIPAAMLEPGAAPKLGVVGVLKGPLRDGVIVP  477

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVV+TET+LTG+R +A EGKRLAAKRRN VDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  478   GANLVVVTETNLTGNRATAVEGKRLAAKRRNTVDPLALTAGDLVVHDQHGIGRFVEMVER  537

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASAKRGGG   +DKLYVPMDSLDQLSRYVGGQAPALSRLGGSDW N
Sbjct  538   TVGGARREYLVLEYASAKRGGG---SDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWTN  594

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKAR+AVREIAGELV+LYAKRQASPGHAF+PDTPWQAE+EDAFGFTETVDQLTAI EV
Sbjct  595   TKTKARKAVREIAGELVALYAKRQASPGHAFAPDTPWQAEMEDAFGFTETVDQLTAITEV  654

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K DMEK IPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +R
Sbjct  655   KGDMEKSIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTDR  714

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTD AESR VI+G+ADGSVD+VIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  715   MAGFPVTVKGLSRFTDPAESRTVIEGMADGSVDVVIGTHRLLQTGVRWKDLGLVVVDEEQ  774

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLR+HVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  775   RFGVEHKEHIKSLRSHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  834

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQ+AAALRRELLRDGQAFYVHNRVSSID  AAR+R+LVPEARVVVAHGQMPEDLLE 
Sbjct  835   HDDKQVAAALRRELLRDGQAFYVHNRVSSIDDTAARIRKLVPEARVVVAHGQMPEDLLER  894

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQ FW RE DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  895   TVQGFWQREFDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  954

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQ PLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLG+EQSGHVAGVGF
Sbjct  955   YFLYPPQAPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGVEQSGHVAGVGF  1014

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADG+TV T EEPKDVRIDLPVDAHLPPDYI SDRLRLE 
Sbjct  1015  DLYVRLVGEAVE----AYRAAADGKTVTTPEEPKDVRIDLPVDAHLPPDYIGSDRLRLEA  1070

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAA+SD  VAAVVDEL DRYGALPEPA RL AVARLRLLCR SGITDV+A S+ATV
Sbjct  1071  YRRLAAATSDSGVAAVVDELIDRYGALPEPALRLVAVARLRLLCRASGITDVSAPSSATV  1130

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RL+P+ LPDSAQVRLKRMYPG HYRATT+TVQVPIPR GG+GAPRIRDVELVQMVA+L+T
Sbjct  1131  RLAPMDLPDSAQVRLKRMYPGGHYRATTSTVQVPIPRDGGVGAPRIRDVELVQMVANLVT  1190

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQ  1233
             ALAGKP+Q IG T+ S   ED      + KERQ
Sbjct  1191  ALAGKPQQDIGRTSLS---EDDAAATASGKERQ  1220


>gi|118619716|ref|YP_908048.1| transcription-repair coupling factor Mfd (TrcF) [Mycobacterium 
ulcerans Agy99]
 gi|118571826|gb|ABL06577.1| transcription-repair coupling factor Mfd (TrcF) [Mycobacterium 
ulcerans Agy99]
Length=1222

 Score = 2078 bits (5383),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1054/1233 (86%), Positives = 1131/1233 (92%), Gaps = 13/1233 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG A  DTPIAGLV+LAL+APTFQQL+ RA  RPDELTL+ PASAR  VASALA+QG
Sbjct  1     MTAPGAASPDTPIAGLVDLALTAPTFQQLIARASDRPDELTLVGPASARSFVASALAQQG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADD+ AELRGVFG+AVAL PSWETLPHERLSPGVDTVG RL+ LRRLAH
Sbjct  61    PLLVVTATGREADDVTAELRGVFGEAVALFPSWETLPHERLSPGVDTVGARLLLLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDD +LGPPL VVVT+VRSLLQPMTPQLG  EP++L+VG E  FD V+ARLVELAYTRVD
Sbjct  121   PDDTRLGPPLRVVVTAVRSLLQPMTPQLGRQEPVSLSVGQEIGFDEVIARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILD+FAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEI++ TLVA 
Sbjct  181   MVGRRGEFAVRGGILDLFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIEVSTLVAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLL+EDVRARAA LAA+HPA+E+TVTGS  DMLAKLAEGI  DGMEA+LPVL  D 
Sbjct  241   ACRELLLTEDVRARAAALAAQHPASENTVTGSVIDMLAKLAEGIPTDGMEALLPVLRPDD  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
             HALLTDQL +GTPVLVCDPEKVRTRAADLI+TGREFLEASWSVAA+GT    APVDVE L
Sbjct  301   HALLTDQLAEGTPVLVCDPEKVRTRAADLIKTGREFLEASWSVAAMGT---DAPVDVEAL  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGF EL+QV+ AA+ +GHPWWTLSQLS+ESA EL+VRAAPSARGHQ+DID+IFAMLRA
Sbjct  358   GGSGFAELEQVQTAASSSGHPWWTLSQLSEESATELEVRAAPSARGHQKDIDDIFAMLRA  417

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H++TGGYA +V PGTGTAHR+VERL+ESD PA ML+PG APK GVVGVL+GPLRDGVI+P
Sbjct  418   HVSTGGYAVMVEPGTGTAHRMVERLAESDIPAAMLEPGAAPKLGVVGVLKGPLRDGVIVP  477

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLVV+TET+LTG+R +A EGKRLAAKRRN VDPLALTAGDLVVHDQHGIGRFVEMVER
Sbjct  478   GANLVVVTETNLTGNRATAVEGKRLAAKRRNTVDPLALTAGDLVVHDQHGIGRFVEMVER  537

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYASA+RGGG   +DKLYVPMDSLDQLSRYVGGQAPALSRLGGSDW N
Sbjct  538   TVGGARREYLVLEYASARRGGG---SDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWTN  594

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKAR+AVREIAGELV+LYAKRQASPGHAF+PDTPWQAE+EDAFGFTETVDQLTAI EV
Sbjct  595   TKTKARKAVREIAGELVALYAKRQASPGHAFAPDTPWQAEMEDAFGFTETVDQLTAITEV  654

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K DMEK IPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +R
Sbjct  655   KRDMEKSIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTDR  714

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTD AESR VI+G+ADGSVD+VIGTHRLLQTGVRWKDLGLVVVDEEQ
Sbjct  715   MAGFPVTVKGLSRFTDPAESRTVIEGMADGSVDVVIGTHRLLQTGVRWKDLGLVVVDEEQ  774

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLR+HVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  775   RFGVEHKEHIKSLRSHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  834

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQ+AAALRRELLRDGQAFYVHNR SSID  AAR+R+LVPEARVV AHGQMPEDLLE 
Sbjct  835   HDDKQVAAALRRELLRDGQAFYVHNRASSIDDTAARIRKLVPEARVVAAHGQMPEDLLER  894

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQ FW RE DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  895   TVQGFWQREFDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  954

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPPQ PLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLG+EQSGHVAGVGF
Sbjct  955   YFLYPPQAPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGVEQSGHVAGVGF  1014

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLY+RLVGEA+E    AYRAAADG+ V T EEPKDVRIDLPVDAHLPPDYI SDRLRLE 
Sbjct  1015  DLYLRLVGEAVE----AYRAAADGKMVTTPEEPKDVRIDLPVDAHLPPDYIGSDRLRLEA  1070

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLA A+SD  VAAVVDEL DRYGALPEPA RL AVARLRLLCR SGITDV+A S+ATV
Sbjct  1071  YRRLATATSDSGVAAVVDELIDRYGALPEPALRLVAVARLRLLCRASGITDVSAPSSATV  1130

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             RL+P+ LPDSAQVRLKRMYPG HYRATT+TVQVPIPR GG+GAPRIRDVELVQMVA+L+T
Sbjct  1131  RLAPMDLPDSAQVRLKRMYPGGHYRATTSTVQVPIPRDGGVGAPRIRDVELVQMVANLVT  1190

Query  1201  ALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQ  1233
             ALAGK +Q IG T+ S   ED  G   + KERQ
Sbjct  1191  ALAGKLQQDIGRTSLS---EDDAGATASGKERQ  1220


>gi|254819273|ref|ZP_05224274.1| hypothetical protein MintA_05066 [Mycobacterium intracellulare 
ATCC 13950]
Length=1200

 Score = 2071 bits (5366),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1031/1208 (86%), Positives = 1105/1208 (92%), Gaps = 9/1208 (0%)

Query  19    LALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTATGREADDLAAE  78
             +AL+APTFQQL+  A   P EL L+ PASARL VASALAR GPLLVVTATGREADDL AE
Sbjct  1     MALTAPTFQQLIDSAAASPAELHLVGPASARLFVASALARLGPLLVVTATGREADDLTAE  60

Query  79    LRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPPLGVVVTSVR  138
             LRGVFGDAVA+ PSWETLPHERLSPGVDTVG RL  LRRLAHPDDA+LGPPL VVVT+ R
Sbjct  61    LRGVFGDAVAVFPSWETLPHERLSPGVDTVGARLTVLRRLAHPDDARLGPPLQVVVTAAR  120

Query  139   SLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIF  198
             SLLQPMTPQLG++EP+TL+VG E  F+GV+ARLVELAYTRVDMVGRRGEFAVRGGILD+F
Sbjct  121   SLLQPMTPQLGLIEPVTLSVGAEVEFEGVIARLVELAYTRVDMVGRRGEFAVRGGILDVF  180

Query  199   APTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSEDVRARAAQL  258
              PTAEHPVR+EFWGDE++EMRMFSVADQRSIPEI++ TL+A  CRELLL+E+VR RAA+L
Sbjct  181   PPTAEHPVRIEFWGDEVSEMRMFSVADQRSIPEIEVDTLIAVPCRELLLTEEVRQRAAEL  240

Query  259   AARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGTPVLVCD  318
             +ARHPA E  +TGS +DMLAKLAEGIAVDGMEA+LPVL    H LLTDQL  GTP+L+CD
Sbjct  241   SARHPATEPAITGSVTDMLAKLAEGIAVDGMEALLPVLRPGEHVLLTDQLAQGTPILLCD  300

Query  319   PEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLGGSGFVELDQVRAAAART  378
             PEK+RTRAADLI+TG EFLEASWS AA+GT    APVDV Q GGSGF ELD V+AAAA+ 
Sbjct  301   PEKIRTRAADLIKTGSEFLEASWSAAAMGT---DAPVDVAQFGGSGFAELDDVQAAAAKG  357

Query  379   GHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRAHIATGGYAALVAPGTGTA  438
             GHPWWTLSQLSDESA+ELD+RAAPSARGHQ DID IFAMLRAH+ TGGYA +VAPG GTA
Sbjct  358   GHPWWTLSQLSDESAVELDIRAAPSARGHQHDIDGIFAMLRAHVTTGGYAVVVAPGAGTA  417

Query  439   HRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDLTGSRVS  498
             HRVVERL+E DTPA ML+ G APK GVVGVL+GPL DGVIIPGA LVVITETDLTGSRV+
Sbjct  418   HRVVERLAECDTPAAMLESGAAPKLGVVGVLKGPLHDGVIIPGATLVVITETDLTGSRVA  477

Query  499   AAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAK  558
             A EGKRLAAKRRN VDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYAS+K
Sbjct  478   AVEGKRLAAKRRNTVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASSK  537

Query  559   -RGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELV  617
              RGG AKNTDKLYVPMDSLDQLSRYVGGQAPALS+LGGSDWANTKTKARRAVREIAGELV
Sbjct  538   NRGGAAKNTDKLYVPMDSLDQLSRYVGGQAPALSKLGGSDWANTKTKARRAVREIAGELV  597

Query  618   SLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGD  677
             SLYAKRQASPGHAF PDTPWQAE+EDAFG+TETVDQLTAI EVK DMEKPIPMDRVICGD
Sbjct  598   SLYAKRQASPGHAFGPDTPWQAEMEDAFGYTETVDQLTAITEVKGDMEKPIPMDRVICGD  657

Query  678   VGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDA  737
             VGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +RM+GFPVT+KGLSRFTD 
Sbjct  658   VGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTDRMTGFPVTVKGLSRFTDP  717

Query  738   AESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHV  797
             AES+AVI+GLADGSVD+VIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHV
Sbjct  718   AESKAVIEGLADGSVDVVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHV  777

Query  798   DVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRD  857
             DVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQ+AAALRRELLRD
Sbjct  778   DVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQVAAALRRELLRD  837

Query  858   GQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTT  917
             GQ FYVHNRVSSID  AA++RELVPEARVVVAHGQMPE+ LE TVQ FWNRE+DILVCTT
Sbjct  838   GQVFYVHNRVSSIDRTAAKIRELVPEARVVVAHGQMPEERLERTVQGFWNREYDILVCTT  897

Query  918   IVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDR  977
             IVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPP  PLTETAYDR
Sbjct  898   IVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPHAPLTETAYDR  957

Query  978   LATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDA  1037
             LATIAQNNELGAGMAVA+KDLEIRGAGNVLG+EQSGHVAGVGFDLYVRLVGEA+E    A
Sbjct  958   LATIAQNNELGAGMAVAMKDLEIRGAGNVLGVEQSGHVAGVGFDLYVRLVGEAVE----A  1013

Query  1038  YRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVV  1097
             YRAAADG TV TAEEPKDVRIDLPVDAHLPPDYIASDRLRLE YRRLAAA+SD E+ AVV
Sbjct  1014  YRAAADGHTVTTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEAYRRLAAAASDGEIDAVV  1073

Query  1098  DELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKR  1157
             +EL DRYGALPEPA RL AVARLRLLCR +GIT+V+A SAATVRLSP+TLPDSAQVRLKR
Sbjct  1074  EELVDRYGALPEPALRLVAVARLRLLCRAAGITEVSAPSAATVRLSPMTLPDSAQVRLKR  1133

Query  1158  MYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITNPSP  1217
             MYP A YRATT+TVQVPIPRAGG+GAPR+RDVELVQMVA+L+TAL GK +  IGIT+ SP
Sbjct  1134  MYPAAGYRATTSTVQVPIPRAGGVGAPRLRDVELVQMVANLVTALQGKAQTDIGITS-SP  1192

Query  1218  PGEDGRGR  1225
                   GR
Sbjct  1193  AVMTSEGR  1200


>gi|221229524|ref|YP_002502940.1| putative transcription-repair coupling factor [Mycobacterium 
leprae Br4923]
 gi|219932631|emb|CAR70345.1| putative transcription-repair coupling factor [Mycobacterium 
leprae Br4923]
Length=1224

 Score = 2035 bits (5273),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1036/1229 (85%), Positives = 1100/1229 (90%), Gaps = 20/1229 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPAC DTPIAGLVELAL+APTF QLM+RAG RP EL L  PA ARL VASALAR G
Sbjct  1     MTAPGPACLDTPIAGLVELALTAPTFGQLMERAGTRPAELILAGPACARLFVASALARLG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREA +L AELRGVFG AVA+ PSWETLPHERLSPGVDTVG RLM LRRLAH
Sbjct  61    PLLVVTATGREASNLTAELRGVFGAAVAMFPSWETLPHERLSPGVDTVGARLMVLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPL VVVT+VRSLLQPMT QLG++EP+TL+VGDE  F+ V+ARLVELAYTRVD
Sbjct  121   PDDARLGPPLQVVVTAVRSLLQPMTAQLGLVEPVTLSVGDEIGFERVIARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIF PTAEHPVRVEFWGDEITEMRMFSV DQRSIPEI + TLVA 
Sbjct  181   MVGRRGEFAVRGGILDIFGPTAEHPVRVEFWGDEITEMRMFSVVDQRSIPEIGVDTLVAI  240

Query  241   ACRELLLSEDVRARAAQLAA----RHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVL  296
             ACRELLLS+DVRARA +LAA    R P  E  ++GS +D+LAKLAEGI VDGMEA+LPVL
Sbjct  241   ACRELLLSDDVRARAVELAAQAAARRPTEEPAISGSVTDVLAKLAEGIPVDGMEALLPVL  300

Query  297   WSDGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVD  356
               D +ALLTDQ    TPVL+CDPEKVR +AADLI+T R FLEASWSVAA+G A+N APVD
Sbjct  301   CPDDYALLTDQFAADTPVLLCDPEKVRIQAADLIKTDRAFLEASWSVAAIG-ADNAAPVD  359

Query  357   VEQLGGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFA  416
             VEQL GSGFVEL  V+AAA R+GHPWWTLSQLSDESA+ELD+RAAPS RGHQ  ID IFA
Sbjct  360   VEQLYGSGFVELGDVQAAAIRSGHPWWTLSQLSDESALELDIRAAPSTRGHQHAIDGIFA  419

Query  417   MLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAP----KPGVVGVLQGP  472
             MLRAH+ATGGYAA+V PGTGTAHRVVERL+ESD P  ML+P  AP    +PG+VGVL+GP
Sbjct  420   MLRAHVATGGYAAIVTPGTGTAHRVVERLAESDIPGAMLEPAAAPGLGLRPGLVGVLKGP  479

Query  473   LRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIG  532
             L DGV+IPGANLV+ITE DLTGSR +  EGKRLAAKRR+  DPLALTAGDLVVHDQHGIG
Sbjct  480   LLDGVVIPGANLVIITEADLTGSRATPVEGKRLAAKRRSAADPLALTAGDLVVHDQHGIG  539

Query  533   RFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSR  592
             RFVEMVERTVGGARREYLVLEYAS K+   +K  DKLYVPMDSLDQLSRYVGGQAPALSR
Sbjct  540   RFVEMVERTVGGARREYLVLEYASNKK---SKQADKLYVPMDSLDQLSRYVGGQAPALSR  596

Query  593   LGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVD  652
             LGGSDWANTKTKAR AVREIAGELVSLYAKRQASPGHAF PDTPWQAE+EDAFGFTETVD
Sbjct  597   LGGSDWANTKTKARCAVREIAGELVSLYAKRQASPGHAFGPDTPWQAEMEDAFGFTETVD  656

Query  653   QLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQ  712
             QLTAI EVK DMEK +PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQ
Sbjct  657   QLTAITEVKGDMEKSVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQ  716

Query  713   HLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLG  772
             HL+TF ERM+GFPVT+KGLSRFTDAAESRAVIDGLA+GSVDIVIGTHRLLQTGV WKDLG
Sbjct  717   HLRTFTERMAGFPVTVKGLSRFTDAAESRAVIDGLAEGSVDIVIGTHRLLQTGVCWKDLG  776

Query  773   LVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY  832
             LVVVDEEQ FGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY
Sbjct  777   LVVVDEEQWFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY  836

Query  833   PVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQ  892
             PVLTYVGPHDDKQ+AAALRRELLRDGQAFYVHNRVSSI  AAARV  LVPEARVVVAHGQ
Sbjct  837   PVLTYVGPHDDKQVAAALRRELLRDGQAFYVHNRVSSIYQAAARVCGLVPEARVVVAHGQ  896

Query  893   MPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVG  952
             MPEDLLETT++ FWNRE+DILVCTTIVETGLDI NANTL+VERADTFGLSQLHQLRGRVG
Sbjct  897   MPEDLLETTMRGFWNREYDILVCTTIVETGLDIPNANTLVVERADTFGLSQLHQLRGRVG  956

Query  953   RSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQS  1012
             RS ERGYAYFLYPPQ PLTE AYDRL TIAQNNELGAGMAVALKDLEIRGAGNVLG+EQS
Sbjct  957   RSHERGYAYFLYPPQAPLTEIAYDRLVTIAQNNELGAGMAVALKDLEIRGAGNVLGVEQS  1016

Query  1013  GHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIA  1072
             GHVAGVGFDLYVRLVGEA+E    AYRA ADG+T  T EEPKDVRIDLPVDAHLPPDYIA
Sbjct  1017  GHVAGVGFDLYVRLVGEAVE----AYRAVADGKTAITPEEPKDVRIDLPVDAHLPPDYIA  1072

Query  1073  SDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDV  1132
             SDRLRLEGYRRLAAASSD EVAAVVDEL DRYGALPEPA+RL AVA+LRLLCRGSGI +V
Sbjct  1073  SDRLRLEGYRRLAAASSDTEVAAVVDELIDRYGALPEPAQRLVAVAQLRLLCRGSGIIEV  1132

Query  1133  TAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGG----LGAPRIRD  1188
             TA SA+T+RLSP+ L DSAQVRLKRMYPGA YRAT ATVQVPIPRAG     LG P IRD
Sbjct  1133  TAPSASTMRLSPIRLIDSAQVRLKRMYPGAQYRATAATVQVPIPRAGSSGGTLGVPCIRD  1192

Query  1189  VELVQMVADLITALAGKPRQHIGITNPSP  1217
             VELVQ VADLITAL G PR+ IGIT P P
Sbjct  1193  VELVQAVADLITALQGLPRKVIGITGPEP  1221


>gi|15827046|ref|NP_301309.1| transcription-repair coupling factor [Mycobacterium leprae TN]
 gi|13092593|emb|CAC29760.1| putative transcription-repair coupling factor [Mycobacterium 
leprae]
Length=1224

 Score = 2034 bits (5270),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1035/1229 (85%), Positives = 1099/1229 (90%), Gaps = 20/1229 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPGPAC DTPIAGLVELAL+APTF QLM+RAG RP EL L  PA ARL VASALAR G
Sbjct  1     MTAPGPACLDTPIAGLVELALTAPTFGQLMERAGTRPAELILAGPACARLFVASALARLG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREA +L AELRGVFG AVA+ PSWETLPHERLSPGVDTVG RLM LRRLAH
Sbjct  61    PLLVVTATGREASNLTAELRGVFGAAVAMFPSWETLPHERLSPGVDTVGARLMVLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPL VVVT+VRSLLQPMT QLG++EP+TL+VGDE  F+ V+ARLVELAYTRVD
Sbjct  121   PDDARLGPPLQVVVTAVRSLLQPMTAQLGLVEPVTLSVGDEIGFERVIARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVGRRGEFAVRGGILDIF PTAEHPVRVEFWGDEITEMRMFSV DQRSIPEI + TLVA 
Sbjct  181   MVGRRGEFAVRGGILDIFGPTAEHPVRVEFWGDEITEMRMFSVVDQRSIPEIGVDTLVAI  240

Query  241   ACRELLLSEDVRARAAQLAA----RHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVL  296
             ACRELLLS+DVRARA +LAA    R P  E  ++GS +D+LAKLAEGI VDGMEA+LPVL
Sbjct  241   ACRELLLSDDVRARAVELAAQAAARRPTEEPAISGSVTDVLAKLAEGIPVDGMEALLPVL  300

Query  297   WSDGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVD  356
               D +ALLTDQ    TPVL+CDPEKVR +AADLI+T R FLEASWSVAA+G A+N APVD
Sbjct  301   CPDDYALLTDQFAADTPVLLCDPEKVRIQAADLIKTDRAFLEASWSVAAIG-ADNAAPVD  359

Query  357   VEQLGGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFA  416
             VEQL GSGFVEL  V+AAA R+GHPWWTLSQLSDESA+ELD+RAAPS RGHQ  ID IFA
Sbjct  360   VEQLYGSGFVELGDVQAAAIRSGHPWWTLSQLSDESALELDIRAAPSTRGHQHAIDGIFA  419

Query  417   MLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAP----KPGVVGVLQGP  472
             MLRAH+ATGGYAA+V PGTGTAHRVVERL+ESD P  ML+P  AP    +PG+VGVL+GP
Sbjct  420   MLRAHVATGGYAAIVTPGTGTAHRVVERLAESDIPGAMLEPAAAPGLGLRPGLVGVLKGP  479

Query  473   LRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIG  532
             L DGV+IPGANLV+ITE DLTGSR +  EGKRLAAKRR+  DPLALTAGDLVVHDQHGIG
Sbjct  480   LLDGVVIPGANLVIITEADLTGSRATPVEGKRLAAKRRSAADPLALTAGDLVVHDQHGIG  539

Query  533   RFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSR  592
             RFVEMVERTVGGARREYLVLEYAS K+   +K  DKLYVPMDSLDQLSRYVGGQAPALSR
Sbjct  540   RFVEMVERTVGGARREYLVLEYASNKK---SKQADKLYVPMDSLDQLSRYVGGQAPALSR  596

Query  593   LGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVD  652
             LGGSDWANTKTKAR AVREIAGELVSLYAKRQASPGHAF PDTPWQAE+EDAFGFTETVD
Sbjct  597   LGGSDWANTKTKARCAVREIAGELVSLYAKRQASPGHAFGPDTPWQAEMEDAFGFTETVD  656

Query  653   QLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQ  712
             QLTAI EVK DMEK +PMDRVICGDVGYGK EIAVRAAFKAVQDGKQVAVLVPTTLLADQ
Sbjct  657   QLTAITEVKGDMEKSVPMDRVICGDVGYGKAEIAVRAAFKAVQDGKQVAVLVPTTLLADQ  716

Query  713   HLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLG  772
             HL+TF ERM+GFPVT+KGLSRFTDAAESRAVIDGLA+GSVDIVIGTHRLLQTGV WKDLG
Sbjct  717   HLRTFTERMAGFPVTVKGLSRFTDAAESRAVIDGLAEGSVDIVIGTHRLLQTGVCWKDLG  776

Query  773   LVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY  832
             LVVVDEEQ FGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY
Sbjct  777   LVVVDEEQWFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY  836

Query  833   PVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQ  892
             PVLTYVGPHDDKQ+AAALRRELLRDGQAFYVHNRVSSI  AAARV  LVPEARVVVAHGQ
Sbjct  837   PVLTYVGPHDDKQVAAALRRELLRDGQAFYVHNRVSSIYQAAARVCGLVPEARVVVAHGQ  896

Query  893   MPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVG  952
             MPEDLLETT++ FWNRE+DILVCTTIVETGLDI NANTL+VERADTFGLSQLHQLRGRVG
Sbjct  897   MPEDLLETTMRGFWNREYDILVCTTIVETGLDIPNANTLVVERADTFGLSQLHQLRGRVG  956

Query  953   RSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQS  1012
             RS ERGYAYFLYPPQ PLTE AYDRL TIAQNNELGAGMAVALKDLEIRGAGNVLG+EQS
Sbjct  957   RSHERGYAYFLYPPQAPLTEIAYDRLVTIAQNNELGAGMAVALKDLEIRGAGNVLGVEQS  1016

Query  1013  GHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIA  1072
             GHVAGVGFDLYVRLVGEA+E    AYRA ADG+T  T EEPKDVRIDLPVDAHLPPDYIA
Sbjct  1017  GHVAGVGFDLYVRLVGEAVE----AYRAVADGKTAITPEEPKDVRIDLPVDAHLPPDYIA  1072

Query  1073  SDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDV  1132
             SDRLRLEGYRRLAAASSD EVAAVVDEL DRYGALPEPA+RL AVA+LRLLCRGSGI +V
Sbjct  1073  SDRLRLEGYRRLAAASSDTEVAAVVDELIDRYGALPEPAQRLVAVAQLRLLCRGSGIIEV  1132

Query  1133  TAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGG----LGAPRIRD  1188
             TA SA+T+RLSP+ L DSAQVRLKRMYPGA YRAT ATVQVPIPRAG     LG P IRD
Sbjct  1133  TAPSASTMRLSPIRLIDSAQVRLKRMYPGAQYRATAATVQVPIPRAGSSGGTLGVPCIRD  1192

Query  1189  VELVQMVADLITALAGKPRQHIGITNPSP  1217
             VELVQ VADLITAL G PR+ IGIT P P
Sbjct  1193  VELVQAVADLITALQGLPRKVIGITGPEP  1221


>gi|296169893|ref|ZP_06851505.1| transcription-repair coupling factor [Mycobacterium parascrofulaceum 
ATCC BAA-614]
 gi|295895449|gb|EFG75151.1| transcription-repair coupling factor [Mycobacterium parascrofulaceum 
ATCC BAA-614]
Length=1201

 Score = 2031 bits (5263),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1031/1199 (86%), Positives = 1100/1199 (92%), Gaps = 13/1199 (1%)

Query  19    LALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTATGREADDLAAE  78
             +AL+APTFQQL++ A  RP EL L+ PASARL VASALAR GPLLVVTATGREADDL AE
Sbjct  1     MALTAPTFQQLIESAADRPPELHLVGPASARLFVASALARLGPLLVVTATGREADDLTAE  60

Query  79    LRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPPLGVVVTSVR  138
             LRGVFGDAVA  PSWETLPHERLSPGVDTVGTRL  LRRLAHP+DA+LGPPL VVVT+VR
Sbjct  61    LRGVFGDAVAAFPSWETLPHERLSPGVDTVGTRLTVLRRLAHPEDARLGPPLRVVVTAVR  120

Query  139   SLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIF  198
             SLLQPMTPQLG++EP+T +VG E  F+ VVARLVELAYTRVDMVGRRGEFAVRGGILD+F
Sbjct  121   SLLQPMTPQLGLVEPVTFSVGQEMAFEEVVARLVELAYTRVDMVGRRGEFAVRGGILDVF  180

Query  199   APTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSEDVRARAAQL  258
              PTAEHPVR+EFWGDE++EMRMF+VADQRSIPEI++ T++A ACRELLLS+DVR RAA L
Sbjct  181   PPTAEHPVRIEFWGDEVSEMRMFAVADQRSIPEIEVETVIAVACRELLLSDDVRERAAAL  240

Query  259   AARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGTPVLVCD  318
             AARH  AE  +TGS +DMLAKLAEGIAVDGMEA+LPVL    H LLTDQL  GTPVL+CD
Sbjct  241   AARHSGAEPAITGSVTDMLAKLAEGIAVDGMEALLPVLRPGEHVLLTDQLAQGTPVLLCD  300

Query  319   PEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLGGSGFVELDQVRAAAART  378
             PEKVRTRAADLI+TG EFLEASWSVAALGT    APVDV Q GGSGF EL+ VRAAAA +
Sbjct  301   PEKVRTRAADLIKTGSEFLEASWSVAALGT---DAPVDVAQFGGSGFTELEDVRAAAATS  357

Query  379   GHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRAHIATGGYAALVAPGTGTA  438
             GHPWWTLSQLSDESA+ELD+RAAPSARGHQ DIDEIFAMLRAH++TGGYAA+VAPG GTA
Sbjct  358   GHPWWTLSQLSDESAVELDIRAAPSARGHQHDIDEIFAMLRAHVSTGGYAAVVAPGIGTA  417

Query  439   HRVVERLSESDTPAGMLDPGQAP---KPGVVGVLQGPLRDGVIIPGANLVVITETDLTGS  495
             HRVVERL++SDTPA ML+P  A    KPGVV VL+GPL DGV++PGANLVVITETDLTGS
Sbjct  418   HRVVERLADSDTPATMLEPDAADTTLKPGVVCVLKGPLHDGVVVPGANLVVITETDLTGS  477

Query  496   RVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYA  555
             R +A EGKRLAAKRRN VDPLALTAGDLVVHDQHGIGRFVEM ERTVGGARREYLVLEYA
Sbjct  478   RATAVEGKRLAAKRRNTVDPLALTAGDLVVHDQHGIGRFVEMTERTVGGARREYLVLEYA  537

Query  556   SAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGE  615
             S+KRGGG   +DKLYVPMDSLDQLSRYVGGQAPALS+LGGSDWANTKTKARRAVREIAGE
Sbjct  538   SSKRGGG---SDKLYVPMDSLDQLSRYVGGQAPALSKLGGSDWANTKTKARRAVREIAGE  594

Query  616   LVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVIC  675
             LV+LYAKRQASPGHAF+PDTPWQAE+EDAFGFTETVDQLTAI EVKADMEKPIPMDRVIC
Sbjct  595   LVALYAKRQASPGHAFAPDTPWQAEMEDAFGFTETVDQLTAITEVKADMEKPIPMDRVIC  654

Query  676   GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFT  735
             GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF +RM+GFPVT+KGLSRFT
Sbjct  655   GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTDRMAGFPVTVKGLSRFT  714

Query  736   DAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRT  795
             D AESRAVI+GLADGSVD+VIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRT
Sbjct  715   DNAESRAVIEGLADGSVDVVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRT  774

Query  796   HVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELL  855
             HVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP DDKQ+AAALRRELL
Sbjct  775   HVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPQDDKQVAAALRRELL  834

Query  856   RDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVC  915
             RDGQ FYVHNRVSSID  AAR+RELVPEARVVVAHGQMPE+ LE TVQ FWNRE+DILVC
Sbjct  835   RDGQVFYVHNRVSSIDRTAARIRELVPEARVVVAHGQMPEERLERTVQGFWNREYDILVC  894

Query  916   TTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAY  975
             TTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPP  PLTETAY
Sbjct  895   TTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPHAPLTETAY  954

Query  976   DRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYR  1035
             DRLATIAQNNELGAGMAVALKDLEIRGAGNVLG+EQSGHVAGVGFDLYVRLVGEA+E   
Sbjct  955   DRLATIAQNNELGAGMAVALKDLEIRGAGNVLGVEQSGHVAGVGFDLYVRLVGEAVE---  1011

Query  1036  DAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAA  1095
              AYRAAADGQTV TAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAA  D  V A
Sbjct  1012  -AYRAAADGQTVTTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAAPDDAAVDA  1070

Query  1096  VVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRL  1155
             VV+EL DRYGALPEPA RL AVARLRLLCR +GIT+V+A SAATVRLSP+TLPDSAQVRL
Sbjct  1071  VVEELVDRYGALPEPALRLVAVARLRLLCRAAGITEVSAPSAATVRLSPMTLPDSAQVRL  1130

Query  1156  KRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITN  1214
             KRMYP A YRATT+TVQVPIPR GG+GA RIRDVELVQMVA+L+TAL GKP+  IGIT 
Sbjct  1131  KRMYPSASYRATTSTVQVPIPRDGGVGAARIRDVELVQMVANLVTALQGKPQTDIGITG  1189


>gi|126437189|ref|YP_001072880.1| transcription-repair coupling factor [Mycobacterium sp. JLS]
 gi|126236989|gb|ABO00390.1| transcription-repair coupling factor [Mycobacterium sp. JLS]
Length=1211

 Score = 1946 bits (5042),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 962/1211 (80%), Positives = 1067/1211 (89%), Gaps = 11/1211 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MT  G     TPIAGL+ELAL  P    L  RA  +PD+L ++ PASARLLV +ALA+ G
Sbjct  1     MTVSGLHHVQTPIAGLIELALRDPCLADLSARAADKPDDLAMVGPASARLLVTAALAQAG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDL AELRGV GD+ AL PSWETLPHERLSPGVDTVG R+M LRRLAH
Sbjct  61    PLLVVTATGREADDLTAELRGVIGDSAALFPSWETLPHERLSPGVDTVGARMMLLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPL VVVT+ RSL+QPM P L  +EP+TLTVG E  FDGV+ RLV+LAYTR D
Sbjct  121   PDDARLGPPLRVVVTTARSLVQPMAPGLAEVEPVTLTVGAEMDFDGVIKRLVDLAYTRCD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MV +RGEFAVRGGILD+F PTAEHPVRVEFWGDEI+EMRMF+VADQRSIPEI++ T++A 
Sbjct  181   MVAKRGEFAVRGGILDVFPPTAEHPVRVEFWGDEISEMRMFAVADQRSIPEIEVDTVIAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELL+S++VR+RAA LAA HP  E++V GS  DMLAKLAEGI VDGMEA+LP+L    
Sbjct  241   PCRELLMSDEVRSRAAVLAAEHPTHENSVPGSVPDMLAKLAEGIPVDGMEALLPLLRPTD  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
              A+L+D LPDG P+LVCDPEKVRTRA DLI+TGREFLEASWS AA+G A   AP+D+E +
Sbjct  301   LAMLSDHLPDGAPILVCDPEKVRTRAGDLIKTGREFLEASWSTAAVGGA---APIDLEAM  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             G SGF+  ++VR  A   GHPWWTLSQLSDE AIELD+R+APSARG Q  ++EIFAMLRA
Sbjct  358   GASGFLGFEEVRTGARAGGHPWWTLSQLSDEKAIELDIRSAPSARGQQSSVEEIFAMLRA  417

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H+ATGGY A+V PG GTAHRVVE+L E+DTPA ML+PG+ PK GVVGVL+GPL DGV++P
Sbjct  418   HVATGGYGAVVTPGAGTAHRVVEQLGENDTPATMLEPGEEPKAGVVGVLKGPLHDGVVLP  477

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLV++TE DLTGSRV+A EGKRLAAKRRN+VDPLALTAGDLVVHDQHGIGRFVEM ER
Sbjct  478   GANLVIVTEADLTGSRVTATEGKRLAAKRRNVVDPLALTAGDLVVHDQHGIGRFVEMTER  537

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
              VGGARREYLVLEYAS+KRGGG   +D+LYVPMDSLDQLSRYVGG+AP+LS+LGGSDWAN
Sbjct  538   VVGGARREYLVLEYASSKRGGG---SDRLYVPMDSLDQLSRYVGGEAPSLSKLGGSDWAN  594

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIA ELV+LYAKRQA+PGHAFSPDTPWQ E+EDAFGFTETVDQLTAIEEV
Sbjct  595   TKTKARRAVREIASELVALYAKRQAAPGHAFSPDTPWQNEMEDAFGFTETVDQLTAIEEV  654

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKP+PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF  R
Sbjct  655   KADMEKPVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTAR  714

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTD AESRA ++G+ DGSVDIVIGTHRLLQTGV WKDLGL++VDEEQ
Sbjct  715   MAGFPVTVKGLSRFTDPAESRAALEGMKDGSVDIVIGTHRLLQTGVVWKDLGLIIVDEEQ  774

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKS+RTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  775   RFGVEHKEHIKSMRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  834

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
              DDKQ+AAALRRELLRDGQAFY+HNRV +ID AA+++  LVPEARVVVAHGQMPE+LLE 
Sbjct  835   QDDKQVAAALRRELLRDGQAFYIHNRVRTIDQAASKIAALVPEARVVVAHGQMPEELLER  894

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TV+ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  895   TVEGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  954

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPP+ PLTETAYDRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG EQSGHVAGVGF
Sbjct  955   YFLYPPEQPLTETAYDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGAEQSGHVAGVGF  1014

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADG+TV T +E KDVRIDLPVDA+LPPDYI SDRLRLE 
Sbjct  1015  DLYVRLVGEAVE----AYRAAADGKTVATPQETKDVRIDLPVDANLPPDYIGSDRLRLEA  1070

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAA  D  V AV+DEL DRYG LPEPA+RL  VARLRL+CR  GITDV++ SA+TV
Sbjct  1071  YRRLAAAQDDAGVDAVIDELVDRYGPLPEPAQRLVGVARLRLVCREYGITDVSSVSASTV  1130

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRA-GGLGAPRIRDVELVQMVADLI  1199
             +LSP+ LPDSAQ+RLKRMYPGA YRATT TV VPIPRA   +GAPRIRD ELV MVA L+
Sbjct  1131  KLSPMELPDSAQLRLKRMYPGATYRATTGTVSVPIPRATDSVGAPRIRDAELVAMVAGLV  1190

Query  1200  TALAGKPRQHI  1210
              AL GKP+  I
Sbjct  1191  LALNGKPQAQI  1201


>gi|108801209|ref|YP_641406.1| transcription-repair coupling factor [Mycobacterium sp. MCS]
 gi|119870360|ref|YP_940312.1| transcription-repair coupling factor [Mycobacterium sp. KMS]
 gi|108771628|gb|ABG10350.1| transcription-repair coupling factor [Mycobacterium sp. MCS]
 gi|119696449|gb|ABL93522.1| transcription-repair coupling factor [Mycobacterium sp. KMS]
Length=1211

 Score = 1943 bits (5034),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 961/1211 (80%), Positives = 1066/1211 (89%), Gaps = 11/1211 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MT  G     TPIAGL+ELAL  P    L  RA  +PD+L ++ PASARLLV +ALA+ G
Sbjct  1     MTVSGLHHVQTPIAGLIELALRDPCLADLSARAADKPDDLAMVGPASARLLVTAALAQAG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATGREADDL AELRGV GD+ AL PSWETLPHERLSPGVDTVG R+M LRRLAH
Sbjct  61    PLLVVTATGREADDLTAELRGVIGDSAALFPSWETLPHERLSPGVDTVGARMMLLRRLAH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPL VVVT+ RSL+QPM P L  +EP+TLTVG E  FDGV+ RLV+LAYTR D
Sbjct  121   PDDARLGPPLRVVVTTARSLVQPMAPGLAEVEPVTLTVGAEMDFDGVIKRLVDLAYTRCD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MV +RGEFAVRGGILD+F PTAEHPVRVEFWGDEI+EMRMF+VADQRSIPEI++ T++A 
Sbjct  181   MVAKRGEFAVRGGILDVFPPTAEHPVRVEFWGDEISEMRMFAVADQRSIPEIEVDTVIAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELL+S++VR+RAA LAA HP  E++V GS  DMLAKLAEGI VDGMEA+LP+L    
Sbjct  241   PCRELLMSDEVRSRAAVLAAEHPTHENSVPGSVPDMLAKLAEGIPVDGMEALLPLLRPTD  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
              A+L+D LPDG P+LVCDPEKVRTRA DLI+TGREFLEASWS AA+G A   AP+D+E +
Sbjct  301   LAMLSDHLPDGAPILVCDPEKVRTRAGDLIKTGREFLEASWSTAAVGGA---APIDLEAM  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             G SGF+  ++VR  A   GHPWWTLSQLSDE AIELD+R+APSARG Q  ++EIFAMLRA
Sbjct  358   GASGFLGFEEVRTGARAGGHPWWTLSQLSDEKAIELDIRSAPSARGQQSSVEEIFAMLRA  417

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H+ATGGY A+V PG GTAHRVVE+L E+DTPA ML+PG+ PK GVVGVL+GPL DGV++P
Sbjct  418   HVATGGYGAVVTPGAGTAHRVVEQLGENDTPATMLEPGEEPKAGVVGVLKGPLHDGVVLP  477

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLV++TE DLTGSRV+A EGKRLAAKRRN+VDPLALTAGDLVVHDQHGIGRFVEM ER
Sbjct  478   GANLVIVTEADLTGSRVTATEGKRLAAKRRNVVDPLALTAGDLVVHDQHGIGRFVEMTER  537

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
              VGGARREYLVLEYAS+KRGGG   +D+LYVPMDSLDQLSRYVGG+AP+LS+LGGSDWAN
Sbjct  538   VVGGARREYLVLEYASSKRGGG---SDRLYVPMDSLDQLSRYVGGEAPSLSKLGGSDWAN  594

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIA ELV+LYAKRQA+PGHAFSPDTPWQ E+EDAFGFTETVDQLTAIEEV
Sbjct  595   TKTKARRAVREIASELVALYAKRQAAPGHAFSPDTPWQNEMEDAFGFTETVDQLTAIEEV  654

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKP+PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF  R
Sbjct  655   KADMEKPVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTAR  714

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTD AESRA ++G+ DGSVDIVIGTHRLLQTGV WKDLGL++VDEEQ
Sbjct  715   MAGFPVTVKGLSRFTDPAESRAALEGMKDGSVDIVIGTHRLLQTGVVWKDLGLIIVDEEQ  774

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKS+RTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  775   RFGVEHKEHIKSMRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  834

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
              DDKQ+AAALRRELLRDGQAFY+HNRV +ID AA+++  LVPEARVVVAHGQMPE+LLE 
Sbjct  835   QDDKQVAAALRRELLRDGQAFYIHNRVRTIDQAASKIAALVPEARVVVAHGQMPEELLER  894

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TV+ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  895   TVEGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  954

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPP+ PLTETAYDRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG EQSGHVAGVGF
Sbjct  955   YFLYPPEQPLTETAYDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGAEQSGHVAGVGF  1014

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADG+TV T +E KDVRIDLPVDA+LPPDYI SDRLRLE 
Sbjct  1015  DLYVRLVGEAVE----AYRAAADGKTVATPQETKDVRIDLPVDANLPPDYIGSDRLRLEA  1070

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAA  D  V AV+DEL DRYG LPEPA+RL  VARLRL+CR  GITDV++ SA+TV
Sbjct  1071  YRRLAAAQDDAGVDAVIDELVDRYGPLPEPAQRLVGVARLRLVCREYGITDVSSVSASTV  1130

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRA-GGLGAPRIRDVELVQMVADLI  1199
             +LSP+ LPDSA +RLKRMYPGA YRATT TV VPIPRA   +GAPRIRD ELV MVA L+
Sbjct  1131  KLSPMELPDSALLRLKRMYPGATYRATTGTVSVPIPRATDSVGAPRIRDAELVAMVAGLV  1190

Query  1200  TALAGKPRQHI  1210
              AL GKP+  I
Sbjct  1191  LALNGKPQAQI  1201


>gi|120405727|ref|YP_955556.1| transcription-repair coupling factor [Mycobacterium vanbaalenii 
PYR-1]
 gi|119958545|gb|ABM15550.1| transcription-repair coupling factor [Mycobacterium vanbaalenii 
PYR-1]
Length=1212

 Score = 1912 bits (4954),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 962/1218 (79%), Positives = 1068/1218 (88%), Gaps = 15/1218 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MT  G     TPIAGLV+LAL  P  Q++ +RAG RP +L L+ PASAR+ VASALA+ G
Sbjct  1     MTVSGTLHVHTPIAGLVDLALRDPALQEIARRAGDRPADLNLVGPASARVFVASALAQPG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
              LLVVTATGREADDL AELRGVFGDAVAL PSWETLPHERLSPGVDTVG R+M LRRL H
Sbjct  61    LLLVVTATGREADDLTAELRGVFGDAVALFPSWETLPHERLSPGVDTVGARMMLLRRLTH  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LGPPL +VVT+ RSLLQPM P L  ++P+TLTVG E+ FD VVARLV+LAY+RVD
Sbjct  121   PDDARLGPPLRIVVTTARSLLQPMAPDLAEVDPVTLTVGGEADFDAVVARLVDLAYSRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVG+RGEFAVRGGILD+F PTAEHPVRVEFWGDE++EMRMFSVADQRSIPEI+I TL+A 
Sbjct  181   MVGKRGEFAVRGGILDVFPPTAEHPVRVEFWGDEVSEMRMFSVADQRSIPEIEIDTLIAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELLL+ +VR RAA LA+ HP  E++VTGS  DMLAKLAEGI VDGMEA+LP+L    
Sbjct  241   PCRELLLTAEVRDRAAALASEHPVLENSVTGSVPDMLAKLAEGIPVDGMEALLPLLRPSD  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
              A L D LP+GTP+LVCDPEKVRTRAADLI+TGREFLEASWS AA+G      P+D+E L
Sbjct  301   FATLPDHLPEGTPLLVCDPEKVRTRAADLIKTGREFLEASWSTAAVG---GDVPIDIEAL  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIE---LDVRAAPSARGHQRDIDEIFAM  417
             G SG+V     R AA   GHPWWTLSQL D  A E   LD+R APSARG Q ++DEIFAM
Sbjct  358   GVSGYVGYGDARDAARAGGHPWWTLSQL-DSGAGESTALDIRPAPSARGQQHNLDEIFAM  416

Query  418   LRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGV  477
             LRAH+ATGG+  +V PG+GTA RVVE+LSESD PA +L+PG  P  GVVGV++GPL DGV
Sbjct  417   LRAHVATGGFGVVVTPGSGTAMRVVEQLSESDIPATVLEPGAVPGEGVVGVIKGPLHDGV  476

Query  478   IIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEM  537
             +IPGANLVVITETDLTG+R +A EGK+LAAKRRN+VDPLALTAGDLVVHDQHGIGRFVEM
Sbjct  477   VIPGANLVVITETDLTGNRAAATEGKKLAAKRRNVVDPLALTAGDLVVHDQHGIGRFVEM  536

Query  538   VERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSD  597
              ER +GGARREYLVLEYASAKRGGG   +D+LYVPMDSLDQLSRYVGG+AP LSRLGGSD
Sbjct  537   TERVIGGARREYLVLEYASAKRGGG---SDRLYVPMDSLDQLSRYVGGEAPTLSRLGGSD  593

Query  598   WANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAI  657
             WANTKTKAR+AVREIA ELV+LYAKRQAS GHAF+PDTPWQ E+EDAFGFTETVDQLTAI
Sbjct  594   WANTKTKARKAVREIAAELVALYAKRQASAGHAFAPDTPWQREMEDAFGFTETVDQLTAI  653

Query  658   EEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF  717
              EVK+DMEKP+PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF
Sbjct  654   TEVKSDMEKPVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF  713

Query  718   GERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVD  777
               RM+GFPVT+KGLSRFTD AESRA I+G+ DGSVDIVIGTHRLLQTGV WKDLGLV+VD
Sbjct  714   TNRMTGFPVTVKGLSRFTDPAESRATIEGMKDGSVDIVIGTHRLLQTGVTWKDLGLVIVD  773

Query  778   EEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTY  837
             EEQRFGVEHKEHIKS+RTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTY
Sbjct  774   EEQRFGVEHKEHIKSMRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTY  833

Query  838   VGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDL  897
             VGPHDDKQ+AAALRRE+LRDGQAFY+HNRV +ID+AAA+VR+LVPEARVVVAHGQMPE+ 
Sbjct  834   VGPHDDKQVAAALRREMLRDGQAFYIHNRVRTIDSAAAKVRQLVPEARVVVAHGQMPEEQ  893

Query  898   LETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRER  957
             LE TV+ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRER
Sbjct  894   LEKTVEGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRER  953

Query  958   GYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAG  1017
             GYAYFLYPP+VPLTETAYDRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG EQSGHVAG
Sbjct  954   GYAYFLYPPEVPLTETAYDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGAEQSGHVAG  1013

Query  1018  VGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLR  1077
             VGFDLYVRLVGEA+E    AYRAAADG+TV   EEPKDVRIDLPVDAHLPPDYI SDRLR
Sbjct  1014  VGFDLYVRLVGEAVE----AYRAAADGKTVAAPEEPKDVRIDLPVDAHLPPDYIGSDRLR  1069

Query  1078  LEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASA  1137
             LE YRRLAAA  D  V AV++EL DRYG LPEPA+RL AVARLRLL R  G+T++ A SA
Sbjct  1070  LEAYRRLAAAPDDAAVDAVIEELVDRYGPLPEPAQRLVAVARLRLLARAHGVTEIGAPSA  1129

Query  1138  ATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAG-GLGAPRIRDVELVQMVA  1196
              T+R+SP+TLPDSAQ+RLKR+Y GA+YRATT+TVQVP+PRAG G+G+PRIRD+ELV  VA
Sbjct  1130  TTLRISPMTLPDSAQLRLKRLYSGANYRATTSTVQVPVPRAGSGVGSPRIRDLELVAFVA  1189

Query  1197  DLITALAGKPRQHIGITN  1214
              L+ A+ GKP + + IT 
Sbjct  1190  GLLLAIDGKPGEEVDITK  1207


>gi|118471657|ref|YP_889663.1| transcription-repair coupling factor [Mycobacterium smegmatis 
str. MC2 155]
 gi|118172944|gb|ABK73840.1| transcription-repair coupling factor [Mycobacterium smegmatis 
str. MC2 155]
Length=1215

 Score = 1892 bits (4901),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 969/1224 (80%), Positives = 1081/1224 (89%), Gaps = 11/1224 (0%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG     TPIAGLVELALS P+ Q +++RA  RP +L L+ PASAR+LVA+ALA+ G
Sbjct  1     MTAPGHTSVQTPIAGLVELALSDPSLQDVIRRAADRPADLALVGPASARVLVAAALAQNG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVV ATGREAD+L AELRGVFGD+VAL PSWETLPHERLSPGV+TVG RLM LRRLA 
Sbjct  61    PLLVVAATGREADELTAELRGVFGDSVALFPSWETLPHERLSPGVETVGARLMLLRRLAR  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDD  LG PL VVVT+ RSLLQPM P L  +EP+TL+VG E  F+ VVARLV+L+YTRVD
Sbjct  121   PDDETLGAPLRVVVTTTRSLLQPMAPDLVDIEPVTLSVGAEMEFEDVVARLVDLSYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVG+RGEFAVRGGILD+F PTAEHPVRVEFWGDEI+EMR F++ADQRSIPE+ + T+VA 
Sbjct  181   MVGKRGEFAVRGGILDVFPPTAEHPVRVEFWGDEISEMRAFAIADQRSIPEVPVQTVVAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELL+++DVR RAA LAA HP  E+TV G+  DMLAKLAEGI VDGMEA+LP+L    
Sbjct  241   PCRELLMTDDVRERAAALAAEHPTTENTVPGTVPDMLAKLAEGIPVDGMEALLPLLHPIE  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
                LT  LP+G PVLVCDPEKVRTRAADLI+TGREFLEASWS AA+G     AP+D+E L
Sbjct  301   PTTLTRHLPEGAPVLVCDPEKVRTRAADLIKTGREFLEASWSTAAVG---GDAPIDLEAL  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             G SGFV  ++ R AA   GHPWWTLSQLSDESA+ELD+R+APSARG Q +++EIFAMLRA
Sbjct  358   GASGFVTFEEAREAAREGGHPWWTLSQLSDESAVELDIRSAPSARGSQHNLEEIFAMLRA  417

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H+ATGGYAA+V PG GTAHRVVE+L E+DT A +L+PG APK GVVGVL+GPL  GV++P
Sbjct  418   HVATGGYAAVVTPGIGTAHRVVEQLGEADTAATILEPGTAPKAGVVGVLKGPLCSGVVLP  477

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLV+ITETDLTG+RV+A EG++LAAKRRN+VDPLALTAGDLVVHDQHGIG+FVEM ER
Sbjct  478   GANLVIITETDLTGNRVTANEGRKLAAKRRNVVDPLALTAGDLVVHDQHGIGKFVEMTER  537

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
              VGGARREYLVLEYAS+KRGGG   TDKLYVPMDSLDQLSRYVGG+AP+LSRLGGSDWAN
Sbjct  538   VVGGARREYLVLEYASSKRGGG---TDKLYVPMDSLDQLSRYVGGEAPSLSRLGGSDWAN  594

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKARRAVREIA ELV+LYAKRQ++PGHAF PDTPWQAE+EDAFGFTET+DQLTAI+EV
Sbjct  595   TKTKARRAVREIASELVALYAKRQSAPGHAFGPDTPWQAEMEDAFGFTETIDQLTAIQEV  654

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K+DMEKP+PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF  R
Sbjct  655   KSDMEKPVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFTNR  714

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTD AESRAVI+GL DGSVD+VIGTHRLLQTGV WKDLGL++VDEEQ
Sbjct  715   MAGFPVTVKGLSRFTDPAESRAVIEGLKDGSVDVVIGTHRLLQTGVTWKDLGLIIVDEEQ  774

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKS+RTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP
Sbjct  775   RFGVEHKEHIKSMRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  834

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQ+AAALRRELLRDGQAFY+HNRV +ID AAARVR+LVPEARVVVAHGQM E+ LE 
Sbjct  835   HDDKQVAAALRRELLRDGQAFYIHNRVRTIDEAAARVRQLVPEARVVVAHGQMNEETLEK  894

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TV+ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  895   TVEGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  954

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPP  PLTETAYDRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG EQSGHVAGVGF
Sbjct  955   YFLYPPNKPLTETAYDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGAEQSGHVAGVGF  1014

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADG+TV T +E KDVRIDLPVDAHLPP+YI SDRLRLE 
Sbjct  1015  DLYVRLVGEAVE----AYRAAADGKTVATPQEQKDVRIDLPVDAHLPPEYIGSDRLRLEA  1070

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAA+ D  VA+VVDEL DRYG LPEPA+RL AVARLRLLCR  GIT++ A SA+TV
Sbjct  1071  YRRLAAAADDDAVASVVDELIDRYGPLPEPAQRLVAVARLRLLCREFGITEIGAVSASTV  1130

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAG-GLGAPRIRDVELVQMVADLI  1199
             RLSP+ LPDSAQ+RLKRMYPG HYRATT+TVQVP+PRAG G+GAPRIRD+ELVQ VA L+
Sbjct  1131  RLSPMVLPDSAQLRLKRMYPGGHYRATTSTVQVPLPRAGEGVGAPRIRDLELVQWVAGLV  1190

Query  1200  TALAGKPRQHIGITNPSPPGEDGR  1223
               L GK +  + ++  S P  + +
Sbjct  1191  LVLNGKGQGDVDMSKFSNPAGEAK  1214


>gi|333989623|ref|YP_004522237.1| transcription-repair coupling factor Mfd (TrcF) [Mycobacterium 
sp. JDM601]
 gi|333485591|gb|AEF34983.1| transcription-repair coupling factor Mfd (TrcF) [Mycobacterium 
sp. JDM601]
Length=1223

 Score = 1884 bits (4880),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 985/1225 (81%), Positives = 1076/1225 (88%), Gaps = 14/1225 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTAPG A   TPIAGLVE ALSAPTF  L++RA  RP EL L+ PA+ R   A+A+AR  
Sbjct  1     MTAPGHASPATPIAGLVEAALSAPTFVDLIERADSRPAELNLVGPAATRPFAAAAVARNT  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             PLLVVTATG EADDLAAELRGV+GD VAL PSWETLPHERLSPGVDTVG R++ LRRLA 
Sbjct  61    PLLVVTATGHEADDLAAELRGVYGDTVALFPSWETLPHERLSPGVDTVGARMLLLRRLAR  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA LGPPL VVVT+ RSLLQPMTP L  +EP+TLTVG+E+PF+ V+ARLVELAYTRVD
Sbjct  121   PDDAHLGPPLRVVVTTARSLLQPMTPHLDAIEPVTLTVGEETPFEAVIARLVELAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             +VGRRGEFAVRGGILD+F PTAEHPVR+EFWGDEITEMR FSVADQRSIPEID  T+VA 
Sbjct  181   LVGRRGEFAVRGGILDVFPPTAEHPVRIEFWGDEITEMRPFSVADQRSIPEIDAGTVVAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
             ACRELLL++DVRARAAQLA  HP  ++TVTG   DMLAKLAEGI VDGMEA+  VL    
Sbjct  241   ACRELLLTDDVRARAAQLAGDHPRTDNTVTGGVGDMLAKLAEGIPVDGMEALGSVLRPGP  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
              ALLTDQL  GTPVL+CDPEKVR RA DLI+TGREFLEASWSVAA+G     AP+DVEQL
Sbjct  301   QALLTDQLAAGTPVLICDPEKVRARAGDLIKTGREFLEASWSVAAIG---GDAPIDVEQL  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRA  420
             GGSGF +L +VR AA   GHPWWTLSQL D  AIEL+VR +PSARG QRDI+ IFAMLRA
Sbjct  358   GGSGFRDLAEVRKAALDAGHPWWTLSQLPDPEAIELEVRPSPSARGRQRDIEAIFAMLRA  417

Query  421   HIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIP  480
             H ATGG AA+V PG GTA R+VE+L+ES+T A +L+PG AP+PGVVGVLQGPL DGV+I 
Sbjct  418   HTATGGAAAIVTPGVGTARRLVEQLAESETAATLLEPGAAPQPGVVGVLQGPLHDGVVIG  477

Query  481   GANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             GANLV++TETDLTG+RV+  EGKRLAAKRRN VDPLALTAGDLVVHDQHGIG+FVEM ER
Sbjct  478   GANLVIVTETDLTGNRVAGPEGKRLAAKRRNAVDPLALTAGDLVVHDQHGIGKFVEMTER  537

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TVGGARREYLVLEYAS KRG  A  TDKLYVPMDSLDQLSRYVGGQAP LS+LGGSDW+ 
Sbjct  538   TVGGARREYLVLEYASGKRG--ANGTDKLYVPMDSLDQLSRYVGGQAPGLSKLGGSDWSQ  595

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TKTKAR+AVREIA ELV+LYAKRQA+PGHAF+PDTPWQAE+EDAFGFTETVDQLTAI EV
Sbjct  596   TKTKARKAVREIADELVALYAKRQAAPGHAFAPDTPWQAEMEDAFGFTETVDQLTAIGEV  655

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADMEKP+PMDRVICGDVGYGKTEIAVRAAFKAVQDG+QVAVLVPTTLLADQHLQTF  R
Sbjct  656   KADMEKPVPMDRVICGDVGYGKTEIAVRAAFKAVQDGRQVAVLVPTTLLADQHLQTFTTR  715

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M+GFPVT+KGLSRFTD  ES+AVIDGLADGSVD+VIGTHRLLQTGV WK+LGLV+VDEEQ
Sbjct  716   MAGFPVTVKGLSRFTDPKESKAVIDGLADGSVDVVIGTHRLLQTGVAWKNLGLVIVDEEQ  775

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE+RYPVLTYVGP
Sbjct  776   RFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEDRYPVLTYVGP  835

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             HDDKQ+AAALRRELLRDGQ FYVHNRVSSIDAAAARVR LVPEARVVVAHGQMPE+LLET
Sbjct  836   HDDKQVAAALRRELLRDGQIFYVHNRVSSIDAAAARVRALVPEARVVVAHGQMPEELLET  895

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQ FWNRE+DILVCTTI+ETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA
Sbjct  896   TVQGFWNREYDILVCTTIIETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  955

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYP   PLTETA+DRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG+EQSGHVAGVGF
Sbjct  956   YFLYPRDTPLTETAHDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGVEQSGHVAGVGF  1015

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E YR AYR    G  V T EEPKDVRIDLPVDAHLPP+YI SDRLRLE 
Sbjct  1016  DLYVRLVGEAVEAYRAAYR----GDLV-TTEEPKDVRIDLPVDAHLPPEYINSDRLRLEA  1070

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YRRLAAA  D  ++AVV+ELTDRYG LPEPA RL AVARLRLLCR  GIT+V+ ASA T+
Sbjct  1071  YRRLAAAPDDAAISAVVEELTDRYGPLPEPAGRLVAVARLRLLCRSVGITEVSVASATTL  1130

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPR----AGGLGAPRIRDVELVQMVA  1196
             +L+P+TLPDSAQ+RLKR++P A YRATTATVQVPIPR       +GAPRIRDVELVQMVA
Sbjct  1131  KLAPMTLPDSAQLRLKRLHPSASYRATTATVQVPIPRAGGAGAPVGAPRIRDVELVQMVA  1190

Query  1197  DLITALAGKPRQHIGITNPSPPGED  1221
             DLI+AL GKP   + +   +P   D
Sbjct  1191  DLISALDGKPAGRLDMAGAAPATRD  1215


>gi|315442986|ref|YP_004075865.1| transcription-repair coupling factor Mfd [Mycobacterium sp. Spyr1]
 gi|315261289|gb|ADT98030.1| transcription-repair coupling factor Mfd [Mycobacterium sp. Spyr1]
Length=1202

 Score = 1866 bits (4834),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 963/1211 (80%), Positives = 1056/1211 (88%), Gaps = 20/1211 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTA G     TPIAGLVELAL  P+ Q++ +R   RP +L  + PASAR  VASALA+ G
Sbjct  1     MTASGTLHVHTPIAGLVELALRDPSLQEIARRGADRPADLHFVGPASARPFVASALAQAG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
              LLVVTATGREADDL AELRGVFGD+VA+ PSWETLPHERLSPGVDTVG R+M LRRLA 
Sbjct  61    LLLVVTATGREADDLTAELRGVFGDSVAMFPSWETLPHERLSPGVDTVGARMMLLRRLAF  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LG PL VVV + RSL+QPM P L  ++P+TLTVG E+ FD VVARLV+LAYTRVD
Sbjct  121   PDDARLGEPLRVVVATARSLVQPMAPDLAQIDPVTLTVGAEADFDSVVARLVDLAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVG+RGEFAVRGGILD+F PTAEHPVRVEFWGDEI+EMRMFSVADQRSIPEI+I T++A 
Sbjct  181   MVGKRGEFAVRGGILDLFPPTAEHPVRVEFWGDEISEMRMFSVADQRSIPEIEIDTVIAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELLL+ DVR RAA L+A HP +E+ V GS  DMLA+LAEGI VDGMEA+LP+L    
Sbjct  241   PCRELLLTADVRERAAALSAEHPVSENNVPGSVPDMLARLAEGIPVDGMEALLPLLRPSD  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
              A L D LP+GTP+LVCDPEKVRTRAADLI+TGREFLEASWS AA+G      P+D+E L
Sbjct  301   FATLPDHLPEGTPLLVCDPEKVRTRAADLIKTGREFLEASWSTAAVG---GDVPIDLEAL  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIE---LDVRAAPSARGHQ---RDIDEI  414
             G SG+V  ++ R AA   GH WWTLSQL D  A E   LD+R APSAR  Q      DEI
Sbjct  358   GASGYVTYNEARDAARDGGHAWWTLSQL-DSGAGESTALDIRPAPSARLAQPIATGPDEI  416

Query  415   FAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLR  474
             FAMLRAH+ATGG+ A+V PG GT  RVVE+LSESDTPA +L+PG APK GVVGVL+GPL 
Sbjct  417   FAMLRAHVATGGFGAVVTPGAGTCQRVVEQLSESDTPAMILEPGMAPKEGVVGVLKGPLH  476

Query  475   DGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRF  534
             DGV+IPGANLVVITETDLTG+R +A EGK+LAAKRRN+VDPLALTAGDLVVHDQHGIGRF
Sbjct  477   DGVVIPGANLVVITETDLTGNRAAATEGKKLAAKRRNVVDPLALTAGDLVVHDQHGIGRF  536

Query  535   VEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLG  594
             VEM ER +GGARREYLVLEYASAKRGGG   +D+LYVPMDSLDQLSRYVGG+AP LSRLG
Sbjct  537   VEMTERVIGGARREYLVLEYASAKRGGG---SDRLYVPMDSLDQLSRYVGGEAPTLSRLG  593

Query  595   GSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQL  654
             GSDWANTKTKARRAVREIA ELV+LYAKRQASPGHAFSPDTPWQ E+EDAFGFTETVDQL
Sbjct  594   GSDWANTKTKARRAVREIAAELVTLYAKRQASPGHAFSPDTPWQVEMEDAFGFTETVDQL  653

Query  655   TAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHL  714
             TAI EVK+DMEKP+PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHL
Sbjct  654   TAITEVKSDMEKPVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHL  713

Query  715   QTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLV  774
             QTF  RM+GFPVT+KGLSRFTD AESRA ++G+ DGSVDIVIGTHRLLQTGV WKDLGLV
Sbjct  714   QTFTNRMTGFPVTVKGLSRFTDPAESRATMEGMKDGSVDIVIGTHRLLQTGVTWKDLGLV  773

Query  775   VVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPV  834
             +VDEEQRFGVEHKEHIKS+RTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPV
Sbjct  774   IVDEEQRFGVEHKEHIKSMRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPV  833

Query  835   LTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMP  894
             LTYVG HDDKQIAAALRRE+LRDGQAFY+HNRV +ID+AAA+VR+LVPEARVVVAHGQMP
Sbjct  834   LTYVGQHDDKQIAAALRREMLRDGQAFYIHNRVRTIDSAAAKVRQLVPEARVVVAHGQMP  893

Query  895   EDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRS  954
             E+ LE TV+ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRS
Sbjct  894   EEQLEKTVEGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRS  953

Query  955   RERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGH  1014
             RERGYAYFLYPP+VPLTETAYDRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG EQSGH
Sbjct  954   RERGYAYFLYPPEVPLTETAYDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGAEQSGH  1013

Query  1015  VAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASD  1074
             VAGVGFDLYVRLVGEA+E    AYRAAADG+TV T EEPKDVRIDLPVDAHLPPDYI SD
Sbjct  1014  VAGVGFDLYVRLVGEAVE----AYRAAADGKTVATPEEPKDVRIDLPVDAHLPPDYIGSD  1069

Query  1075  RLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA  1134
             RLRLE YRRLAAA  D  V AV++EL DRYG LPEPA  L AVARLRLL R +GIT+V A
Sbjct  1070  RLRLEAYRRLAAAPDDAAVDAVIEELVDRYGPLPEPAELLVAVARLRLLARAAGITEVGA  1129

Query  1135  --ASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAG-GLGAPRIRDVEL  1191
               ASA+T+R+SPLTLPDSAQ+RLKR+Y GA+YRATT+TVQVPIPRAG G+GAPRIRD EL
Sbjct  1130  VSASASTLRISPLTLPDSAQLRLKRLYSGANYRATTSTVQVPIPRAGQGVGAPRIRDREL  1189

Query  1192  VQMVADLITAL  1202
             V  VA LI  L
Sbjct  1190  VDFVAGLIKVL  1200


>gi|145222538|ref|YP_001133216.1| transcription-repair coupling factor [Mycobacterium gilvum PYR-GCK]
 gi|145215024|gb|ABP44428.1| transcription-repair coupling factor [Mycobacterium gilvum PYR-GCK]
Length=1198

 Score = 1864 bits (4828),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 962/1208 (80%), Positives = 1056/1208 (88%), Gaps = 18/1208 (1%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             MTA G     TPIAGLV LAL  P+ Q++ +R   RP +L  + PASARL VASALA+ G
Sbjct  1     MTASGTLHVHTPIAGLVGLALRDPSLQEIARRGVDRPADLHFVGPASARLFVASALAQAG  60

Query  61    PLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
              LLVVTATGREADDL AELRGVFGDAVA+ PSWETLPHERLSPGVDTVG R+M LRRLA 
Sbjct  61    LLLVVTATGREADDLTAELRGVFGDAVAMFPSWETLPHERLSPGVDTVGARMMLLRRLAF  120

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDA+LG PL VVVT+ RSLLQPM P L  ++P+TLTVG E+ FD  VARLV+LAYTRVD
Sbjct  121   PDDARLGEPLRVVVTTARSLLQPMAPDLARIDPVTLTVGGEADFDETVARLVDLAYTRVD  180

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVG+RGEFAVRGGILD+F PTAEHPVRVEFWGDEI+EMRMFSVADQRSIPEI+I T++A 
Sbjct  181   MVGKRGEFAVRGGILDLFPPTAEHPVRVEFWGDEISEMRMFSVADQRSIPEIEIDTVIAV  240

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELLL+ DVR RAA LA  HP +E+ V GS  DMLA+LAEGI VDGMEA+LP+L    
Sbjct  241   PCRELLLTADVRERAAALAEEHPVSENNVPGSVPDMLARLAEGIPVDGMEALLPLLRPSD  300

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
              A L D LP+GTP+LVCDPEKVRTRAADLI+TGREFLEASWS AA+G      P+D+E L
Sbjct  301   FATLPDHLPEGTPLLVCDPEKVRTRAADLIKTGREFLEASWSTAAVG---GDVPIDLEAL  357

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIE---LDVRAAPSARGHQRDIDEIFAM  417
             G SG+V  ++ R AA   GH WWTLSQL D  A E   LD+R APSARG Q +++EIFAM
Sbjct  358   GASGYVTYNEARDAARDGGHGWWTLSQL-DSGAGESTALDIRPAPSARG-QHNLEEIFAM  415

Query  418   LRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGV  477
             LRAH+ATGG   +V PG GT  RVVE+LSESDTPA +L+PG APK GVVGVL+GPL DGV
Sbjct  416   LRAHVATGGCGVVVTPGAGTCQRVVEQLSESDTPAMILEPGMAPKDGVVGVLKGPLHDGV  475

Query  478   IIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEM  537
             +IPGANLVVITETDLTG+R +A EGK+LAAKRRN+VDPLALTAGDLVVHDQHGIGRFVEM
Sbjct  476   VIPGANLVVITETDLTGNRAAATEGKKLAAKRRNVVDPLALTAGDLVVHDQHGIGRFVEM  535

Query  538   VERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSD  597
              ER +GGARREYLVLEYASAKRGGGA   D+LYVPMDSLDQLSRYVGG+AP LSRLGGSD
Sbjct  536   TERVIGGARREYLVLEYASAKRGGGA---DRLYVPMDSLDQLSRYVGGEAPTLSRLGGSD  592

Query  598   WANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAI  657
             WANTKTKARRAVREIA ELV+LYAKRQASPGHAFSPDTPWQ E+EDAFGFTETVDQLTAI
Sbjct  593   WANTKTKARRAVREIAAELVTLYAKRQASPGHAFSPDTPWQVEMEDAFGFTETVDQLTAI  652

Query  658   EEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF  717
              EVK+DMEKP+PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF
Sbjct  653   TEVKSDMEKPVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTF  712

Query  718   GERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVD  777
               RM+GFPVT++GLSRFTD A SRA ++G+ DGSVDIVIGTHRL+QTGV WKDLGLV+VD
Sbjct  713   TARMTGFPVTVRGLSRFTDPASSRATLEGMKDGSVDIVIGTHRLIQTGVTWKDLGLVIVD  772

Query  778   EEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTY  837
             EEQRFGVEHKEHIKS+RTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTY
Sbjct  773   EEQRFGVEHKEHIKSMRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTY  832

Query  838   VGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDL  897
             VG HDDKQ+AAALRRE+LRDGQAFY+HNRV +ID+AAA++R+LVPEARVVVAHGQMPE+ 
Sbjct  833   VGQHDDKQVAAALRREMLRDGQAFYIHNRVRTIDSAAAKIRQLVPEARVVVAHGQMPEEQ  892

Query  898   LETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRER  957
             LE TV+ FWNRE+DILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRER
Sbjct  893   LEKTVEGFWNREYDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRER  952

Query  958   GYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAG  1017
             GYAYFLYPP+VPLTETAYDRLATIAQNNELGAGMAVA+KDLEIRGAGNVLG EQSGHVAG
Sbjct  953   GYAYFLYPPEVPLTETAYDRLATIAQNNELGAGMAVAMKDLEIRGAGNVLGAEQSGHVAG  1012

Query  1018  VGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLR  1077
             VGFDLYVRLVGEA+E    AYRAAADG+TV T EEPKDVRIDLPVDAHLPPDYI SDRLR
Sbjct  1013  VGFDLYVRLVGEAVE----AYRAAADGKTVATPEEPKDVRIDLPVDAHLPPDYIGSDRLR  1068

Query  1078  LEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA--A  1135
             LEGYRRLAAA  D  V AVV+EL DRYG LPEPA  L AVARLRLL R +GIT+V A  A
Sbjct  1069  LEGYRRLAAAPDDAAVDAVVEELVDRYGPLPEPAELLVAVARLRLLARAAGITEVGAVSA  1128

Query  1136  SAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAG-GLGAPRIRDVELVQM  1194
             SA+T+R+SPLTLPDSAQ+RLKR+Y GA+YRATT+TVQVPIPRAG G+GAPRIRD ELV  
Sbjct  1129  SASTLRISPLTLPDSAQLRLKRLYSGANYRATTSTVQVPIPRAGQGVGAPRIRDRELVDF  1188

Query  1195  VADLITAL  1202
             VA LI  L
Sbjct  1189  VAGLIKVL  1196


>gi|169628250|ref|YP_001701899.1| transcription-repair coupling factor [Mycobacterium abscessus 
ATCC 19977]
 gi|169240217|emb|CAM61245.1| Probable transcription-repair coupling factor (TrcF) [Mycobacterium 
abscessus]
Length=1216

 Score = 1740 bits (4507),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 900/1224 (74%), Positives = 1027/1224 (84%), Gaps = 25/1224 (2%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALA--R  58
             MTA  P     P+AG++  AL  P F  L      +   L L AP  AR  V + +A   
Sbjct  1     MTATTP-----PLAGVIRTALRDPAFDVLAPAIAAKTG-LDLTAPTCARAFVVTGMADAS  54

Query  59    QGPLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRL  118
               P+LVVTAT REA DL AELR V+GDAV LLPSWETLPHERLSPGVDTVG RL  L RL
Sbjct  55    DAPVLVVTATTREAQDLTAELRDVYGDAVTLLPSWETLPHERLSPGVDTVGARLQVLHRL  114

Query  119   AHPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTR  178
             AHP+D+++G PL VV+T+VRSLLQPM+P+L  +EP+ L VG E  FDGV+ARLVELAYTR
Sbjct  115   AHPEDSRMGVPLRVVITTVRSLLQPMSPELFDLEPVELAVGAELEFDGVIARLVELAYTR  174

Query  179   VDMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLV  238
             VDMV  RGEFAVRGGILD+F+PTA+HPVRVEFWGDE++EMR FSVADQRSIPE+ + +++
Sbjct  175   VDMVAGRGEFAVRGGILDVFSPTADHPVRVEFWGDEVSEMRYFSVADQRSIPELQVDSVL  234

Query  239   AFACRELLLSEDVRARAAQLAARHPAAEST----VTGSASDMLAKLAEGIAVDGMEAVLP  294
             A  CRELLL++ VRARAA+LA+    + S     +     +MLAKLA+GI VDGME++LP
Sbjct  235   AMPCRELLLTDQVRARAAELASAAGVSGSEEGHRLGAGVGEMLAKLADGICVDGMESLLP  294

Query  295   VLWSDGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAP  354
             VL S    +L D LPD  PVLVCDPEKVRTRAADL RTGREFLEASWSVAA+G+    AP
Sbjct  295   VLHSGKLTMLVDHLPDHAPVLVCDPEKVRTRAADLERTGREFLEASWSVAAIGS---DAP  351

Query  355   VDVEQLGGSGFVELDQVRAAAARTGHPWWTLSQL--SDESAIELDVRAAPSARGHQRDID  412
             +DVE L  SGF ELD V+ AA   G+PWW+LS L   ++ AI L VR +PSARGH+    
Sbjct  352   IDVEALADSGFRELDDVKHAAGEAGYPWWSLSPLGMDNDQAIGLAVRPSPSARGHKEGAA  411

Query  413   EIFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGP  472
             EIFAMLRAH+ TGG AA+VA G GT HR++E+L+E++TPA +L+PG  P  GVVGVL+G 
Sbjct  412   EIFAMLRAHVMTGGRAAVVAAGAGTTHRIIEQLAETETPATLLEPGAEPAEGVVGVLRGH  471

Query  473   LRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIG  532
             L DGV++ GAN+V++TETDLTGSRV+A +GKRL AKRRN VDPLAL+AGDLVVHDQHGIG
Sbjct  472   LTDGVVLTGANIVIVTETDLTGSRVAATDGKRLPAKRRNQVDPLALSAGDLVVHDQHGIG  531

Query  533   RFVEMVERTVGGARREYLVLEYASAKRGGGAK-NTDKLYVPMDSLDQLSRYVGGQAPALS  591
             RFVEMVERTVGGARREYLVLEYAS KRG  A   +D+LYVPMDSLDQLSRYVGG++P LS
Sbjct  532   RFVEMVERTVGGARREYLVLEYASGKRGAAAGGQSDRLYVPMDSLDQLSRYVGGESPGLS  591

Query  592   RLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETV  651
             RLGGSDW NTKTKAR+AVREIAGELV+LYA RQA+PGHAF+PDTPWQ E+EDAFGF ETV
Sbjct  592   RLGGSDWTNTKTKARKAVREIAGELVALYAARQAAPGHAFAPDTPWQREMEDAFGFVETV  651

Query  652   DQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAD  711
             DQLTAI EVK+DMEKP+PMDRV+CGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAD
Sbjct  652   DQLTAITEVKSDMEKPVPMDRVVCGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAD  711

Query  712   QHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDL  771
             QHLQTF  R +GFPV + GLSRFTD   S+ V++G+ADGSVDIVIGTHRLLQTGVRWKDL
Sbjct  712   QHLQTFTNRTAGFPVKVAGLSRFTDPLTSKLVVEGMADGSVDIVIGTHRLLQTGVRWKDL  771

Query  772   GLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEER  831
             GLV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEER
Sbjct  772   GLVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEER  831

Query  832   YPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHG  891
             YPVLTYVGPHDDKQ+AAALRRELLRDGQAFYVHNRVS+ID AAAR+R+LVPEARVVVAHG
Sbjct  832   YPVLTYVGPHDDKQVAAALRRELLRDGQAFYVHNRVSTIDKAAARIRDLVPEARVVVAHG  891

Query  892   QMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRV  951
             QMPE++LE TVQ FWNRE+DILVCTTI+ETGLDISNANTLIVERAD FGLSQLHQLRGRV
Sbjct  892   QMPEEMLERTVQGFWNREYDILVCTTIIETGLDISNANTLIVERADIFGLSQLHQLRGRV  951

Query  952   GRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQ  1011
             GRSRERGYAYFLY P+VPLTETAYDRL+TIAQNN+LGAGMAVA+KDLEIRGAGNVLG+EQ
Sbjct  952   GRSRERGYAYFLYSPEVPLTETAYDRLSTIAQNNDLGAGMAVAMKDLEIRGAGNVLGVEQ  1011

Query  1012  SGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYI  1071
             SGHVAGVGFDLYVRLVGEA+E    AYRAAADG+TV TAEEPK+VRIDLPVDAHLP DYI
Sbjct  1012  SGHVAGVGFDLYVRLVGEAVE----AYRAAADGKTVLTAEEPKEVRIDLPVDAHLPTDYI  1067

Query  1072  ASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITD  1131
              SDRLRLE YRRLAAA+   ++ A V+EL DRYG LP P +RL AVA LRLLCR  GITD
Sbjct  1068  GSDRLRLEAYRRLAAAADAAQINAAVEELADRYGPLPLPVQRLVAVASLRLLCREMGITD  1127

Query  1132  VTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRA--GGLGAPRIRDV  1189
             ++      +R+ PL L DSAQ+RLKR++P A YRATT+ VQVPIPRA  GG+G+ RIRD+
Sbjct  1128  LSVV-GTNIRIQPLPLLDSAQLRLKRLHPAAQYRATTSVVQVPIPRAGDGGVGSDRIRDL  1186

Query  1190  ELVQMVADLITALAGKPRQHIGIT  1213
             ELV M+A+L+ AL+G+P   + IT
Sbjct  1187  ELVHMIAELLVALSGRPAGSVDIT  1210


>gi|226365233|ref|YP_002783016.1| transcription-repair coupling factor [Rhodococcus opacus B4]
 gi|226243723|dbj|BAH54071.1| transcription-repair coupling factor [Rhodococcus opacus B4]
Length=1215

 Score = 1658 bits (4294),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 842/1214 (70%), Positives = 985/1214 (82%), Gaps = 34/1214 (2%)

Query  8     CSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTA  67
              SDTP+AGL ++AL      Q+ +  G R   L ++APA AR  VA+ALA +  LL+VTA
Sbjct  11    SSDTPLAGLAKIALGDAVVAQVTEALGRR--HLDIVAPAPARPFVAAALAERTHLLLVTA  68

Query  68    TGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLG  127
             TGREADDL AEL+ + GDAVA  PSWETLPHERLSP  DTVG R+  LRRLA PDD   G
Sbjct  69    TGREADDLTAELQEMIGDAVAQFPSWETLPHERLSPSADTVGRRVEVLRRLARPDDRSYG  128

Query  128   PPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGE  187
              PL VVVT+VRSL+QPM P LG +EP+TL VG E  FDG++ RLVE+AYTRVDMVG+RGE
Sbjct  129   APLQVVVTTVRSLVQPMAPGLGEIEPVTLRVGVEHDFDGLIQRLVEMAYTRVDMVGKRGE  188

Query  188   FAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLL  247
             FAVRGGILD+F+PTA+HPVRVEFWGDE+TE+R FSVADQRS+ E+DI  ++A  CRELLL
Sbjct  189   FAVRGGILDLFSPTADHPVRVEFWGDEVTELRAFSVADQRSLAELDIDAVIAPPCRELLL  248

Query  248   SEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQ  307
             +EDVR RAAQLA  + A  + V     +ML K++ GI V+GMEA+LPVL      LLTD 
Sbjct  249   TEDVRDRAAQLAVDNQADAALV-----EMLDKMSAGIPVEGMEALLPVLRPGQLQLLTDV  303

Query  308   LPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE-------QL  360
             LP+   VL+CDPEK+RTRA DL+RTG+EFLEASW+ A++G A   AP+D          L
Sbjct  304   LPESAHVLLCDPEKIRTRATDLVRTGQEFLEASWTAASIGGA---APLDTSVLKGDGIDL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESA--IELDVRAAPSARGHQRDIDEIFAML  418
             G S +  L QVR +A   G PWWTLS L+  S   +EL +  AP  RG    + E+F  L
Sbjct  361   GASAYRTLSQVRESAETAGLPWWTLSPLASGSGEELELAITPAPQVRGSDELLSELFVSL  420

Query  419   RAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVI  478
             RAH++TGG A +V  G GTAHRV+ERL E++ PA  L PG  P  G VGVL+G L DG++
Sbjct  421   RAHVSTGGRAVIVVAGAGTAHRVLERLREAEVPAAELTPGSEPARGQVGVLRGSLHDGLV  480

Query  479   IPGAN----LVVITETDLTGSRVSA-AEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGR  533
              PG +    LVV+TE+DLTG+RV+A  +G+RL AKRRN VDPLALTAGD+VVHDQHGIGR
Sbjct  481   FPGGDTTPGLVVVTESDLTGNRVAAVGDGRRLPAKRRNQVDPLALTAGDMVVHDQHGIGR  540

Query  534   FVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRL  593
             FVEMVERT+GGARREYLV+EYA++KRG      D+L+VPM+SLDQLSRYVGG+ PALS+L
Sbjct  541   FVEMVERTIGGARREYLVIEYAASKRG---HPGDRLFVPMESLDQLSRYVGGELPALSKL  597

Query  594   GGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQ  653
             GGSDWANTK KAR+AVREIAGELV LYA RQA+PGHAF PDTPWQ E+EDAF FTET DQ
Sbjct  598   GGSDWANTKRKARKAVREIAGELVQLYAARQAAPGHAFGPDTPWQKEMEDAFAFTETHDQ  657

Query  654   LTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQH  713
             LT I EVKADMEK +PMDRV+ GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA QH
Sbjct  658   LTVISEVKADMEKAVPMDRVVIGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQQH  717

Query  714   LQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGL  773
             LQTF ERM+ FPV ++GLSRFTDA ES+ ++ G+ADG +D+V+GTHRLLQT VRWKDLGL
Sbjct  718   LQTFTERMAAFPVKVRGLSRFTDAGESKEIVAGMADGEIDVVVGTHRLLQTAVRWKDLGL  777

Query  774   VVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYP  833
             V+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+P
Sbjct  778   VIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERHP  837

Query  834   VLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQM  893
             +LTYVG + DKQ+AAA+RRELLRDGQ FYVHNRVSSID AA R+RELVPEARVVVAHGQM
Sbjct  838   ILTYVGAYADKQVAAAIRRELLRDGQVFYVHNRVSSIDKAAQRIRELVPEARVVVAHGQM  897

Query  894   PEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGR  953
              ED LE TVQ FW R++D+LVCTTI+ETGLDISNANTLIVERAD+ GLSQLHQLRGRVGR
Sbjct  898   NEDTLERTVQGFWERDYDVLVCTTIIETGLDISNANTLIVERADSLGLSQLHQLRGRVGR  957

Query  954   SRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSG  1013
             SRERGYAYFLYPP+ PLTETAYDRLATI+QN++LGAGMAVA+KDLEIRGAGNVLG EQSG
Sbjct  958   SRERGYAYFLYPPEKPLTETAYDRLATISQNSDLGAGMAVAMKDLEIRGAGNVLGAEQSG  1017

Query  1014  HVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIAS  1073
             HVAGVGFDLYVRLVGEA+E    A+RAAADG+ + T + PK+VRIDLPVDAH+PPDY+ S
Sbjct  1018  HVAGVGFDLYVRLVGEAVE----AFRAAADGKPITTDDAPKEVRIDLPVDAHIPPDYVTS  1073

Query  1074  DRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVT  1133
             DRLRLEGYR+LAAA+    + AVVDEL DRYG LPE  RRL +VA+LRLL R  G+ ++ 
Sbjct  1074  DRLRLEGYRKLAAATELDGITAVVDELVDRYGPLPEEVRRLVSVAKLRLLAREYGLEEI-  1132

Query  1134  AASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRA--GGLGAPRIRDVEL  1191
             A     +++SP+ LPDS Q+RLKR+YP A YRATT  VQ+P+PRA  GG+GA R+RDVEL
Sbjct  1133  AVVGTQLKISPMALPDSKQLRLKRIYPSAQYRATTGMVQLPLPRAGSGGIGAERVRDVEL  1192

Query  1192  VQMVADLITALAGK  1205
             +Q +ADL+ AL GK
Sbjct  1193  LQYIADLVLALDGK  1206


>gi|111022724|ref|YP_705696.1| transcription repair coupling factor [Rhodococcus jostii RHA1]
 gi|110822254|gb|ABG97538.1| transcription repair coupling factor [Rhodococcus jostii RHA1]
Length=1215

 Score = 1654 bits (4284),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 840/1214 (70%), Positives = 982/1214 (81%), Gaps = 34/1214 (2%)

Query  8     CSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTA  67
              SDTP+AGL ++AL      Q+ +  G     L ++AP  AR  VA+ALA +  LL+VTA
Sbjct  11    SSDTPLAGLAKIALGDAVIAQVTEALGRH--HLDIVAPGPARPFVAAALAERTHLLLVTA  68

Query  68    TGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLG  127
             TGREADDL AELR + GDAVA  PSWETLPHERLSP  DTVG R+  LRRLA PDD   G
Sbjct  69    TGREADDLTAELREMIGDAVAQFPSWETLPHERLSPSADTVGRRVEVLRRLARPDDRSYG  128

Query  128   PPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGE  187
              PL V+VT+VRSL+QPM P LG +EP+TL VG E  FDG++ RLVE+AYTRVDMVG+RGE
Sbjct  129   APLQVIVTTVRSLVQPMAPGLGEIEPVTLRVGVEHDFDGLIQRLVEMAYTRVDMVGKRGE  188

Query  188   FAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLL  247
             FAVRGGILD+F+PTA+HPVRVEFWGDE+TE+R FSVADQRS+PE+DI  ++A  CRELLL
Sbjct  189   FAVRGGILDLFSPTADHPVRVEFWGDEVTELRAFSVADQRSLPELDIDAVIAPPCRELLL  248

Query  248   SEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQ  307
             +EDVR RAAQLA  + A  + V     +ML K++ GI V+GMEA+LPVL      LLTD 
Sbjct  249   TEDVRDRAAQLAVDNQADAALV-----EMLDKMSAGIPVEGMEALLPVLRPGQLQLLTDV  303

Query  308   LPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE-------QL  360
             LP+   VL+CDPEK+RTRA DL+RTG+EFLEASW+ A++G A   AP+D          L
Sbjct  304   LPESAHVLLCDPEKIRTRATDLVRTGQEFLEASWTAASIGGA---APLDTSVLRGDGIDL  360

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQLSDESA--IELDVRAAPSARGHQRDIDEIFAML  418
             G S +  L QVR +A   G PWWTLS L+  +   +EL V  AP  RG    + E+F  L
Sbjct  361   GASAYRSLSQVRESAEARGLPWWTLSPLASGNGEELELAVTPAPQVRGSDDLLSELFVSL  420

Query  419   RAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVI  478
             RAH+ TGG A +V  G GTAHRV+ERL E++ PA  L PG  P  G VGVL+G L DG++
Sbjct  421   RAHVTTGGRAVIVVAGAGTAHRVLERLREAEVPAAELAPGTEPPRGQVGVLRGSLHDGLV  480

Query  479   IPG----ANLVVITETDLTGSRVSA-AEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGR  533
              PG    A LV++TE DLTG+RV+A  +GKRL AKRRN VDPLALTAGD+VVHDQHGIGR
Sbjct  481   FPGDDSTAGLVIVTEADLTGNRVAAVGDGKRLPAKRRNQVDPLALTAGDMVVHDQHGIGR  540

Query  534   FVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRL  593
             FVEMVERT+GGARREYLV+EYA++KRG      D+L+VPM+SLDQLSRYVGG+ PALS+L
Sbjct  541   FVEMVERTIGGARREYLVIEYAASKRG---HPGDRLFVPMESLDQLSRYVGGELPALSKL  597

Query  594   GGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQ  653
             GGSDWANTK KAR+AVREIAGELV LYA RQA+PGHAF PDTPWQ E+EDAF FTET DQ
Sbjct  598   GGSDWANTKRKARKAVREIAGELVQLYAARQAAPGHAFGPDTPWQKEMEDAFAFTETHDQ  657

Query  654   LTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQH  713
             LT I EVKADMEK +PMDRV+ GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA QH
Sbjct  658   LTVISEVKADMEKAVPMDRVVIGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQQH  717

Query  714   LQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGL  773
             LQTF ERM+ FPVT++GLSRFTDA +S+  I G+ADG +D+V+GTHRLLQTG+RWKDLGL
Sbjct  718   LQTFTERMAAFPVTVRGLSRFTDAGDSKETIAGMADGEIDVVVGTHRLLQTGIRWKDLGL  777

Query  774   VVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYP  833
             V+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+P
Sbjct  778   VIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERHP  837

Query  834   VLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQM  893
             +LTYVG + DKQ+AAA+RRELLRDGQ FYVHNRVSSID +A R+RELVPEARVVVAHGQM
Sbjct  838   ILTYVGAYADKQVAAAIRRELLRDGQVFYVHNRVSSIDKSAQRIRELVPEARVVVAHGQM  897

Query  894   PEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGR  953
              ED LE TVQ FW R++D+LVCTTI+ETGLDISNANTLIVERAD+ GLSQLHQLRGRVGR
Sbjct  898   NEDTLERTVQGFWERDYDVLVCTTIIETGLDISNANTLIVERADSLGLSQLHQLRGRVGR  957

Query  954   SRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSG  1013
             SRERGYAYFLYPP+ PLTETAYDRLATI+QN++LGAGMAVA+KDLEIRGAGNVLG EQSG
Sbjct  958   SRERGYAYFLYPPEKPLTETAYDRLATISQNSDLGAGMAVAMKDLEIRGAGNVLGAEQSG  1017

Query  1014  HVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIAS  1073
             HVAGVGFDLYVRLVGEA+E    A+RAAADG+ + T + PK+VRIDLPVDAH+PPDY+ S
Sbjct  1018  HVAGVGFDLYVRLVGEAVE----AFRAAADGRPITTEDAPKEVRIDLPVDAHIPPDYVTS  1073

Query  1074  DRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVT  1133
             DRLRLEGYR+LAAA+    + AVVDEL DRYG LPE  RRL +VA+LRLL R  G+ ++ 
Sbjct  1074  DRLRLEGYRKLAAATELDGITAVVDELADRYGPLPEEVRRLVSVAKLRLLAREYGLEEI-  1132

Query  1134  AASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRA--GGLGAPRIRDVEL  1191
             A     ++++P+ LPDS Q+RLKR+YP A YRATT  VQ+P+PRA  GG+GA R+RDVEL
Sbjct  1133  AVVGTQLKIAPMALPDSKQLRLKRIYPSAQYRATTGMVQLPLPRAGSGGIGAERVRDVEL  1192

Query  1192  VQMVADLITALAGK  1205
             +Q +AD + AL GK
Sbjct  1193  LQYIADFVVALDGK  1206


>gi|325676609|ref|ZP_08156287.1| transcription-repair coupling factor [Rhodococcus equi ATCC 33707]
 gi|325552787|gb|EGD22471.1| transcription-repair coupling factor [Rhodococcus equi ATCC 33707]
Length=1225

 Score = 1640 bits (4248),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 837/1221 (69%), Positives = 989/1221 (81%), Gaps = 35/1221 (2%)

Query  2     TAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGP  61
              +  P  + TP+AGL   AL+     ++ Q + GR   + ++AP +AR  VA+ALA +  
Sbjct  6     NSSAPVAAATPLAGLASTALADGAIGRV-QDSVGRTG-VDIVAPVAARPFVAAALADRTQ  63

Query  62    LLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHP  121
             LL+VTATGREADDL  EL+ +FGD VA  PSWETLPHERLSP  DTVG RL  LRRLA P
Sbjct  64    LLLVTATGREADDLTTELQEIFGDGVAQFPSWETLPHERLSPSADTVGRRLQVLRRLACP  123

Query  122   DDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDM  181
             D+A  GPPL V+VT+VRSL+QPM P LG +EP+ L +G E  F  +V+RL ELAYTRVDM
Sbjct  124   DEADYGPPLRVIVTTVRSLVQPMAPGLGDIEPVVLRIGSEHDFGELVSRLAELAYTRVDM  183

Query  182   VGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFA  241
             VG+RGEFAVRGGILD+F PT++HPVRVEFWGDE+TE+R FSVADQRS+PE+++ T+VA  
Sbjct  184   VGKRGEFAVRGGILDVFPPTSDHPVRVEFWGDEVTELRAFSVADQRSLPELELSTVVAPP  243

Query  242   CRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGH  301
             CRELLL+E VR RAAQLA  +PA  + V     +ML KL+ GI V+GMEA+LP+L     
Sbjct  244   CRELLLTEAVRDRAAQLATENPADAALV-----EMLDKLSAGIPVEGMEALLPLLQPGEL  298

Query  302   ALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLG  361
              LLT+ LP  T VL+CDPEK+RTRA DL+RTG+EFLEASW+ A++G A   AP+D   LG
Sbjct  299   QLLTEVLPRETHVLLCDPEKIRTRATDLVRTGQEFLEASWTAASIGGA---APIDTSVLG  355

Query  362   G------SGFVELDQVRAAAARTGHPWWTLSQLSD--ESAIELDVRAAPSARGHQRDIDE  413
             G      S +  L QVR  A   G PWWT+S L+   E  + L V++AP  RG +  +  
Sbjct  356   GGIDLGASAYRSLRQVRENAEAQGRPWWTISPLASGSEDELVLPVQSAPEVRGSEELLSM  415

Query  414   IFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPL  473
             +F  LRAH+ TGG A +V  G+GTAHRV+ERL E+D PAG L PG  P  G+V VL+G L
Sbjct  416   LFVNLRAHVTTGGRAVVVVAGSGTAHRVLERLKEADVPAGELAPGAEPARGLVQVLRGSL  475

Query  474   RDGVIIPGAN------LVVITETDLTGSRVSAA-EGKRLAAKRRNIVDPLALTAGDLVVH  526
              +G+++PG +      LV++TE+DLTG+RV+AA +GK++ AKRRN VDPLALTAGD+VVH
Sbjct  476   HEGIVLPGDDAAGVPGLVIVTESDLTGNRVAAAGDGKKMPAKRRNQVDPLALTAGDMVVH  535

Query  527   DQHGIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQ  586
             DQHGIGRFVEMVERT+GGARREYLV+EYA++KRG      D+L+VPM+SLDQLSRYVGG+
Sbjct  536   DQHGIGRFVEMVERTIGGARREYLVIEYAASKRG---HPGDRLFVPMESLDQLSRYVGGE  592

Query  587   APALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFG  646
              PALS+LGGSDW NTK KAR+AVREIAGELV LYA RQA+PGHAF PDTPWQ E+EDAF 
Sbjct  593   MPALSKLGGSDWQNTKRKARKAVREIAGELVQLYAARQAAPGHAFGPDTPWQKEMEDAFA  652

Query  647   FTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPT  706
             FTET DQLT I+EVKADMEKP+PMDRV+ GDVGYGKTE+AVRAAFKAVQDGKQVAVLVPT
Sbjct  653   FTETHDQLTVIDEVKADMEKPVPMDRVVIGDVGYGKTEVAVRAAFKAVQDGKQVAVLVPT  712

Query  707   TLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGV  766
             TLLA QHLQTF ERM+ FPV ++GLSRFTDAAES+ +I  LADG +DIV+GTHRLLQTGV
Sbjct  713   TLLAQQHLQTFSERMANFPVKVRGLSRFTDAAESKEIIAQLADGEIDIVVGTHRLLQTGV  772

Query  767   RWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILT  826
             RWKDLGLV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILT
Sbjct  773   RWKDLGLVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILT  832

Query  827   PPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARV  886
             PPEER+P+LTYVG + DKQ+AAA+RRELLRDGQ FYVHNRVSSID AA R+RE+VPEARV
Sbjct  833   PPEERHPILTYVGAYADKQVAAAIRRELLRDGQVFYVHNRVSSIDKAAKRIREMVPEARV  892

Query  887   VVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQ  946
             VVAHGQM E+ LE TVQ FW RE D+LVCTTI+ETGLDISNANTLIVERAD+ GLSQLHQ
Sbjct  893   VVAHGQMNEETLEKTVQGFWEREFDVLVCTTIIETGLDISNANTLIVERADSLGLSQLHQ  952

Query  947   LRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNV  1006
             LRGRVGRSRERGYAYFLYPP+ PLTETAYDRLATI+QN++LGAGMAVA+KDLEIRGAGNV
Sbjct  953   LRGRVGRSRERGYAYFLYPPEKPLTETAYDRLATISQNSDLGAGMAVAMKDLEIRGAGNV  1012

Query  1007  LGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHL  1066
             LG EQSGHVAGVGFDLYVRLVGEA+E    AYRA ADG+ V T  E K+VRIDLPVDAH+
Sbjct  1013  LGAEQSGHVAGVGFDLYVRLVGEAVE----AYRAVADGRPVTTEPEVKEVRIDLPVDAHI  1068

Query  1067  PPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRG  1126
             PPDY+ SDRLRLEGYR+LAAA+    +AAVV+EL DRYG LPE   RL +VA+LRLLCR 
Sbjct  1069  PPDYVTSDRLRLEGYRKLAAAADTDAIAAVVEELVDRYGPLPEEVGRLVSVAKLRLLCRE  1128

Query  1127  SGITDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRA--GGLGAP  1184
              GI +V A +   +++SP+ LPDS Q+RLKRMYP A YRATT  VQ+P+PRA  GG+GA 
Sbjct  1129  YGIEEV-AVTGTQLKISPMQLPDSKQLRLKRMYPSAQYRATTGMVQMPLPRAGSGGVGAE  1187

Query  1185  RIRDVELVQMVADLITALAGK  1205
             R+RDVEL+Q +A+ + A+ GK
Sbjct  1188  RVRDVELLQYIANFLLAMDGK  1208


>gi|312138702|ref|YP_004006038.1| transcription repair coupling factor mfd [Rhodococcus equi 103S]
 gi|311888041|emb|CBH47353.1| transcription repair coupling factor Mfd [Rhodococcus equi 103S]
Length=1228

 Score = 1639 bits (4243),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 837/1217 (69%), Positives = 988/1217 (82%), Gaps = 35/1217 (2%)

Query  6     PACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVV  65
             P  + TP+AGL   AL+     ++ Q + GR   + ++AP +AR  VA+ALA +  LL+V
Sbjct  13    PVAAATPLAGLASTALADGAIGRV-QDSVGRTG-VDIVAPVAARPFVAAALADRTQLLLV  70

Query  66    TATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQ  125
             TATGREADDL  EL+ +FGD VA  PSWETLPHERLSP  DTVG RL  LRRLA PD+A 
Sbjct  71    TATGREADDLTTELQEIFGDGVAQFPSWETLPHERLSPSADTVGRRLQVLRRLACPDEAD  130

Query  126   LGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRR  185
              GPPL V+VT+VRSL+QPM P LG +EP+ L +G E  F  +V+RL ELAYTRVDMVG+R
Sbjct  131   YGPPLRVIVTTVRSLVQPMAPGLGDIEPVVLRIGSEHDFGELVSRLAELAYTRVDMVGKR  190

Query  186   GEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACREL  245
             GEFAVRGGILD+F PT++HPVRVEFWGDE+TE+R FSVADQRS+PE+++ T+VA  CREL
Sbjct  191   GEFAVRGGILDVFPPTSDHPVRVEFWGDEVTELRAFSVADQRSLPELELSTVVAPPCREL  250

Query  246   LLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLT  305
             LL+E VR RAAQLA  +PA  + V     +ML KL+ GI V+GMEA+LP+L      LLT
Sbjct  251   LLTEAVRDRAAQLATENPADAALV-----EMLDKLSAGIPVEGMEALLPLLQPGELQLLT  305

Query  306   DQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLGG---  362
             + LP  T VL+CDPEK+RTRA DL+RTG+EFLEASW+ A++G A   AP+D   LGG   
Sbjct  306   EVLPRETHVLLCDPEKIRTRATDLVRTGQEFLEASWTAASIGGA---APIDTSVLGGGID  362

Query  363   ---SGFVELDQVRAAAARTGHPWWTLSQLSD--ESAIELDVRAAPSARGHQRDIDEIFAM  417
                S +  L QVR  A   G PWWT+S L+   E  + L V++AP  RG +  +  +F  
Sbjct  363   LGASAYRSLRQVRENAEAQGRPWWTISPLASGSEDELVLPVQSAPEVRGSEELLSMLFVN  422

Query  418   LRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGV  477
             LRAH+ TGG A +V  G+GTAHRV+ERL E+D PAG L PG  P  G+V VL+G L +G+
Sbjct  423   LRAHVTTGGRAVVVVAGSGTAHRVLERLKEADVPAGELAPGAEPARGLVQVLRGSLHEGI  482

Query  478   IIPGAN------LVVITETDLTGSRVSAA-EGKRLAAKRRNIVDPLALTAGDLVVHDQHG  530
             ++PG +      LV++TE+DLTG+RV+AA +GK++ AKRRN VDPLALTAGD+VVHDQHG
Sbjct  483   VLPGDDAAGVPGLVIVTESDLTGNRVAAAGDGKKMPAKRRNQVDPLALTAGDMVVHDQHG  542

Query  531   IGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPAL  590
             IGRFVEMVERT+GGARREYLV+EYA++KRG      D+L+VPM+SLDQLSRYVGG+ PAL
Sbjct  543   IGRFVEMVERTIGGARREYLVIEYAASKRG---HPGDRLFVPMESLDQLSRYVGGEMPAL  599

Query  591   SRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTET  650
             S+LGGSDW NTK KAR+AVREIAGELV LYA RQA+PGHAF PDTPWQ E+EDAF FTET
Sbjct  600   SKLGGSDWQNTKRKARKAVREIAGELVQLYAARQAAPGHAFGPDTPWQKEMEDAFAFTET  659

Query  651   VDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA  710
              DQLT I+EVKADMEKP+PMDRV+ GDVGYGKTE+AVRAAFKAVQDGKQVAVLVPTTLLA
Sbjct  660   HDQLTVIDEVKADMEKPVPMDRVVIGDVGYGKTEVAVRAAFKAVQDGKQVAVLVPTTLLA  719

Query  711   DQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKD  770
              QHLQTF ERM+ FPV ++GLSRFTDAAES+ +I  LADG VDIV+GTHRLLQTGVRWKD
Sbjct  720   QQHLQTFSERMANFPVKVRGLSRFTDAAESKEIIAQLADGEVDIVVGTHRLLQTGVRWKD  779

Query  771   LGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEE  830
             LGLV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEE
Sbjct  780   LGLVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEE  839

Query  831   RYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAH  890
             R+P+LTYVG + DKQ+AAA+RRELLRDGQ FYVHNRVSSID AA R+RE+VPEARVVVAH
Sbjct  840   RHPILTYVGAYADKQVAAAIRRELLRDGQVFYVHNRVSSIDKAAKRIREMVPEARVVVAH  899

Query  891   GQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGR  950
             GQM E+ LE TVQ FW RE D+LVCTTI+ETGLDISNANTLIVERAD+ GLSQLHQLRGR
Sbjct  900   GQMNEETLEKTVQGFWEREFDVLVCTTIIETGLDISNANTLIVERADSLGLSQLHQLRGR  959

Query  951   VGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIE  1010
             VGRSRERGYAYFLYPP+ PLTETAYDRLATI+QN++LGAGMAVA+KDLEIRGAGNVLG E
Sbjct  960   VGRSRERGYAYFLYPPEKPLTETAYDRLATISQNSDLGAGMAVAMKDLEIRGAGNVLGAE  1019

Query  1011  QSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDY  1070
             QSGHVAGVGFDLYVRLVGEA+E    AYRA ADG+ V T  E K+VRIDLPVDAH+PPDY
Sbjct  1020  QSGHVAGVGFDLYVRLVGEAVE----AYRAVADGRPVTTEPEVKEVRIDLPVDAHIPPDY  1075

Query  1071  IASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGIT  1130
             + SDRLRLEGYR+LAAA+    +AAVV+EL DRYG LPE   RL +VA+LRLLCR  GI 
Sbjct  1076  VTSDRLRLEGYRKLAAAADTDAIAAVVEELVDRYGPLPEEVGRLVSVAKLRLLCREYGIE  1135

Query  1131  DVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRA--GGLGAPRIRD  1188
             +V+  +   +++SP+ LPDS Q+RLKRMYP A YRATT  VQ+P+PRA  GG+GA R+RD
Sbjct  1136  EVS-VTGTQLKISPMQLPDSKQLRLKRMYPSAQYRATTGMVQMPLPRAGSGGVGAERVRD  1194

Query  1189  VELVQMVADLITALAGK  1205
             VEL+Q +A+ + A+ GK
Sbjct  1195  VELLQYIANFLLAMDGK  1211


>gi|229494982|ref|ZP_04388731.1| transcription-repair coupling factor [Rhodococcus erythropolis 
SK121]
 gi|229318076|gb|EEN83948.1| transcription-repair coupling factor [Rhodococcus erythropolis 
SK121]
Length=1208

 Score = 1628 bits (4215),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 821/1213 (68%), Positives = 982/1213 (81%), Gaps = 32/1213 (2%)

Query  7     ACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVT  66
             + + T +AGL E+AL+   F  +++  G     L ++AP  AR  +A+ALA + P+L+VT
Sbjct  5     SSAQTALAGLAEVALADAAFTPVIESIGSAA--LDIVAPKPARPFIAAALAARTPVLLVT  62

Query  67    ATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQL  126
             ATGREADDL +EL  + G  VA  PSWETLPHERLSP  DTVG R+  LRRLA PDDA  
Sbjct  63    ATGREADDLTSELTEMLGGGVAQFPSWETLPHERLSPSADTVGRRVEVLRRLARPDDASY  122

Query  127   GPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRG  186
             G PL V+VT+VRSL+QPM P LG +EP+TL VG E  FD V+ RLVE+AY+RVDMVG+RG
Sbjct  123   GSPLRVIVTTVRSLVQPMAPGLGEIEPITLRVGTEIDFDSVLVRLVEMAYSRVDMVGKRG  182

Query  187   EFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELL  246
             EFAVRGGILD+F+PTA+HPVR+EFWGDE++E+R FSVADQRS+ ++D+ +++A  CREL+
Sbjct  183   EFAVRGGILDLFSPTADHPVRIEFWGDEVSELRYFSVADQRSLADVDVDSVIAPPCRELI  242

Query  247   LSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTD  306
             L+ DVR RAA LAA + A  S V     +ML K++ GI V+GMEA+LPVL      LL+D
Sbjct  243   LTADVRDRAAALAAENQADASLV-----EMLDKISAGIPVEGMEALLPVLKPGELQLLSD  297

Query  307   QLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE-------Q  359
              LP+G  +L+CDPEKVRTRA DL+RTG+EFLEASW+ A++G A   AP+D          
Sbjct  298   VLPEGAHILLCDPEKVRTRATDLVRTGQEFLEASWTAASIGGA---APLDTSILNGGGVD  354

Query  360   LGGSGFVELDQVRAAAARTGHPWWTLSQLSDESA--IELDVRAAPSARGHQRDIDEIFAM  417
             LG S +  L  VR +A   G PWWT+S L+  +   +EL V AAP  RG    + E+F  
Sbjct  355   LGASAYRSLRHVRESAEAAGRPWWTVSPLASGNGEELELPVHAAPQVRGSDDLLAELFVS  414

Query  418   LRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGV  477
             LRAH++TGG AA+V  G GTA RVVERL E++ PA MLD G  P  G V VL+G L DG+
Sbjct  415   LRAHVSTGGRAAIVVAGAGTASRVVERLGEAEVPAKMLDAGATPARGQVAVLRGSLHDGL  474

Query  478   IIPGAN----LVVITETDLTGSRVSA-AEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIG  532
             ++ G +    +V++TE+DLTG+RV+A  +GKRL AKRRN VDPLAL+AGD+VVHDQHGIG
Sbjct  475   VLAGDDSTPGMVIVTESDLTGNRVAAVGDGKRLPAKRRNQVDPLALSAGDMVVHDQHGIG  534

Query  533   RFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSR  592
             RFVEMVERT+GGARREYLV+EYA +KRG      D+L+VPM+SLDQLSRYVGG+ PALS+
Sbjct  535   RFVEMVERTIGGARREYLVIEYAPSKRG---HPGDRLFVPMESLDQLSRYVGGELPALSK  591

Query  593   LGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVD  652
             LGGSDWANTK KAR+AVREIAGELV LYA RQA+PGHAF PDTPWQ ELEDAF FTET+D
Sbjct  592   LGGSDWANTKRKARKAVREIAGELVQLYAARQAAPGHAFGPDTPWQKELEDAFAFTETID  651

Query  653   QLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQ  712
             QLT I EVKADMEKP+PMDRV+ GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA Q
Sbjct  652   QLTVISEVKADMEKPVPMDRVVIGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQQ  711

Query  713   HLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLG  772
             HLQTF ERM+ FPV ++GLSRFTDA +S+ +I G+A+G +DIV+GTHRLLQTG+RWKDLG
Sbjct  712   HLQTFTERMASFPVKVRGLSRFTDAKDSKEIIAGMAEGEIDIVVGTHRLLQTGIRWKDLG  771

Query  773   LVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY  832
             LV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+
Sbjct  772   LVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERH  831

Query  833   PVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQ  892
             P+LTYVG + DKQ+AAA+RRELLRDGQ FYVHNRVSSID AA ++RELVPEARVVVAHGQ
Sbjct  832   PILTYVGAYADKQVAAAIRRELLRDGQVFYVHNRVSSIDKAAKKIRELVPEARVVVAHGQ  891

Query  893   MPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVG  952
             M ED LE TVQ FW R+ D+LVCTTI+ETGLDISNANTLIVERAD+ GLSQLHQLRGRVG
Sbjct  892   MNEDTLEKTVQGFWERDFDVLVCTTIIETGLDISNANTLIVERADSLGLSQLHQLRGRVG  951

Query  953   RSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQS  1012
             RSRERGYAYFLYP + PLTETAYDRLATI+QN++LGAGMAVA+KDLEIRGAGNVLG EQS
Sbjct  952   RSRERGYAYFLYPAEKPLTETAYDRLATISQNSDLGAGMAVAMKDLEIRGAGNVLGAEQS  1011

Query  1013  GHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIA  1072
             GHVAGVGFDLYVRLVGEA+E    A+RAAADG+ +   E  K+VRIDLPVDAH+PPDY+ 
Sbjct  1012  GHVAGVGFDLYVRLVGEAVE----AFRAAADGKPITMDEGTKEVRIDLPVDAHIPPDYVT  1067

Query  1073  SDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDV  1132
             SDRLRLEGYR+LAAA+    +AAVV+EL DRYG LPE  RRL +VA+LRLLCR   + +V
Sbjct  1068  SDRLRLEGYRKLAAATDSDGIAAVVEELVDRYGPLPEEVRRLISVAKLRLLCREYQLEEV  1127

Query  1133  TAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELV  1192
              A +   +++SP++LPDS Q+RLKR+YP A YRATT  VQ+P+PR GG+G+ R+RDVEL+
Sbjct  1128  -AVTGTQLKISPMSLPDSKQIRLKRIYPSAQYRATTGLVQLPLPRTGGVGSDRLRDVELL  1186

Query  1193  QMVADLITALAGK  1205
             Q +AD I A+ G+
Sbjct  1187  QYIADFILAIDGR  1199


>gi|226307788|ref|YP_002767748.1| transcription-repair coupling factor [Rhodococcus erythropolis 
PR4]
 gi|226186905|dbj|BAH35009.1| transcription-repair coupling factor [Rhodococcus erythropolis 
PR4]
Length=1229

 Score = 1626 bits (4210),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 821/1213 (68%), Positives = 982/1213 (81%), Gaps = 32/1213 (2%)

Query  7     ACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVT  66
             + + T +AGL E+AL+   F  ++   G     L ++AP  AR  +A+ALA + P+L+VT
Sbjct  26    SSAQTALAGLAEVALADAAFTPVIDSIGA--PALDIVAPKPARPFIAAALAARTPVLLVT  83

Query  67    ATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQL  126
             ATGREADDL +EL  + G  VA  PSWETLPHERLSP  DTVG R+  LRRLA PDDA  
Sbjct  84    ATGREADDLTSELTEMLGGGVAQFPSWETLPHERLSPSADTVGRRVEVLRRLARPDDASY  143

Query  127   GPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRG  186
             G PL V+VT+VRSL+QPM P LG +EP+TL VG E  FD V+ RLVE+AY+RVDMVG+RG
Sbjct  144   GSPLRVIVTTVRSLVQPMAPGLGEIEPITLRVGTEIDFDSVLVRLVEMAYSRVDMVGKRG  203

Query  187   EFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELL  246
             EFAVRGGILD+F+PTA+HPVR+EFWGDE++E+R FSVADQRS+P++D+ +++A  CREL+
Sbjct  204   EFAVRGGILDLFSPTADHPVRIEFWGDEVSELRYFSVADQRSLPDVDVDSVIAPPCRELI  263

Query  247   LSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTD  306
             L+ DVR RAA LAA + A  S V     +ML K++ GI V+GMEA+LPVL      LL+D
Sbjct  264   LTADVRDRAAALAAENQADASLV-----EMLDKISAGIPVEGMEALLPVLKPGELQLLSD  318

Query  307   QLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE-------Q  359
              LP G  +L+CDPEKVRTRA DL+RTG+EFLEASW+ A++G A   AP+D          
Sbjct  319   VLPVGAHILLCDPEKVRTRATDLVRTGQEFLEASWTAASIGGA---APLDTSILNGGGVD  375

Query  360   LGGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELD--VRAAPSARGHQRDIDEIFAM  417
             LG S +  L  VR +A   G PWWT+S L+  +  EL+  V+AAP  RG    + E+F  
Sbjct  376   LGASAYRSLRHVRESAEAAGRPWWTVSPLASGNGEELEIPVQAAPQVRGSDDLLAELFVS  435

Query  418   LRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGV  477
             LRAH++TGG AA+V  G GTA RVVERL E++ PA ML+ G  P  G V VL+G L DG+
Sbjct  436   LRAHVSTGGRAAIVVAGAGTASRVVERLGEAEVPAKMLEGGATPARGQVAVLRGSLHDGL  495

Query  478   IIPGAN----LVVITETDLTGSRVSA-AEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIG  532
             ++ G +    +V++TE+DLTG+RV+A  +GKRL AKRRN VDPLAL+AGD+VVHDQHGIG
Sbjct  496   VLAGDDSTPGMVIVTESDLTGNRVAAVGDGKRLPAKRRNQVDPLALSAGDMVVHDQHGIG  555

Query  533   RFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSR  592
             RFVEMVERT+GGARREYLV+EYA +KRG      D+L+VPM+SLDQLSRYVGG+ PALS+
Sbjct  556   RFVEMVERTIGGARREYLVIEYAPSKRG---HPGDRLFVPMESLDQLSRYVGGELPALSK  612

Query  593   LGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVD  652
             LGGSDWANTK KAR+AVREIAGELV LYA RQA+PGHAF PDTPWQ ELEDAF FTET+D
Sbjct  613   LGGSDWANTKRKARKAVREIAGELVQLYAARQAAPGHAFGPDTPWQKELEDAFAFTETID  672

Query  653   QLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQ  712
             QLT I EVKADMEKP+PMDRV+ GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA Q
Sbjct  673   QLTVISEVKADMEKPVPMDRVVIGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQQ  732

Query  713   HLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLG  772
             HLQTF ERM+ FPV ++GLSRFTDA +S+ +I G+A+G +DIV+GTHRLLQTG+RWKDLG
Sbjct  733   HLQTFTERMASFPVKVRGLSRFTDAKDSKEIIAGMAEGEIDIVVGTHRLLQTGIRWKDLG  792

Query  773   LVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY  832
             LV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+
Sbjct  793   LVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERH  852

Query  833   PVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQ  892
             P+LTYVG + DKQ+AAA+RRELLRDGQ FYVHNRVSSID AA ++RELVPEARVVVAHGQ
Sbjct  853   PILTYVGAYADKQVAAAIRRELLRDGQVFYVHNRVSSIDKAAKKIRELVPEARVVVAHGQ  912

Query  893   MPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVG  952
             M ED LE TVQ FW R+ D+LVCTTI+ETGLDISNANTLIVERAD+ GLSQLHQLRGRVG
Sbjct  913   MNEDTLEKTVQGFWERDFDVLVCTTIIETGLDISNANTLIVERADSLGLSQLHQLRGRVG  972

Query  953   RSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQS  1012
             RSRERGYAYFLYP + PLTETAYDRLATI+QN++LGAGMAVA+KDLEIRGAGNVLG EQS
Sbjct  973   RSRERGYAYFLYPAEKPLTETAYDRLATISQNSDLGAGMAVAMKDLEIRGAGNVLGAEQS  1032

Query  1013  GHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIA  1072
             GHVAGVGFDLYVRLVGEA+E    A+RAAADG+ +   E  K+VRIDLPVDAH+PPDY+ 
Sbjct  1033  GHVAGVGFDLYVRLVGEAVE----AFRAAADGKPITMDEGTKEVRIDLPVDAHIPPDYVT  1088

Query  1073  SDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDV  1132
             SDRLRLEGYR+LAAA+    +AAVV+EL DRYG LPE  RRL +VA+LRLLCR   + +V
Sbjct  1089  SDRLRLEGYRKLAAATDSDGIAAVVEELVDRYGPLPEEVRRLISVAKLRLLCREYQLEEV  1148

Query  1133  TAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELV  1192
              A +   +++SP++LPDS Q+RLKR+YP A YRATT  VQ+P+PR GG+G+ R+RDVEL+
Sbjct  1149  -AVTGTQLKISPMSLPDSKQIRLKRIYPSAQYRATTGLVQLPLPRTGGVGSDRLRDVELL  1207

Query  1193  QMVADLITALAGK  1205
             Q +AD I A+ G+
Sbjct  1208  QYIADFILAIDGR  1220


>gi|54026849|ref|YP_121091.1| putative transcription-repair coupling factor [Nocardia farcinica 
IFM 10152]
 gi|54018357|dbj|BAD59727.1| putative transcription-repair coupling factor [Nocardia farcinica 
IFM 10152]
Length=1205

 Score = 1617 bits (4188),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 834/1179 (71%), Positives = 968/1179 (83%), Gaps = 24/1179 (2%)

Query  42    LIAPASARLLVASALARQGPLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERL  101
             ++APA+AR  VA+ +A + P++VVTATGREADDL  EL  + GD+VA  PSWETLPHERL
Sbjct  35    MVAPAAARSFVAATVAGKRPVVVVTATGREADDLTVELTEILGDSVAQFPSWETLPHERL  94

Query  102   SPGVDTVGTRLMALRRLAHPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDE  161
             SP  DTVG RL  LRRLAHPDD     PL VVVT+VRSL+QPM   LG +EP+ L  G E
Sbjct  95    SPSADTVGRRLAVLRRLAHPDDPVFPVPLRVVVTTVRSLMQPMAAGLGDIEPIVLREGAE  154

Query  162   SPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMF  221
               FD ++ RLVE AYTRVDMVG+RGEFAVRGGILD+F PTA+HPVRVEFWGDE+T++R F
Sbjct  155   LDFDDLLTRLVEFAYTRVDMVGKRGEFAVRGGILDLFPPTADHPVRVEFWGDEVTQVRAF  214

Query  222   SVADQRSIPEIDIHTLVAFACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLA  281
             +VADQRS+PEI+I T+VA  CRELLL+  VR RAAQ+AA + A  + V     +ML KLA
Sbjct  215   AVADQRSLPEIEIDTVVATPCRELLLTAPVRERAAQVAAANAADAALV-----EMLDKLA  269

Query  282   EGIAVDGMEAVLPVLWSDGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASW  341
             EGI V+GMEA+LPVL      LLT+QL  GT VL+CDPEK+RTRAADL+RTG EFLEASW
Sbjct  270   EGIPVEGMEALLPVLQPGELTLLTEQLAAGTHVLLCDPEKIRTRAADLVRTGAEFLEASW  329

Query  342   SVAALGTAENQAPV--DVEQLGGSGFVELDQVRAAAARTGHPWWTLSQLS--DESAIELD  397
             + A+ G     AP+  +   L  S +  L Q+R  A R G  WWTLS L+  D + + L 
Sbjct  330   TAASFGA---DAPLGGNGLDLAASSYRALPQIREDADRHGLAWWTLSPLASGDPAEVVLP  386

Query  398   VRAAPSARGHQRDIDEIFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDP  457
             +  AP+ARG    +  IFA LRAH+ TGG A +V  G GTA RV+ERL++++ PA  L  
Sbjct  387   LHQAPTARGSDELVATIFASLRAHVTTGGRAVVVVAGHGTAQRVLERLADAEVPATALTA  446

Query  458   GQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDLTGSRVSA-AEGKRLAAKRRNIVDPL  516
             G  P PGVVGVL G L DGV+   A LVV+ E+DLTG+RV+A  EGKRL AKRRN VDPL
Sbjct  447   GAEPAPGVVGVLCGTLHDGVVFADAALVVVAESDLTGNRVTAPGEGKRLPAKRRNQVDPL  506

Query  517   ALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSL  576
             AL+AGD+VVHDQHGIGRFVEM+ERTVGGARREYLV+EYA +KRG   +  D+L+VPM+SL
Sbjct  507   ALSAGDMVVHDQHGIGRFVEMIERTVGGARREYLVIEYAPSKRG---QPGDRLFVPMESL  563

Query  577   DQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTP  636
             DQLSRYVGG+ P+LS+LGGSDWANTK KAR+AVREIAGELV LYA RQA+PGHAF PDTP
Sbjct  564   DQLSRYVGGEMPSLSKLGGSDWANTKRKARKAVREIAGELVQLYAARQAAPGHAFGPDTP  623

Query  637   WQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQD  696
             WQ E+EDAF FTETVDQ+TAI EVKADMEKP+PMDRV+CGDVGYGKTEIAVRAAFKAVQD
Sbjct  624   WQKEMEDAFAFTETVDQMTAIAEVKADMEKPVPMDRVVCGDVGYGKTEIAVRAAFKAVQD  683

Query  697   GKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVI  756
             GKQV VLVPTTLLA QHLQTF ER++GFPVT+KGLSRFTD AESRAV++G+ADGSVDIV+
Sbjct  684   GKQVVVLVPTTLLAQQHLQTFTERVAGFPVTVKGLSRFTDPAESRAVLEGMADGSVDIVV  743

Query  757   GTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLA  816
             GTHRLLQTGVRWKDLGLV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMSLA
Sbjct  744   GTHRLLQTGVRWKDLGLVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSLA  803

Query  817   GIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAAR  876
             GIREMSTILTPPEER+PVLTYVG ++DKQ+ AA+RRELLRDGQ FYVHNRVSSID AA R
Sbjct  804   GIREMSTILTPPEERHPVLTYVGAYNDKQVTAAIRRELLRDGQVFYVHNRVSSIDKAAKR  863

Query  877   VRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERA  936
             +R+LVPEARVVVAHGQM ED LE TVQ FW RE+D+LVCTTI+ETGLDISNANTLIVERA
Sbjct  864   IRDLVPEARVVVAHGQMNEDTLERTVQGFWQREYDVLVCTTIIETGLDISNANTLIVERA  923

Query  937   DTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALK  996
             DT GLSQLHQLRGRVGRSRERGYAYFLYPP+ PLTETAYDRLATIAQN++LGAGMAVA+K
Sbjct  924   DTLGLSQLHQLRGRVGRSRERGYAYFLYPPEKPLTETAYDRLATIAQNSDLGAGMAVAMK  983

Query  997   DLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDV  1056
             DLEIRGAGNVLG EQSGHVAGVGFDLYVRLVGEA+E    AYRAAADG+ + T EE K+V
Sbjct  984   DLEIRGAGNVLGAEQSGHVAGVGFDLYVRLVGEAVE----AYRAAADGKPI-TTEEVKEV  1038

Query  1057  RIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAA  1116
             RIDLPVDAH+PPDY+ASDRLRLE YR+LAAA  D  +A+VV+EL DRYG LP    RL +
Sbjct  1039  RIDLPVDAHIPPDYVASDRLRLEAYRKLAAAQDDSALASVVEELVDRYGPLPVEVGRLVS  1098

Query  1117  VARLRLLCRGSGITDVTAASAATVRLSP-LTLPDSAQVRLKRMYPGAHYRATTATVQVPI  1175
             VA+LRLL R  GIT++ A +  T+++SP L LPDS Q+RLKR+YP A Y+A +  VQ+P+
Sbjct  1099  VAKLRLLAREYGITEI-AVTGTTLKISPLLNLPDSKQLRLKRLYPSAGYKAASGVVQLPL  1157

Query  1176  PRA-GGLGAPRIRDVELVQMVADLITALAGKPRQHIGIT  1213
             PR    +GA R+RDV+L+Q VADL+ AL GK +  + +T
Sbjct  1158  PRVEDSVGAERVRDVQLLQFVADLLLALDGKAQGAVDLT  1196


>gi|296140872|ref|YP_003648115.1| transcription-repair coupling factor [Tsukamurella paurometabola 
DSM 20162]
 gi|296029006|gb|ADG79776.1| transcription-repair coupling factor [Tsukamurella paurometabola 
DSM 20162]
Length=1218

 Score = 1588 bits (4111),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 817/1213 (68%), Positives = 962/1213 (80%), Gaps = 30/1213 (2%)

Query  2     TAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGP  61
             +AP PA S     GL     + P        A GRPD LT+ A   AR  + SALA Q P
Sbjct  6     SAPTPALS-----GLTRAVAADPDVVAFAG-AAGRPD-LTVTAVDGARPFLLSALAGQAP  58

Query  62    LLVVTATGREADDLAAELRGVFG-DAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAH  120
             +LVVTATGREADDL +ELR   G DAV   PSWETLPHERLSPG DTVG RL  LRRLA 
Sbjct  59    VLVVTATGREADDLTSELRETLGADAVTQFPSWETLPHERLSPGADTVGRRLQVLRRLAW  118

Query  121   PDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVD  180
             PDDAQ G PL  VV +VRSL+QPM P LG    +TL  G+E  F+ ++  LVELAYTRVD
Sbjct  119   PDDAQYGAPLRAVVATVRSLVQPMAPGLGDAPSVTLREGEEFDFEELIETLVELAYTRVD  178

Query  181   MVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAF  240
             MVG+RGEFAVRGGILDIF  T + PVRVEFWGDEIT++R FSVADQRS PE+ + T+  +
Sbjct  179   MVGKRGEFAVRGGILDIFPTTTDLPVRVEFWGDEITDLRAFSVADQRSQPEVQVGTVHVY  238

Query  241   ACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDG  300
              CRELLL+ DVR RAA L A H +       + ++ML KLA+GI V+GMEA++P L    
Sbjct  239   PCRELLLTADVRDRAATLKAEHES-----DAALAEMLEKLAQGIPVEGMEALIPALVPGE  293

Query  301   HALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQL  360
               LLTD LPDGT  ++ DPEK+RTRAADL RTG+EFLEASW+ AALG++    P  ++ L
Sbjct  294   LQLLTDVLPDGTHTVLLDPEKIRTRAADLARTGQEFLEASWTAAALGSSAPLDPSGID-L  352

Query  361   GGSGFVELDQVRAAAARTGHPWWTLSQL-----SDESAIELDVRAAPSARGHQRDIDEIF  415
             G S +  LD V A+ +  GHPWWT+S L     +D+  + +    AP+ RG + + +++F
Sbjct  353   GASAYRGLDDVHASVSAQGHPWWTISPLAAGPDTDDDHLTVHAEHAPAPRGSEAEAEKLF  412

Query  416   AMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRD  475
             A LRAH A+GG   +V  G GT  R++ERL +++ PA  L+ G+ P+PG VGVL+G L+ 
Sbjct  413   ATLRAHAASGGSGVIVVAGRGTRARILERLRDAEVPASELEAGEGPRPGTVGVLRGSLQT  472

Query  476   GVIIPGANLVVITETDLTGSRVSA-AEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRF  534
             G+ +P   LV++ E DLTG+RV+   +G+RL AKRRN VDPLALTAGDLVVHD+HGIG+F
Sbjct  473   GLTVPSQQLVLLAEPDLTGNRVAGVGDGRRLPAKRRNQVDPLALTAGDLVVHDEHGIGKF  532

Query  535   VEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLG  594
             VEM+ERTV GARREYLV+EYA +KRG   +  DKL+VPM+SLDQLSRYVGG+ PALS++G
Sbjct  533   VEMIERTVAGARREYLVIEYAPSKRG---QPGDKLFVPMESLDQLSRYVGGEMPALSKMG  589

Query  595   GSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQL  654
             GSDW NTK KAR+AVREIAGELV LYA R A+PGHAF+PD+PWQ E+EDAF FTETVDQ+
Sbjct  590   GSDWQNTKRKARKAVREIAGELVQLYAARNAAPGHAFAPDSPWQREMEDAFPFTETVDQM  649

Query  655   TAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHL  714
             T I +VK+DMEK +PMDRV+ GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA QHL
Sbjct  650   TVIGDVKSDMEKAVPMDRVVIGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQQHL  709

Query  715   QTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLV  774
             +TF +RM GFPVT+KGLSRFTD  E+  V++GLADGSVDIV+GTHRLLQTGVRWKDLGLV
Sbjct  710   KTFVDRMQGFPVTVKGLSRFTDRHETEQVLEGLADGSVDIVVGTHRLLQTGVRWKDLGLV  769

Query  775   VVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPV  834
             VVDEEQRFGVEHKEHIK+LRT+VDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+PV
Sbjct  770   VVDEEQRFGVEHKEHIKALRTNVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERHPV  829

Query  835   LTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMP  894
             LTYVGP+D+KQ+AAA+RRELLRDGQ FYVHNRVSSID AA ++R++VPEARVVVAHGQM 
Sbjct  830   LTYVGPYDNKQVAAAIRRELLRDGQVFYVHNRVSSIDKAAKQIRDMVPEARVVVAHGQMG  889

Query  895   EDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRS  954
             E+ LE+TVQ FWNRE D+LVCTTIVETGLDISNANTLIVERA+  GLSQLHQLRGRVGRS
Sbjct  890   EEALESTVQGFWNREFDVLVCTTIVETGLDISNANTLIVERAENLGLSQLHQLRGRVGRS  949

Query  955   RERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGH  1014
             RERGYAYFLYP + PLTETAYDRL+TIAQNNELGAGMAVA+KDLEIRGAGNVLG EQSGH
Sbjct  950   RERGYAYFLYPSEKPLTETAYDRLSTIAQNNELGAGMAVAMKDLEIRGAGNVLGAEQSGH  1009

Query  1015  VAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASD  1074
             VAGVGFDLYVRLVGEA+E    A+RAAADG  +   EE K+VRIDLPVDAH+PPDY+ SD
Sbjct  1010  VAGVGFDLYVRLVGEAVE----AFRAAADGTPITLPEEQKEVRIDLPVDAHIPPDYVTSD  1065

Query  1075  RLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA  1134
             RLRLE YR+LAAA  D  VA V+ ELTDRYG  P    RLAA+ARLR L R +G+T+V+ 
Sbjct  1066  RLRLEAYRKLAAAHDDSAVAEVLTELTDRYGPPPVEVERLAAIARLRSLARAAGVTEVS-  1124

Query  1135  ASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPR--AGGLGAPRIRDVELV  1192
              S  TVR+SP+ L DS Q+RLKR+YPG  YRATT TV  PIPR   GG+G+ R+RD+ L+
Sbjct  1125  VSGTTVRVSPMELRDSQQLRLKRLYPGGSYRATTRTVTFPIPRVEGGGVGSERVRDIALL  1184

Query  1193  QMVADLITALAGK  1205
             Q+VAD + A+ GK
Sbjct  1185  QVVADFLAAMDGK  1197


>gi|289555197|ref|ZP_06444407.1| LOW QUALITY PROTEIN: transcription-repair coupling factor mfd 
[Mycobacterium tuberculosis KZN 605]
 gi|289439829|gb|EFD22322.1| LOW QUALITY PROTEIN: transcription-repair coupling factor mfd 
[Mycobacterium tuberculosis KZN 605]
Length=824

 Score = 1572 bits (4070),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 790/802 (99%), Positives = 790/802 (99%), Gaps = 7/802 (0%)

Query  433   PGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDL  492
             P  GTA RV         PAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDL
Sbjct  30    PRGGTAVRVRH-------PAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDL  82

Query  493   TGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVL  552
             TGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVL
Sbjct  83    TGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVL  142

Query  553   EYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREI  612
             EYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREI
Sbjct  143   EYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREI  202

Query  613   AGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDR  672
             AGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDR
Sbjct  203   AGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDR  262

Query  673   VICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLS  732
             VICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLS
Sbjct  263   VICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLS  322

Query  733   RFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKS  792
             RFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKS
Sbjct  323   RFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKS  382

Query  793   LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRR  852
             LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRR
Sbjct  383   LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRR  442

Query  853   ELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDI  912
             ELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDI
Sbjct  443   ELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDI  502

Query  913   LVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTE  972
             LVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTE
Sbjct  503   LVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTE  562

Query  973   TAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALE  1032
             TAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALE
Sbjct  563   TAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALE  622

Query  1033  TYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDRE  1092
             TYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDRE
Sbjct  623   TYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDRE  682

Query  1093  VAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQ  1152
             VAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQ
Sbjct  683   VAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQ  742

Query  1153  VRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGI  1212
             VRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGI
Sbjct  743   VRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGI  802

Query  1213  TNPSPPGEDGRGRNTTIKERQP  1234
             TNPSPPGEDGRGRNTTIKERQP
Sbjct  803   TNPSPPGEDGRGRNTTIKERQP  824


>gi|289757102|ref|ZP_06516480.1| LOW QUALITY PROTEIN: transcription-repair coupling factor Mfd 
[Mycobacterium tuberculosis T85]
 gi|289712666|gb|EFD76678.1| LOW QUALITY PROTEIN: transcription-repair coupling factor Mfd 
[Mycobacterium tuberculosis T85]
Length=849

 Score = 1541 bits (3989),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 772/784 (99%), Positives = 773/784 (99%), Gaps = 0/784 (0%)

Query  451   PAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRR  510
             P G   P + P     GVLQGPLRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRR
Sbjct  66    PRGCSIPARRPSRESSGVLQGPLRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRR  125

Query  511   NIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLY  570
             NIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLY
Sbjct  126   NIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLY  185

Query  571   VPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHA  630
             VPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHA
Sbjct  186   VPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHA  245

Query  631   FSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAA  690
             FSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAA
Sbjct  246   FSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAA  305

Query  691   FKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADG  750
             FKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADG
Sbjct  306   FKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADG  365

Query  751   SVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRT  810
             SVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRT
Sbjct  366   SVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRT  425

Query  811   LEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSI  870
             LEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSI
Sbjct  426   LEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSI  485

Query  871   DAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANT  930
             DAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANT
Sbjct  486   DAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANT  545

Query  931   LIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAG  990
             LIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAG
Sbjct  546   LIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAG  605

Query  991   MAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTA  1050
             MAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTA
Sbjct  606   MAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTA  665

Query  1051  EEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEP  1110
             EEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEP
Sbjct  666   EEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEP  725

Query  1111  ARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTAT  1170
             ARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTAT
Sbjct  726   ARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTAT  785

Query  1171  VQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITNPSPPGEDGRGRNTTIK  1230
             VQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITNPSPPGEDGRGRNTTIK
Sbjct  786   VQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITNPSPPGEDGRGRNTTIK  845

Query  1231  ERQP  1234
             ERQP
Sbjct  846   ERQP  849


>gi|343926966|ref|ZP_08766456.1| transcription-repair coupling factor [Gordonia alkanivorans NBRC 
16433]
 gi|343763125|dbj|GAA13382.1| transcription-repair coupling factor [Gordonia alkanivorans NBRC 
16433]
Length=1191

 Score = 1535 bits (3975),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 803/1206 (67%), Positives = 937/1206 (78%), Gaps = 35/1206 (2%)

Query  13    IAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALAR--QGPLLVVTATGR  70
             ++GL  LA +  +F+++ +R   R   L + AP +AR  + S LA   + PLLVV+A GR
Sbjct  7     LSGLAALACADKSFREVHERRAER--RLDITAPDAARPFLVSCLAAGAEAPLLVVSANGR  64

Query  71    EADDLAAELRGVFGDA--VALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGP  128
             EADDL AEL  +  DA  VA  PSWETLPHERLSP  DTVG RL  L RLA+P D     
Sbjct  65    EADDLTAELAELLDDADSVAQFPSWETLPHERLSPSADTVGQRLAVLHRLANPGDN----  120

Query  129   PLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEF  188
             PL VVVT+VRSL+QPM P LG +  +TL  G E  FDG++A+LVE+AY RVDMVGRRGEF
Sbjct  121   PLRVVVTTVRSLVQPMAPGLGEVATVTLREGIEVDFDGLLAQLVEMAYERVDMVGRRGEF  180

Query  189   AVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLS  248
             AVRGGILD+F  TA+HPVRVEFWGDEITE+R FSVADQRS PE+D   +     RELLLS
Sbjct  181   AVRGGILDVFPTTADHPVRVEFWGDEITEIRAFSVADQRSQPEVDASEVRIHPGRELLLS  240

Query  249   EDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQL  308
             E VR RA+ LAA++P        + ++ML KLAEGI V+GMEA++P L      LLT+ +
Sbjct  241   EKVRTRASDLAAKNPD-----DTALTEMLGKLAEGIPVEGMEALIPALVDGEMQLLTEVV  295

Query  309   PDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQ-----LGGS  363
             PDGT VL+ DPEKVRTRAADL +TG EFLEASW+ AA+G     AP+D        L  S
Sbjct  296   PDGTRVLILDPEKVRTRAADLSKTGAEFLEASWTAAAMGA---NAPIDPRSGTGIDLQAS  352

Query  364   GFVELDQVRAAAARTGHPWWTLSQLSDESA--IELDVRAAPSARGHQRDIDEIFAMLRAH  421
              +  L  VR A  +   PWWTLS LS  S   +ELD+   P+ RG +R+I   FA LRAH
Sbjct  353   AYRSLGDVREATLQAKRPWWTLSPLSTGSGNELELDLTPGPAPRGDEREIAATFAQLRAH  412

Query  422   IATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPG  481
             ++ G  AA+V  G GTA RV ERLSE++ P  + +PG  P+PG V V    LR G++   
Sbjct  413   VSDGKTAAIVVTGKGTAQRVGERLSEAEVPYVIAEPGHRPEPGEVTVFGATLRAGIVCAD  472

Query  482   ANLVVITETDLTGSRVSAA-EGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             A LVV+TE DLTG+RV+   +G++L AKRRN VDPLAL AGDLVVHDQHGIG+FVEM+ER
Sbjct  473   AGLVVVTEADLTGTRVANVRDGRKLPAKRRNQVDPLALAAGDLVVHDQHGIGKFVEMIER  532

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TV GARREYLVLEYAS+KRG  A   D+LYVPMD+LDQLSRYVGG+ P+LS+LGGSDW N
Sbjct  533   TVSGARREYLVLEYASSKRGQPA---DRLYVPMDALDQLSRYVGGEQPSLSKLGGSDWQN  589

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TK KAR+AVREIAGELV LYA R A+PGHAF PDTPWQ E+EDAF FTETVDQLT I EV
Sbjct  590   TKRKARKAVREIAGELVQLYAARHAAPGHAFGPDTPWQQEMEDAFDFTETVDQLTVIAEV  649

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K+DME+P+PMDRVI GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTT+LA QHLQTF ER
Sbjct  650   KSDMERPVPMDRVIVGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTILAQQHLQTFTER  709

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             MSGFPV ++GLSRFTDA ESR + + +A G VDIVIGTHRLLQTG+ WKDLGLV+VDEEQ
Sbjct  710   MSGFPVRVRGLSRFTDAKESREITEAMAKGEVDIVIGTHRLLQTGITWKDLGLVIVDEEQ  769

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+PVLTYVG 
Sbjct  770   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERHPVLTYVGA  829

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             +  KQ+AAA+RRELLRDGQ FYVHNRVS+ID  A  +  ++PEARVVVAHGQM ED LE 
Sbjct  830   YAPKQVAAAIRRELLRDGQVFYVHNRVSTIDKTAKDIAAMIPEARVVVAHGQMGEDQLER  889

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TV  FWNRE+D+LVCTTI+ETGLDISNANTLIV+RA+  GLSQLHQLRGRVGRSRERGYA
Sbjct  890   TVSGFWNREYDVLVCTTIIETGLDISNANTLIVDRAENLGLSQLHQLRGRVGRSRERGYA  949

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             Y LY P  PLTETAYDRLATIAQNNELGAGMAVALKDLE+RGAGNVLG EQSGHVAGVGF
Sbjct  950   YLLYSPDRPLTETAYDRLATIAQNNELGAGMAVALKDLELRGAGNVLGAEQSGHVAGVGF  1009

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADG+ V T +E  +VRIDLPVDAH+P +Y+ SDRLRLE 
Sbjct  1010  DLYVRLVGEAVE----AYRAAADGKPVET-QETGEVRIDLPVDAHIPVEYVDSDRLRLEA  1064

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YR+LA+A+ D EV AV+ EL DRYG  P    RLA++ARLRL CR  GIT++  A    V
Sbjct  1065  YRKLASATDDAEVDAVLVELNDRYGPPPVETTRLASIARLRLRCRERGITEIGLAGQG-V  1123

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             ++SPL L DS QVRL+R+Y  A +RATT+ V +PIPR GG+G+ R+RD EL++ +   +T
Sbjct  1124  KISPLPLLDSEQVRLRRLYSSATFRATTSVVTLPIPRTGGVGSARLRDDELIEYLTTFLT  1183

Query  1201  ALAGKP  1206
              L  +P
Sbjct  1184  QLKPEP  1189


>gi|262201520|ref|YP_003272728.1| transcription-repair coupling factor [Gordonia bronchialis DSM 
43247]
 gi|262084867|gb|ACY20835.1| transcription-repair coupling factor [Gordonia bronchialis DSM 
43247]
Length=1195

 Score = 1518 bits (3930),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 796/1210 (66%), Positives = 929/1210 (77%), Gaps = 50/1210 (4%)

Query  7     ACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG--PLLV  64
             AC+DT I+G+               RA      + L AP +AR  V + LA+    PLLV
Sbjct  14    ACADTAISGI---------------RARRDEVHVDLTAPDAARPFVVACLAKDADAPLLV  58

Query  65    VTATGREADDLAAELRGVFG--DAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPD  122
             V+A GREADDL AEL  +    DAVA  PSWETLPHERLSP  DTVG RL  L RLA+P 
Sbjct  59    VSANGREADDLTAELAELLDEPDAVAQFPSWETLPHERLSPSADTVGARLAVLHRLANPG  118

Query  123   DAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMV  182
             D+    PL VVVT+VRSL+QPM P LG +  ++L  G E  FDG++  LVE+AY RVDMV
Sbjct  119   DS----PLRVVVTTVRSLVQPMAPGLGDVATISLAEGFEIDFDGLLTDLVEMAYERVDMV  174

Query  183   GRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFAC  242
             GRRGEFAVRGGILD+F  TA++PVRVEFWGDEITEMR FSVADQRS PE++   +    C
Sbjct  175   GRRGEFAVRGGILDVFPTTADYPVRVEFWGDEITEMRAFSVADQRSQPEVEATRVDIHPC  234

Query  243   RELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHA  302
             RELLL++++R RAA+LA++     +      ++ML KLAEGI V+GMEA++P L      
Sbjct  235   RELLLTDEIRTRAAELASQFEGDPTL-----AEMLTKLAEGIPVNGMEALIPALVDGRMQ  289

Query  303   LLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQ---  359
             LLT+ +P GT VL+ DPEKVRTRAADL +TG EFLEASW+ AA+G    Q P+D      
Sbjct  290   LLTEVVPAGTRVLILDPEKVRTRAADLSKTGAEFLEASWTAAAMGA---QGPLDGRSSQA  346

Query  360   ----LGGSGFVELDQVRAAAARTGHPWWTLSQLS--DESAIELDVRAAPSARGHQRDIDE  413
                 L  S +  LD+VR      G  WWT+S L+  D+  + LD+   P+ RG   +I  
Sbjct  347   LGVDLQASAYRPLDEVRETTLAAGRSWWTISPLATGDDHEVVLDLAPGPAPRGDDNEIVA  406

Query  414   IFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPL  473
             +FA LRAH+  G  AA+V  G GTA RV ERL++++ P  + +PG  P PG V V  G L
Sbjct  407   VFAQLRAHVRAGQTAAIVVAGKGTAQRVGERLADAEVPHVIAEPGHRPAPGEVSVFGGTL  466

Query  474   RDGVIIPGANLVVITETDLTGSRVSAA-EGKRLAAKRRNIVDPLALTAGDLVVHDQHGIG  532
             R G++ P A LV++TE DLTG+RV+   +G++L AKRRN VDPLALTAGDLVVHDQHGIG
Sbjct  467   RHGLVCPDAGLVIVTEADLTGTRVANVRDGRKLPAKRRNQVDPLALTAGDLVVHDQHGIG  526

Query  533   RFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSR  592
             +FVEM+ERTV GARREYLVLEYA +KRG   +  D+LYVPMD+LDQLSRYVGG+ P+LS+
Sbjct  527   KFVEMIERTVSGARREYLVLEYAPSKRG---QPGDRLYVPMDALDQLSRYVGGEQPSLSK  583

Query  593   LGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVD  652
             LGGSDW NTK KAR+AVREIAGELV LYA R A+PGHAF PDTPWQ E+EDAF FTETVD
Sbjct  584   LGGSDWQNTKRKARKAVREIAGELVQLYAARHAAPGHAFGPDTPWQQEMEDAFDFTETVD  643

Query  653   QLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQ  712
             Q+T I EVKADME+P+PMDRVI GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTT+LA Q
Sbjct  644   QMTVIGEVKADMERPVPMDRVIVGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTILAQQ  703

Query  713   HLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLG  772
             HLQTF ERMSGFPV ++GLSRFTDA ESR +ID +A G VDIVIGTHRLLQTGV WKDLG
Sbjct  704   HLQTFSERMSGFPVRVRGLSRFTDARESREIIDAMATGEVDIVIGTHRLLQTGVTWKDLG  763

Query  773   LVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERY  832
             LV+VDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+
Sbjct  764   LVIVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERH  823

Query  833   PVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQ  892
             PVLTYVG +  KQ+AAA+RRELLRDGQ FYVHNRVS+ID  A  +  +VPEARVVVAHGQ
Sbjct  824   PVLTYVGAYAPKQVAAAIRRELLRDGQVFYVHNRVSTIDKTARDIAAMVPEARVVVAHGQ  883

Query  893   MPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVG  952
             M ED LE TV  FWNRE D+LVCTTI+ETGLDISNANTLIV+RA+  GLSQLHQLRGRVG
Sbjct  884   MNEDQLEKTVSGFWNREFDVLVCTTIIETGLDISNANTLIVDRAENLGLSQLHQLRGRVG  943

Query  953   RSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQS  1012
             RSRERGYAY LY P+ PLTETAYDRLATIAQNNELGAGMAVALKDLE+RGAGNVLG EQS
Sbjct  944   RSRERGYAYLLYSPERPLTETAYDRLATIAQNNELGAGMAVALKDLELRGAGNVLGAEQS  1003

Query  1013  GHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIA  1072
             GHVAGVGFDLYVRLVGEA+E    AYRAAADGQ V T+ E ++VRIDLPVDAH+P +Y+ 
Sbjct  1004  GHVAGVGFDLYVRLVGEAVE----AYRAAADGQPV-TSRETEEVRIDLPVDAHIPVEYVD  1058

Query  1073  SDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDV  1132
             SDRLRLE YR+LA+A  D  V  V+ ELTDRYG  P    RLAA+ARLRL CR  GIT++
Sbjct  1059  SDRLRLEAYRKLASAIDDAAVDGVIAELTDRYGEPPVETTRLAAIARLRLRCRERGITEI  1118

Query  1133  TAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELV  1192
               A    +++SPL L DS QVRLKR+Y  A+YRATT+ V +PIPR GG+G+ R+RD EL+
Sbjct  1119  GLAGTG-LKISPLPLLDSEQVRLKRLYSAANYRATTSVVTLPIPRTGGVGSARLRDDELI  1177

Query  1193  QMVADLITAL  1202
               +   +T L
Sbjct  1178  VYLTTFLTQL  1187


>gi|333921138|ref|YP_004494719.1| transcription-repair coupling factor [Amycolicicoccus subflavus 
DQS3-9A1]
 gi|333483359|gb|AEF41919.1| Transcription-repair coupling factor [Amycolicicoccus subflavus 
DQS3-9A1]
Length=1201

 Score = 1506 bits (3900),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 793/1200 (67%), Positives = 938/1200 (79%), Gaps = 24/1200 (2%)

Query  14    AGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTATGREAD  73
             + L + AL     QQ+ + A GR  E TL+AP  AR  +A+ALA   P+L+VTA  REA+
Sbjct  12    SALFDFALGDAALQQV-RDAVGR-TERTLVAPLGARPFIAAALASVAPVLLVTANRREAE  69

Query  74    DLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPPLGVV  133
             DL +EL+GV GD VAL PSWETLPHERLSPG DTVG RL  LRRLA PDDA  G PL V+
Sbjct  70    DLTSELQGVLGDTVALFPSWETLPHERLSPGADTVGQRLQVLRRLARPDDATFGAPLKVI  129

Query  134   VTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGG  193
             V  VR+++QPM+  LG   P+ L +G+E  FD ++A L E AY RVDMV +RGE+AVRGG
Sbjct  130   VAPVRAVIQPMSRGLGERAPIVLRIGEERGFDDLLAELTEFAYKRVDMVAKRGEYAVRGG  189

Query  194   ILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSEDVRA  253
             ILDIF PTAEHP+R+EFWGDE+TE+R FSVADQRS+    +  ++A  CRELLL++  R 
Sbjct  190   ILDIFPPTAEHPIRIEFWGDEVTELREFSVADQRSLSGGAVEVVIAPPCRELLLTDSARE  249

Query  254   RAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGTP  313
             RAA LAA H   +S V     ++  KL+ GI V+GMEA++P L      LL + LP GT 
Sbjct  250   RAAALAAAHAGNDSLV-----ELFDKLSSGIPVEGMEALIPALTEGPLELLPELLPQGTV  304

Query  314   VLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE--QLGGSGFVELDQV  371
             V++CDPEK   RA DL  +G EFLEASW+ A+ G      P+D     L  S F  L  V
Sbjct  305   VVICDPEKTNARADDLRSSGTEFLEASWAAASFGGG---VPIDSRTLDLSASAFKPLPFV  361

Query  372   RAAAARTGHPWWTLSQLSDESAIEL--DVRAAPSARGHQRDIDEIFAMLRAHIATGGYAA  429
             R  A   G  WW L+QL+  S  EL   V+AAP+ RG +++I   FAMLRAHI+ GG AA
Sbjct  362   RERAVAVGRGWWDLTQLASGSDDELVLPVQAAPAMRGSEQEIATTFAMLRAHISQGGRAA  421

Query  430   LVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITE  489
             +V PG GTA R  ERL +++ PA +L+PG+    GVV +L   L  GV+   A L+V+TE
Sbjct  422   IVVPGAGTAQRYKERLLDAEVPAALLEPGKPLSEGVVNLLCATLSSGVVFEDAQLIVLTE  481

Query  490   TDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREY  549
             +DLTG+R +    ++LA+KRRN VDPLAL AGDLVVHDQHGIGRFVEM ERTV GARREY
Sbjct  482   SDLTGNRATTTPTRKLASKRRNQVDPLALQAGDLVVHDQHGIGRFVEMAERTVSGARREY  541

Query  550   LVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAV  609
             LV+EYA++KRG      D+L+VPM+SLDQLSRYVGG+AP LS++GGSDW NTK KAR+AV
Sbjct  542   LVIEYAASKRG---HPGDRLFVPMESLDQLSRYVGGEAPGLSKMGGSDWQNTKRKARKAV  598

Query  610   REIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIP  669
             REIA ELV LYAKRQASPGHAF PD+PWQ+ELEDAF F ET DQLTAI EVK DME+ +P
Sbjct  599   REIAAELVQLYAKRQASPGHAFGPDSPWQSELEDAFAFVETDDQLTAISEVKGDMERGVP  658

Query  670   MDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIK  729
             MDRV+CGDVG+GKTEIAVRAAFKAVQD KQVAVLVPTTLLA QH +TF +RM+GFPV IK
Sbjct  659   MDRVVCGDVGFGKTEIAVRAAFKAVQDNKQVAVLVPTTLLAQQHTETFTQRMAGFPVKIK  718

Query  730   GLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEH  789
              LSRFT   +SRAVI GLADG+VD+VIGTHRLLQTGVRWKDLGLV+VDEEQRFGVEHKEH
Sbjct  719   QLSRFTGPTDSRAVIAGLADGTVDVVIGTHRLLQTGVRWKDLGLVIVDEEQRFGVEHKEH  778

Query  790   IKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAA  849
             IK+LR+HVD+LTMSATPIPRTLEMSLAGIREMSTILTPPEER PVLTYVG ++DKQ+ AA
Sbjct  779   IKALRSHVDMLTMSATPIPRTLEMSLAGIREMSTILTPPEERLPVLTYVGAYEDKQVGAA  838

Query  850   LRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNRE  909
             +RRELLRDGQ FYVHNRVSSI+ AA  +R+LVPEARVVVAHGQM E+ LETTVQ FWNRE
Sbjct  839   IRRELLRDGQVFYVHNRVSSIEKAAKHIRDLVPEARVVVAHGQMNEEALETTVQGFWNRE  898

Query  910   HDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVP  969
              D+LVCTTIVETGLDISNANTLIVERADT GLSQLHQLRGRVGR RERGYAYFLYP    
Sbjct  899   FDVLVCTTIVETGLDISNANTLIVERADTLGLSQLHQLRGRVGRGRERGYAYFLYPSNRV  958

Query  970   LTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGE  1029
             LTETAYDRLATI+QN++LGAGMAVA+KDLEIRGAGNVLG EQSGHVAGVGFDLY+RLVGE
Sbjct  959   LTETAYDRLATISQNSDLGAGMAVAMKDLEIRGAGNVLGAEQSGHVAGVGFDLYIRLVGE  1018

Query  1030  ALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASS  1089
             A+E    A++A ADG+ V   EE K+V+IDLPVDAH+PPDY++SDRLRLE YR++AAA  
Sbjct  1019  AVE----AFKAVADGRPVEAPEEKKEVKIDLPVDAHIPPDYVSSDRLRLEAYRKIAAAQG  1074

Query  1090  DREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPD  1149
             D E+ A  +EL DRYG LPE  +RL +VARLRL+CR  G+TDV A     +RL+P+TLPD
Sbjct  1075  DDELDAATEELLDRYGPLPEEVKRLLSVARLRLMCRERGLTDV-AVVGTQLRLTPMTLPD  1133

Query  1150  SAQVRLKRMYPGAHYRATTATVQVPIPRAG-GLGA-PRIRDVELVQMVADLITALAGKPR  1207
             S QVRLKR+YP A YR TT+ +Q+P+PR+G G  A PR+RD ++VQ VAD +T+L G P+
Sbjct  1134  SKQVRLKRLYPSAQYRPTTSQIQLPLPRSGRGTPADPRVRDNDVVQFVADFLTSLDGLPK  1193


>gi|326385186|ref|ZP_08206853.1| transcription-repair coupling factor [Gordonia neofelifaecis 
NRRL B-59395]
 gi|326196090|gb|EGD53297.1| transcription-repair coupling factor [Gordonia neofelifaecis 
NRRL B-59395]
Length=1193

 Score = 1493 bits (3865),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 784/1203 (66%), Positives = 913/1203 (76%), Gaps = 33/1203 (2%)

Query  13    IAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALAR--QGPLLVVTATGR  70
             + GL   A     F QL +R G     L + AP +AR  V + LA   + P+LVVTA GR
Sbjct  6     LTGLTSFAFRDAAFGQLRERIG--QARLDITAPDAARPFVVAQLAEVSEHPVLVVTANGR  63

Query  71    EADDLAAELR-----GVFGD-AVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDA  124
             EADDL  EL      G  G   VA  PSWETLPHERLSP  DTVG RL  L RLA P  A
Sbjct  64    EADDLTTELAELLPCGAGGTPVVAQFPSWETLPHERLSPSADTVGARLAVLSRLADPSVA  123

Query  125   QLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGR  184
                 PL VV+ +VRSL+QPM P LG M  +TLT G E+ FD ++ +LVE+AY RVDMVG 
Sbjct  124   ----PLRVVIATVRSLVQPMAPGLGGMRAVTLTEGSEAEFDALIEKLVEMAYERVDMVGA  179

Query  185   RGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRE  244
             RGEFAVRGGILDIF  TA++PVRVEFWGDEIT++R FSVADQR+ PEID   +    CRE
Sbjct  180   RGEFAVRGGILDIFPTTADYPVRVEFWGDEITDIRAFSVADQRTQPEIDTSVVQIHPCRE  239

Query  245   LLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALL  304
             L+L+  VR RAA LA      E        ++L KLAEGI V+GMEA++P L      +L
Sbjct  240   LVLTAGVRERAAALA------EDVTDEGLREILTKLAEGIPVEGMEALIPALVDGRMQML  293

Query  305   TDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALG-TAENQAPVDVEQLGGS  363
             T+ +PDGT VLV DPEKVRTRA DL RTG EFLEASW+ AALG TA   A      L  S
Sbjct  294   TEVMPDGTRVLVLDPEKVRTRAVDLARTGEEFLEASWNAAALGATAPVSAGEPAIDLSAS  353

Query  364   GFVELDQVRAAAARTGHPWWTLSQLSDESA--IELDVRAAPSARGHQRDIDEIFAMLRAH  421
              +  +D V+AA    G  WWT+S LS  S   +ELD++  P+  G+  ++    + LRA 
Sbjct  354   AYRSVDDVQAATVDAGRSWWTMSPLSAGSGEELELDLQPGPAPHGNPDELTAFMSSLRAQ  413

Query  422   IATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPG  481
             IA+GG AAL+A G GTA R V+RL E++ PA +++PG       VGV  G LR G++ P 
Sbjct  414   IASGGRAALIAAGRGTAMRFVDRLGEAEVPARLVEPGDELPDDAVGVFHGTLRRGLVCPS  473

Query  482   ANLVVITETDLTGSRV-SAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             A  V+ TE D+TG+RV  A +G+RL AKRRN VDPLALTAGDLVVHDQHGIG+FVEM+ER
Sbjct  474   AGFVIATEADVTGARVVGAKDGRRLPAKRRNQVDPLALTAGDLVVHDQHGIGKFVEMIER  533

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TV GARREYLV+EYA  KRG   +  D+LYVPMD+LDQLSRYVGG+ P LS+LGGSDWAN
Sbjct  534   TVSGARREYLVIEYAPGKRG---QPGDRLYVPMDALDQLSRYVGGEQPGLSKLGGSDWAN  590

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TK KAR+AVREIAGELV LYA R A+PG AFS DTPWQ E+EDAF +TETVDQ+T I EV
Sbjct  591   TKRKARKAVREIAGELVRLYAARHAAPGFAFSADTPWQREMEDAFDYTETVDQMTVIGEV  650

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             K+DMEKP+PMDRV+ GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTT+LA QHLQTF ER
Sbjct  651   KSDMEKPVPMDRVVVGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTILAGQHLQTFTER  710

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M GFPV ++GLSRFTD AES+ +I  +A G VD+VIGTHRLLQTG+RWKDLGLV+VDEEQ
Sbjct  711   MDGFPVKVRGLSRFTDPAESKEIIAQMASGEVDVVIGTHRLLQTGIRWKDLGLVIVDEEQ  770

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPEER+PVLTYVG 
Sbjct  771   RFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPEERHPVLTYVGA  830

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             + DKQ+AA++RRELLRDGQ FYVHNRVS+ID  A  +  +VPEARVVVAHGQM E+ LE 
Sbjct  831   YSDKQVAASIRRELLRDGQVFYVHNRVSTIDKTAKHIANMVPEARVVVAHGQMGEEQLER  890

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
             TVQ FW+RE+D+LVCTTI+ETGLDISNANTLIV+RA+ FGLSQLHQLRGRVGRSRERGYA
Sbjct  891   TVQGFWDREYDVLVCTTIIETGLDISNANTLIVDRAENFGLSQLHQLRGRVGRSRERGYA  950

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             Y LY P  PLTETAYDRLATIAQNNELGAGMAVALKDLE+RGAGNVLG EQSGHVAGVGF
Sbjct  951   YLLYSPDKPLTETAYDRLATIAQNNELGAGMAVALKDLELRGAGNVLGAEQSGHVAGVGF  1010

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA+E    AYRAAADG+ V T EE  +VRIDLPVDAH+P +Y+ +DRLRLE 
Sbjct  1011  DLYVRLVGEAVE----AYRAAADGKPVAT-EENVEVRIDLPVDAHIPVEYVEADRLRLEA  1065

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YR+LA+A  D +V  V+ EL DRYG  P   +RLAA+ARLRL CR  G+ +V  A   ++
Sbjct  1066  YRKLASAGGDDDVDEVMSELADRYGEPPVETQRLAAIARLRLRCRERGVAEVGLA-GQSI  1124

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLIT  1200
             R+SPL L DS QVRL RMY  A YRA T  + +PIPR GG+G+ R+RD EL+  V   + 
Sbjct  1125  RISPLLLLDSQQVRLARMYSSASYRAATHMITLPIPRTGGVGSARLRDTELIDYVVTFLQ  1184

Query  1201  ALA  1203
              +A
Sbjct  1185  TIA  1187


>gi|134097431|ref|YP_001103092.1| transcription-repair coupling factor [Saccharopolyspora erythraea 
NRRL 2338]
 gi|291004579|ref|ZP_06562552.1| transcription-repair coupling factor [Saccharopolyspora erythraea 
NRRL 2338]
 gi|133910054|emb|CAM00166.1| transcription-repair coupling factor [Saccharopolyspora erythraea 
NRRL 2338]
Length=1195

 Score = 1429 bits (3699),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 743/1161 (64%), Positives = 888/1161 (77%), Gaps = 38/1161 (3%)

Query  61    PLLVVTATGREADDLAAELRGVFG-DAVALLPSWETLPHERLSPGVDTVGTRLMALRRLA  119
             P+L+VTATGREA+++AA +  + G D V + PSWETLPHERLSP  DTVG RL  LRRLA
Sbjct  54    PVLLVTATGREAEEVAAAVSDLIGSDGVEVFPSWETLPHERLSPRADTVGRRLAVLRRLA  113

Query  120   HPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRV  179
             HP++   G  + V+VT+VRSL+QP+ P LG + P+ L VGDE  F+ +V +L  LAY RV
Sbjct  114   HPEEHDHGR-IRVLVTTVRSLIQPIAPGLGELAPVRLRVGDEHDFEELVEKLAALAYNRV  172

Query  180   DMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVA  239
             DMV +RGEFAVRGGI+D+F PT EHP+RVEFWGDE+TE+R FSVADQRS+PE    TL A
Sbjct  173   DMVEKRGEFAVRGGIVDVFPPTEEHPLRVEFWGDEVTEVRPFSVADQRSLPEAQDTTLFA  232

Query  240   FACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSD  299
              ACRELL++E V+ RAA+LA +H A         ++ML K+A G  V+GMEA++P L   
Sbjct  233   PACRELLITEQVQERAAKLAEQHEA-----DAHLNEMLGKIAGGAPVEGMEALIPALCEG  287

Query  300   GHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQ  359
                LLTD +P GT V+V DPEKVR RAADL+RTG+EFLEASW VAA G    +AP+D   
Sbjct  288   EMRLLTDLVPGGTHVVVADPEKVRARAADLVRTGQEFLEASWMVAADG---GRAPID---  341

Query  360   LGGSGFVELDQVRAAAARTGHPWWTLSQLS------DESAIELDVRAAPSARGHQRDIDE  413
             LG S +  L +V A    TG PWWTL+QLS      D+  + L ++   + RG   +++ 
Sbjct  342   LGASAYRGLAEVAAHTESTGLPWWTLTQLSSEDTEDDDGVVRLALKQVDAYRG---EVER  398

Query  414   IFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPG--QAPKPGVVGVLQG  471
              FA LRAH   GG A LV  G GTA R V++L E + PA + + G    P+PGVV V +G
Sbjct  399   AFADLRAHTTAGGAAVLVVAGAGTAQRAVQQLREGELPARLAEDGLTAEPEPGVVTVARG  458

Query  472   PLRDGVIIPGANLVVITETDLTGSR--VSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQH  529
              L DG   P   LVV+TE DLTG R   S  + +R+ ++RRN VDPLAL AGD VVH+QH
Sbjct  459   GLEDGFAAPEVALVVLTEADLTGGRGGTSTKDMRRMPSRRRNAVDPLALKAGDFVVHEQH  518

Query  530   GIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPA  589
             GIG++VEMV+RTVGGA REYLVLEYAS+KRG   +  D+L+VP D LD++SRYVGG+ P 
Sbjct  519   GIGKYVEMVQRTVGGATREYLVLEYASSKRG---QPGDRLFVPTDQLDEVSRYVGGELPT  575

Query  590   LSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTE  649
             L++LGGSDW NTK KAR+AV+EIA ELV LYA RQ++PGHAF  DTPWQ ELEDAF +TE
Sbjct  576   LNKLGGSDWKNTKAKARKAVKEIAAELVQLYAARQSAPGHAFGADTPWQRELEDAFPYTE  635

Query  650   TVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLL  709
             T DQL AI+EVKADM++ +PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLL
Sbjct  636   TGDQLAAIDEVKADMQRAVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLL  695

Query  710   ADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWK  769
             A QHL TF +RM  FPVT+KGLSRFTD  ES     GLA+G+VD+VIGTHRLLQTGVR+K
Sbjct  696   AQQHLNTFTDRMRSFPVTVKGLSRFTDPLESEQTTTGLAEGTVDVVIGTHRLLQTGVRYK  755

Query  770   DLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE  829
             DLGLV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMS+AGIREMSTILTPPE
Sbjct  756   DLGLVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSMAGIREMSTILTPPE  815

Query  830   ERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVA  889
             ER+PVLTYVG +D+KQ+AAA+RRELLRDGQ F+VHNRV +I+ AA  +RELVPEAR+V A
Sbjct  816   ERHPVLTYVGAYDEKQVAAAIRRELLRDGQVFFVHNRVQTIEKAARHLRELVPEARIVTA  875

Query  890   HGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRG  949
             HGQM ED LE  +Q FW REHD+LVCTTIVETGLDISNANTLIVER+D  GLSQLHQLRG
Sbjct  876   HGQMNEDRLEKIIQGFWEREHDVLVCTTIVETGLDISNANTLIVERSDVLGLSQLHQLRG  935

Query  950   RVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGI  1009
             RVGR+RERGYAYFLYP + PLT+TA+DRLATIAQN+ELGAGMAVA+KDLEIRGAGN+LG 
Sbjct  936   RVGRARERGYAYFLYPEEKPLTDTAHDRLATIAQNSELGAGMAVAMKDLEIRGAGNILGA  995

Query  1010  EQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPD  1069
             EQSGH+AGVGFDLYVRLVGEA+E    A+R  A  +     EE  +VR+DLPVDAH+P D
Sbjct  996   EQSGHIAGVGFDLYVRLVGEAVE----AFRRHAGAEPGAGEEELPEVRVDLPVDAHIPHD  1051

Query  1070  YIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGI  1129
             Y+  +RLRLE YR++AAA     + AV  ELTDRYG+LPEP  RL  VA  R LCR  G+
Sbjct  1052  YVPGERLRLEAYRKIAAAGDTEALDAVRAELTDRYGSLPEPVERLLKVAAFRQLCRAHGV  1111

Query  1130  TDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGG----LGAPR  1185
             T+VT     ++R +PL L DS  VRLKR+YP A Y+A   TV VP P  G     +GAP 
Sbjct  1112  TEVT-QQGTSLRAAPLELADSQLVRLKRLYPKAVYKAAVRTVSVPRPTEGAAGGRIGAPP  1170

Query  1186  IRDVELVQMVADLITALAGKP  1206
             +RD  L+   A L+ +LAG+P
Sbjct  1171  LRDEALLDWCAKLLESLAGRP  1191


>gi|256374814|ref|YP_003098474.1| transcription-repair coupling factor [Actinosynnema mirum DSM 
43827]
 gi|255919117|gb|ACU34628.1| transcription-repair coupling factor [Actinosynnema mirum DSM 
43827]
Length=1187

 Score = 1419 bits (3672),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 770/1216 (64%), Positives = 913/1216 (76%), Gaps = 46/1216 (3%)

Query  1     MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQG  60
             M+ PGP      ++GL+   L     + L   AG    EL L  P +AR LVA+AL+R  
Sbjct  1     MSQPGP------LSGLLTAVLPDKALRALADAAGS--PELELEGPPAARPLVAAALSRTS  52

Query  61    PLLVVTATGREADDLAAELRGVFG-DAVALLPSWETLPHERLSPGVDTVGTRLMALRRLA  119
             P+L VTATGREA++LA+ LR + G +AVA+ PSWETLPHERLSP  DTVG RL  LRRLA
Sbjct  53    PVLAVTATGREAEELASVLRDLVGPEAVAIFPSWETLPHERLSPRADTVGARLQVLRRLA  112

Query  120   HPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRV  179
             HP D     PL  VV +VRSL+QPM P LG +EPL L  G E  FD ++ RL ELAYTRV
Sbjct  113   HPGDR----PLRAVVATVRSLIQPMAPGLGDLEPLDLATGSEHDFDALLHRLAELAYTRV  168

Query  180   DMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVA  239
             DMV +RGEFAVRGGILD+F PTAEHP+RVEFWGDE+TE+R FSVADQRS+P+  +    A
Sbjct  169   DMVEKRGEFAVRGGILDVFPPTAEHPLRVEFWGDEVTEIRPFSVADQRSLPK-QVDAFTA  227

Query  240   FACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSD  299
               CRELLL+E VRARA +LAA H A         ++ML KLAEGI  +GMEA++P L   
Sbjct  228   PPCRELLLTERVRARAQELAAEHEA-----DAQLAEMLTKLAEGIPSEGMEALIPALCDG  282

Query  300   GHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQ  359
                LLTD +PDGT VLV DPEK+R RA DL+RTG+EFLEASW  AA G    +AP+D   
Sbjct  283   ELQLLTDLVPDGTHVLVNDPEKIRARARDLVRTGQEFLEASWMAAAGG---GKAPID---  336

Query  360   LGGSGFVELDQVRAAAARTGHPWWTLSQLSDESA--IELDVRAAPSARGHQRDIDEIFAM  417
             LG S +  LD+V  AA     PWWTLSQL+ E +  + L+ +       +Q D+D  FA 
Sbjct  337   LGASAYRSLDEVADAARAADKPWWTLSQLTTEGSDVLRLEFK---HVHAYQGDVDRAFAD  393

Query  418   LRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDP-GQAPKPGVVGVLQGPLRDG  476
             LRAH A GG A LV PGTGTA R  E+L E+   A  +D   + P+ G V V++G L DG
Sbjct  394   LRAHTAAGGTAVLVVPGTGTAQRATEQLREAQVGAVCVDSLDEPPRTGAVTVVRGALEDG  453

Query  477   VIIPGANLVVITETDLTGSR--VSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRF  534
               +P   LVV+TETDLTG R   S  + +R+ ++RRN VDPLAL  GD VVH+QHGIGR+
Sbjct  454   FALPELALVVLTETDLTGGRGGTSTKDMRRMPSRRRNAVDPLALRTGDYVVHEQHGIGRY  513

Query  535   VEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLG  594
             VEMV+RTV GA REYLVLEYAS+KRG   +  D+L+VP D LD++SRYVGG+ P L++LG
Sbjct  514   VEMVQRTVAGATREYLVLEYASSKRG---QPGDRLFVPTDQLDEVSRYVGGELPTLNKLG  570

Query  595   GSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQL  654
             GSDW NTK KA++AV++IA ELV LYA RQ++PGHAF+PDTPWQ ELEDAF FTETVDQ+
Sbjct  571   GSDWKNTKAKAKKAVKQIAAELVQLYAARQSAPGHAFAPDTPWQRELEDAFPFTETVDQM  630

Query  655   TAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHL  714
              AI+EVKADME+ +PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQV VLVPTTLLA QHL
Sbjct  631   AAIDEVKADMERGVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVVVLVPTTLLAQQHL  690

Query  715   QTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLV  774
              TF ERM  FPV ++GLSRFTD  E+     GLA+G VD+VIGTHRLLQ G+R+KDLGLV
Sbjct  691   NTFTERMRAFPVVVRGLSRFTDPTEAEQTTTGLAEGDVDVVIGTHRLLQKGLRYKDLGLV  750

Query  775   VVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPV  834
             +VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEER+P+
Sbjct  751   IVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERHPI  810

Query  835   LTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMP  894
             LTYVG + DKQ+ AA+RRELLRDGQ FYVHNRVSSI+ AA R+REL PEARVV AHGQM 
Sbjct  811   LTYVGGYADKQVGAAIRRELLRDGQVFYVHNRVSSIEKAARRIRELAPEARVVTAHGQMN  870

Query  895   EDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRS  954
             ED LE  +Q FW RE+D+LV TTIVETGLDISNANTLIVER D  GLSQLHQLRGRVGR 
Sbjct  871   EDKLEKIIQGFWEREYDVLVSTTIVETGLDISNANTLIVERGDLLGLSQLHQLRGRVGRG  930

Query  955   RERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGH  1014
             RERGYAYFLYPP+ PL+ETA+DRLATIAQN ELGAGMAVA+KDLEIRGAGN+LG EQSGH
Sbjct  931   RERGYAYFLYPPESPLSETAHDRLATIAQNTELGAGMAVAMKDLEIRGAGNILGAEQSGH  990

Query  1015  VAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASD  1074
             +AGVGFDLYVRLVGEA+E +R +  A ADG+      EP +VR++LPVDAH+P DY+  +
Sbjct  991   IAGVGFDLYVRLVGEAVEAFRRS--AGADGE---LEVEPAEVRVELPVDAHIPHDYVPGE  1045

Query  1075  RLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA  1134
             RLRLE YR++AAA  +  + AV DEL DRYGA P P  RL  VARLR  CR  G+T+V A
Sbjct  1046  RLRLEAYRKIAAAVDEAGLTAVRDELKDRYGAPPLPVERLLDVARLRHTCRAHGVTEV-A  1104

Query  1135  ASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGG----LGAPRIRDVE  1190
                +++R +PL L DS  VRL+R++P A Y+   +T+  P P  G     +GAP +RD E
Sbjct  1105  LQGSSIRFAPLELKDSQVVRLRRLHPKAVYKQAVSTITTPRPTEGAAGGRMGAPPLRDQE  1164

Query  1191  LVQMVADLITALAGKP  1206
             L+   A  + +LAG P
Sbjct  1165  LLAWCAHFLESLAGAP  1180


>gi|319949680|ref|ZP_08023714.1| transcription-repair coupling factor [Dietzia cinnamea P4]
 gi|319436671|gb|EFV91757.1| transcription-repair coupling factor [Dietzia cinnamea P4]
Length=1222

 Score = 1415 bits (3664),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 757/1240 (62%), Positives = 905/1240 (73%), Gaps = 49/1240 (3%)

Query  1     MTAPGPACSDT--PIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALAR  58
             MT+  PA + T   ++GL    +S P    L  RAG   D   + AP S R  +  ALA 
Sbjct  1     MTSTAPAVTSTTAALSGLAGAVISNPALADL--RAGLDRDAAVVRAPESLRPFLVGALAE  58

Query  59    QGPLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRL  118
             + PLLVVTAT RE ++LA EL G++   VA  PSWETLPHERLSP  DT+G RL  L  +
Sbjct  59    RAPLLVVTATERECEELADELSGMYDGEVAQFPSWETLPHERLSPAADTIGRRLEVLSAV  118

Query  119   AHPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTR  178
                     G    ++V + RS++QP++P     EP+ LT GDE     ++ARL E AYTR
Sbjct  119   ------MAGRAPRIIVAAARSVVQPISPAAARREPVRLTRGDEVDPTDLMARLAEFAYTR  172

Query  179   VDMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLV  238
              DMV RRG+ AVRGGI+D+F  TA+HP+R+EF GDEI E+R FSVADQRS+P+ ++  +V
Sbjct  173   EDMVARRGDIAVRGGIVDVFPTTADHPLRIEFDGDEIAEIREFSVADQRSLPDGEVEQVV  232

Query  239   AFACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWS  298
              + CRELLL +DVRARA QLAA H A       + +++L  LAEGI  DGMEA+  VL  
Sbjct  233   LYPCRELLLDDDVRARAGQLAAEHRA-----NPTLAELLDSLAEGIPRDGMEALTSVLVP  287

Query  299   DGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE  358
                A L   +PD T V+VCDP+KVR RAADL   GREFLEASW+ A +G     APVD E
Sbjct  288   GEMATLPMLMPDDTRVVVCDPDKVRRRAADLASAGREFLEASWTAATMG---GDAPVDSE  344

Query  359   --QLGGSGFVELDQVRAAAARTGHPWWTL------SQLSDESAIELDVRAAPSARGHQRD  410
                L GSG+     VR  AA  G  WW L      +   D + I +     P+ RG   +
Sbjct  345   TLDLSGSGYRTFSSVREEAAGAGRAWWQLVPPGFLTDPEDGAVITVPAGDPPAPRGKDSE  404

Query  411   IDEIFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQ  470
             ++ +F  LRA +  GG AA+V PG GT  R++ERLSE++ PA     G  P  G+V V +
Sbjct  405   MEAMFVRLRALVGAGGRAAMVVPGHGTVARILERLSEAEVPATAAQAGSEPADGLVSVYE  464

Query  471   GPLRDGVIIPGA------NLVVITETDLTGSRV-SAAEGKRLAAKRRNIVDPLALTAGDL  523
               L  G  + G       +LVV++ETDLTG+R+ S A  K   +KRRN VDPLAL AGDL
Sbjct  465   AVLHAGFALTGGADGASGDLVVVSETDLTGNRLGSTARPKARHSKRRNQVDPLALKAGDL  524

Query  524   VVHDQHGIGRFVEMVERTV----GGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQL  579
             VVHDQHGIGRFVEMVER V    G +RREYLV+EYA  KRG      D+LYVPM+SL QL
Sbjct  525   VVHDQHGIGRFVEMVERQVRGGDGSSRREYLVIEYAPGKRGAAG---DRLYVPMESLGQL  581

Query  580   SRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQA  639
             SRYVGG+AP LS++GG+DW NTK KAR+AVREIA ELV LYAKRQ++PG AF PDTPWQ 
Sbjct  582   SRYVGGEAPTLSKMGGADWQNTKRKARKAVREIATELVQLYAKRQSAPGRAFGPDTPWQR  641

Query  640   ELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQ  699
             E+EDAF FTETVDQL+AIEEVKADMEK  PMDRV+ GDVGYGKTE+AVRAAFKAVQDG Q
Sbjct  642   EMEDAFPFTETVDQLSAIEEVKADMEKSAPMDRVVVGDVGYGKTEVAVRAAFKAVQDGTQ  701

Query  700   VAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTH  759
             VAVLVPTTLLA QHL TF ERM+GFPVTIKGLSRFT  AE++ ++ GLADG+VD+VIGTH
Sbjct  702   VAVLVPTTLLAQQHLATFTERMTGFPVTIKGLSRFTSDAEAKEILKGLADGTVDVVIGTH  761

Query  760   RLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIR  819
             RLL TGVRWK+LGLV+VDEEQRFGVEHKEHI SLRTHVDVLTMSATPIPRTLEMSLAGIR
Sbjct  762   RLLATGVRWKNLGLVIVDEEQRFGVEHKEHITSLRTHVDVLTMSATPIPRTLEMSLAGIR  821

Query  820   EMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRE  879
             EMS ILTPPEER PVLTYVG + DK +AAA+RRELLR+GQ FYVHNRV +ID+ AAR+R+
Sbjct  822   EMSQILTPPEERLPVLTYVGAYSDKHVAAAIRRELLREGQVFYVHNRVRTIDSTAARIRD  881

Query  880   LVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTF  939
             LVPEARVVVAHGQM E+ LE TV  FWNRE+D+LVCTTIVETGLDISNANTLIV+R+D  
Sbjct  882   LVPEARVVVAHGQMGEEQLEQTVGGFWNREYDVLVCTTIVETGLDISNANTLIVDRSDQL  941

Query  940   GLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLE  999
             GLSQ+HQLRGRVGRSRERGYAYFLY P+ PLTETAYDRLATIAQNN+LGAGMAVA+KDLE
Sbjct  942   GLSQMHQLRGRVGRSRERGYAYFLYDPEKPLTETAYDRLATIAQNNDLGAGMAVAMKDLE  1001

Query  1000  IRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRID  1059
             +RGAGNVLG EQSGH+AGVGFDLY+RLVGEA+E    AYRA ADG+ V T EE  ++RI+
Sbjct  1002  LRGAGNVLGAEQSGHIAGVGFDLYIRLVGEAVE----AYRAIADGEKVETQEELGEIRIE  1057

Query  1060  LPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVAR  1119
             LPVDA +PPDY+  DRLRLE YR+L+ A    ++ AVV+EL DRYG LP  ARR+ +VAR
Sbjct  1058  LPVDAFIPPDYVDGDRLRLEAYRKLSQAREPGDIDAVVEELLDRYGPLPVEARRVVSVAR  1117

Query  1120  LRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPR--  1177
             LRL+ +   + ++  A  + +R+ PL L DS Q+RLKRMYP A YRAT  TV +P+P+  
Sbjct  1118  LRLVAQKYRVREIVLA-GSRLRVGPLDLLDSQQMRLKRMYPAAQYRATQKTVLLPLPKAA  1176

Query  1178  --AGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITNP  1215
                 G G  + RD E++Q  AD +TA+AG P     +  P
Sbjct  1177  GARAGAGGEKARDDEMLQYAADFLTAMAGDPEGSNPVIQP  1216


>gi|302530260|ref|ZP_07282602.1| transcription-repair coupling factor [Streptomyces sp. AA4]
 gi|302439155|gb|EFL10971.1| transcription-repair coupling factor [Streptomyces sp. AA4]
Length=1192

 Score = 1405 bits (3636),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 762/1219 (63%), Positives = 908/1219 (75%), Gaps = 51/1219 (4%)

Query  8     CSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALA----RQG---  60
              +D  ++GL++  L  P  + +++RAG     L L    + R LVA+ALA    R G   
Sbjct  2     VTDAVLSGLLQAILPDPALRGVVERAGA--PLLELQGAVAVRQLVAAALAEDPERGGAGR  59

Query  61    PLLVVTATGREADDLAAELRGVFG-DAVALLPSWETLPHERLSPGVDTVGTRLMALRRLA  119
             P+L VTATGREAD+L A L  + G D VA  PSWETLPHERLSP  DTVG RL  L RL 
Sbjct  60    PVLAVTATGREADELTASLSALLGPDRVADFPSWETLPHERLSPRADTVGRRLEVLHRL-  118

Query  120   HPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRV  179
             H  D QL     VVV +VRSL+QPM P LG + P+ L VG+E  F+ ++ RLVELAYTRV
Sbjct  119   HTGDEQLR----VVVATVRSLIQPMAPGLGSLAPIDLVVGEEQSFEDLLERLVELAYTRV  174

Query  180   DMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVA  239
             DMV +RGEFAVRGGILD+F PTA+HPVRVEFWGDE++E+R F+V+DQRS+P  +I  + A
Sbjct  175   DMVEKRGEFAVRGGILDLFGPTAQHPVRVEFWGDEVSEIRAFAVSDQRSLPG-EIQRVTA  233

Query  240   FACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSD  299
               CRELLL+ DV+ARAA+LA  + A         ++ML KL+ G+ V+GMEA++PVL   
Sbjct  234   PPCRELLLTPDVKARAAELATTYEA-----DAHLAEMLTKLSGGVPVEGMEALIPVLCEG  288

Query  300   GHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQ  359
               ALLTD +P G+ VL+ DPEK+R RAADL+RTG+EFLEASW+ AA G    QAP+D   
Sbjct  289   ELALLTDAMPQGSHVLLADPEKIRARAADLVRTGQEFLEASWTTAAAG---GQAPID---  342

Query  360   LGGSGFVELDQVRAAAARTGHPWWTLSQLSDES--AIELDVRAAPSARGHQRDIDEIFAM  417
             LG S + EL ++ + A  T  PWWTL+QL+ E      + +  AP+ RG   +++     
Sbjct  343   LGASAYRELSEIASHAQETKRPWWTLTQLTSEDPDVYRVGIEPAPAYRG---ELERAMTD  399

Query  418   LRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDP-GQAPKPGVVGVLQGPLRDG  476
             LRAH+A GG   LV  G GTA R VE+L  ++ PA  ++     P  GVV V  G L +G
Sbjct  400   LRAHLAAGGTGVLVVAGQGTASRAVEQLMAAEVPAKHVEVLSDVPPAGVVTVTCGGLAEG  459

Query  477   VIIPGANLVVITETDLTGSRVSAAE-----GKRLAAKRRNIVDPLALTAGDLVVHDQHGI  531
              + P   LVV++E DLTG   +A         ++ ++RR  VDPLAL AGD VVHDQHGI
Sbjct  460   FVSPERALVVLSEADLTGRGATAGSSTKDLNTKMPSRRRGAVDPLALKAGDYVVHDQHGI  519

Query  532   GRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALS  591
             GRFVEMV+RTV GA REYL+LEYAS+KRG   +  D+L+VP D LD++SRYVGG+ P L+
Sbjct  520   GRFVEMVQRTVAGATREYLLLEYASSKRG---QPGDRLFVPTDQLDEVSRYVGGELPTLN  576

Query  592   RLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETV  651
             +LGGSDW NTK +A++AV+EIA ELV LYA RQA+PGHAF PDTPWQ+ELEDAF FTET 
Sbjct  577   KLGGSDWKNTKARAKKAVKEIAAELVQLYAARQAAPGHAFGPDTPWQSELEDAFPFTETN  636

Query  652   DQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAD  711
             DQL AI+EVKADME+ +PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA 
Sbjct  637   DQLAAIDEVKADMERGVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQ  696

Query  712   QHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDL  771
             QHL TF ERM  FPVTIKGLSRFT  AES  +++ LADG VDIVIGTHRLLQTG+R+KDL
Sbjct  697   QHLNTFTERMRSFPVTIKGLSRFTHKAESDRILEQLADGEVDIVIGTHRLLQTGIRYKDL  756

Query  772   GLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEER  831
             GLV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE+R
Sbjct  757   GLVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEDR  816

Query  832   YPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHG  891
             +P+LTYVG +DDKQ+ AA+RRELLRDGQ FYVHNRVSSI+ AA R+RELVPEARVV AHG
Sbjct  817   HPILTYVGAYDDKQVGAAVRRELLRDGQVFYVHNRVSSIEKAAKRIRELVPEARVVTAHG  876

Query  892   QMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRV  951
             QM ED LE  +Q FW  E+D+LVCTTIVETGLDISNANTLIVER D  GL+QLHQLRGRV
Sbjct  877   QMNEDKLEKIIQGFWENEYDVLVCTTIVETGLDISNANTLIVERGDMLGLAQLHQLRGRV  936

Query  952   GRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQ  1011
             GR RERGYAYFLYPP+ PLTETA+DRLATIAQN ELGAGMAVA+KDLEIRGAGN+LG EQ
Sbjct  937   GRGRERGYAYFLYPPEAPLTETAHDRLATIAQNTELGAGMAVAMKDLEIRGAGNILGAEQ  996

Query  1012  SGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYI  1071
             SGH+AGVGFDLYVRLVGEA+E +R   R A  G      EE  +VR+DLPVDAH+P DY+
Sbjct  997   SGHIAGVGFDLYVRLVGEAVEAFR---RHA--GAEPAEDEELAEVRVDLPVDAHIPHDYV  1051

Query  1072  ASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITD  1131
               +RLRLE YR++A+A     + AV +EL DRYG  P P  RL AVA  R  CR +G+T+
Sbjct  1052  PGERLRLEAYRKIASAPDTAALDAVREELVDRYGQPPAPVTRLLAVAAFRHACRAAGVTE  1111

Query  1132  VTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPR---AGG-LGAPRIR  1187
             V AA   T+R +PL L DS  VRLKR+YP A Y+A T TV VP P    AGG +GAP +R
Sbjct  1112  V-AAQGNTIRFAPLPLMDSQLVRLKRLYPKAMYKAITNTVSVPKPTEGPAGGRMGAPVLR  1170

Query  1188  DVELVQMVADLITALAGKP  1206
             D EL+     L+  L   P
Sbjct  1171  DQELLDWCTKLLAQLTKTP  1189


>gi|300790028|ref|YP_003770319.1| transcription-repair coupling factor [Amycolatopsis mediterranei 
U32]
 gi|299799542|gb|ADJ49917.1| transcription-repair coupling factor [Amycolatopsis mediterranei 
U32]
Length=1184

 Score = 1390 bits (3599),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 753/1210 (63%), Positives = 898/1210 (75%), Gaps = 45/1210 (3%)

Query  13    IAGLVELALSAPTFQQLMQRAGGRPDELT--LIAPASARLLVASALARQGPLLVVTATGR  70
             ++GL+   L  P  + +++RAG    EL   + A       +A+      P+L VTATGR
Sbjct  1     MSGLLTAILPDPALRGVVERAGAPLLELQGPIAARQLVAAALAADDGAGKPVLAVTATGR  60

Query  71    EADDLAAELRGVFGDA-VALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPP  129
             EAD+L A L+ + G++ VA  PSWETLPHERLSP  DTVG RL  L RL   DD      
Sbjct  61    EADELTASLKALIGESRVADFPSWETLPHERLSPRADTVGRRLEVLHRLKTGDD-----D  115

Query  130   LGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFA  189
             L VVV +VRSL+QPM P LG + P+ L VG+E  F+G++ RLVELAYTRVDMV +RGEFA
Sbjct  116   LRVVVATVRSLIQPMAPGLGSLAPVDLVVGEEQSFEGLLERLVELAYTRVDMVEKRGEFA  175

Query  190   VRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSE  249
             VRGGILD+F PTA+HPVRVEFWGDE++E+R F+V+DQRS+P  DI  + A  CRELLL+ 
Sbjct  176   VRGGILDLFGPTAQHPVRVEFWGDEVSEIRAFAVSDQRSLPG-DIPRVTAPPCRELLLTR  234

Query  250   DVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLP  309
              VR +AA+LA  + +         ++ML KLA+GI V+GMEA++PVL      LLTD +P
Sbjct  235   PVREKAAELAKTYES-----DAHLAEMLTKLADGIPVEGMEALIPVLCEGELELLTDAMP  289

Query  310   DGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLGGSGFVELD  369
              GT VL+ DPEK+R RAADL+RTG+EFLEASW+ AA G    QAP+D   LG S +  LD
Sbjct  290   AGTHVLLTDPEKIRARAADLVRTGQEFLEASWTTAAAG---GQAPID---LGASAYRGLD  343

Query  370   QVRAAAARTGHPWWTLSQLSDES--AIELDVRAAPSARGHQRDIDEIFAMLRAHIATGGY  427
             ++ + A  T   WWT++QL+ E      + V AAP+ RG   +++   A LRAH A GG 
Sbjct  344   EIASHAQDTKRAWWTITQLTSEDPDVYRVSVEAAPAYRG---ELERATADLRAHTAAGGT  400

Query  428   AALVAPGTGTAHRVVERLSESDTPAGMLDPG--QAPKPGVVGVLQGPLRDGVIIPGANLV  485
             A LV  G GTA R VE+ S +D PA +   G   AP PGVV V  G L DG I P   LV
Sbjct  401   AVLVVAGHGTAARAVEQFSAADVPASLAGDGLKGAPAPGVVTVTCGGLTDGFISPERALV  460

Query  486   VITETDLTGSRVSAAEGKR-----LAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             V+TE DLTG    A    +     + ++RRN VDPLAL +GD VVH+QHGIGRFVEMV+R
Sbjct  461   VLTEADLTGRGSGAGTSTKDLTTKMPSRRRNAVDPLALKSGDYVVHEQHGIGRFVEMVQR  520

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TV GA REYL+LEY S+KRG      D+L+VP D LD++S+YVGG+ P L++LGGSDW N
Sbjct  521   TVAGATREYLLLEYGSSKRG---HPGDRLFVPTDQLDEVSKYVGGELPTLNKLGGSDWKN  577

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TK +A++AV+EIA ELV LYA RQA+PGHAF PDTPWQ ELEDAF FTET DQL AI+EV
Sbjct  578   TKARAKKAVKEIAAELVQLYAARQAAPGHAFGPDTPWQGELEDAFPFTETNDQLAAIDEV  637

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADME+ +PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA QHL TF ER
Sbjct  638   KADMERGVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQQHLNTFHER  697

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M  FPVTIKGLSRFT+  ES  +++ LA G VDIVIGTHRLLQTG+R+KDLGLV+VDEEQ
Sbjct  698   MRSFPVTIKGLSRFTNKTESDIILEQLASGEVDIVIGTHRLLQTGIRYKDLGLVIVDEEQ  757

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE+R+P+LTYVG 
Sbjct  758   RFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEDRHPILTYVGA  817

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             +DDKQ+ AA+RRELLRDGQ FYVHNRVSSI+ AA R+RELVPEARVV AHGQM ED LE 
Sbjct  818   YDDKQVGAAIRRELLRDGQVFYVHNRVSSIEKAARRIRELVPEARVVTAHGQMNEDKLEK  877

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
              +Q FW  E+D+LVCTTIVETGLDISNANTL+VER D  GL+QLHQLRGRVGR RERGYA
Sbjct  878   IIQGFWENEYDVLVCTTIVETGLDISNANTLLVERGDLLGLAQLHQLRGRVGRGRERGYA  937

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPP+ PLTETA+DRLATIAQN ELGAGMAVA+KDLEIRGAGN+LG EQSGH+AGVGF
Sbjct  938   YFLYPPEAPLTETAHDRLATIAQNTELGAGMAVAMKDLEIRGAGNILGAEQSGHIAGVGF  997

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA++ +R    A          EE  DVR+DLP+DAH+P DY+  +RLRLE 
Sbjct  998   DLYVRLVGEAVDAFRRHAGAEP-----AEEEEMADVRVDLPIDAHIPHDYVPGERLRLEA  1052

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YR++AAA     + AV +EL DRYG  P P  RL +VAR R  CR +G+T+V A    T+
Sbjct  1053  YRKIAAAPDTEGLDAVREELIDRYGQPPAPVNRLLSVARFRHTCREAGVTEV-AVQGNTI  1111

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPR---AGG-LGAPRIRDVELVQMVA  1196
             R +PL L DS  VRLKR+YP A ++A T TV VP P    AGG +GAP +RD EL++   
Sbjct  1112  RFAPLPLLDSQMVRLKRLYPKAVFKAVTNTVSVPKPTEGPAGGRIGAPTLRDEELLEWCT  1171

Query  1197  DLITALAGKP  1206
              L+  L  KP
Sbjct  1172  KLLVQLTKKP  1181


>gi|340531704|gb|AEK46909.1| transcription-repair coupling factor [Amycolatopsis mediterranei 
S699]
Length=1184

 Score = 1389 bits (3596),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 752/1210 (63%), Positives = 898/1210 (75%), Gaps = 45/1210 (3%)

Query  13    IAGLVELALSAPTFQQLMQRAGGRPDELT--LIAPASARLLVASALARQGPLLVVTATGR  70
             ++GL+   L  P  + +++RAG    EL   + A       +A+      P+L VTATGR
Sbjct  1     MSGLLTAILPDPALRGVVERAGAPLLELQGPIAARQLVAAALAADDGAGKPVLAVTATGR  60

Query  71    EADDLAAELRGVFGDA-VALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPP  129
             EAD+L A L+ + G++ VA  PSWETLPHERLSP  DTVG RL  L RL   DD      
Sbjct  61    EADELTASLKALIGESRVADFPSWETLPHERLSPRADTVGRRLEVLHRLKTGDD-----D  115

Query  130   LGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFA  189
             L VVV +VRSL+QPM P LG + P+ L VG+E  F+G++ RLVELAYTRVDMV +RGEFA
Sbjct  116   LRVVVATVRSLIQPMAPGLGSLAPVDLVVGEEQSFEGLLERLVELAYTRVDMVEKRGEFA  175

Query  190   VRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSE  249
             VRGGILD+F PTA+HPVRV+FWGDE++E+R F+V+DQRS+P  DI  + A  CRELLL+ 
Sbjct  176   VRGGILDLFGPTAQHPVRVKFWGDEVSEIRAFAVSDQRSLPG-DIPRVTAPPCRELLLTR  234

Query  250   DVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLP  309
              VR +AA+LA  + +         ++ML KLA+GI V+GMEA++PVL      LLTD +P
Sbjct  235   PVREKAAELAKTYES-----DAHLAEMLTKLADGIPVEGMEALIPVLCEGELELLTDAMP  289

Query  310   DGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLGGSGFVELD  369
              GT VL+ DPEK+R RAADL+RTG+EFLEASW+ AA G    QAP+D   LG S +  LD
Sbjct  290   AGTHVLLTDPEKIRARAADLVRTGQEFLEASWTTAAAG---GQAPID---LGASAYRGLD  343

Query  370   QVRAAAARTGHPWWTLSQLSDES--AIELDVRAAPSARGHQRDIDEIFAMLRAHIATGGY  427
             ++ + A  T   WWT++QL+ E      + V AAP+ RG   +++   A LRAH A GG 
Sbjct  344   EIASHAQDTKRAWWTITQLTSEDPDVYRVSVEAAPAYRG---ELERATADLRAHTAAGGT  400

Query  428   AALVAPGTGTAHRVVERLSESDTPAGMLDPG--QAPKPGVVGVLQGPLRDGVIIPGANLV  485
             A LV  G GTA R VE+ S +D PA +   G   AP PGVV V  G L DG I P   LV
Sbjct  401   AVLVVAGHGTAARAVEQFSAADVPASLAGDGLKGAPAPGVVTVTCGGLTDGFISPERALV  460

Query  486   VITETDLTGSRVSAAEGKR-----LAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVER  540
             V+TE DLTG    A    +     + ++RRN VDPLAL +GD VVH+QHGIGRFVEMV+R
Sbjct  461   VLTEADLTGRGSGAGTSTKDLTTKMPSRRRNAVDPLALKSGDYVVHEQHGIGRFVEMVQR  520

Query  541   TVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWAN  600
             TV GA REYL+LEY S+KRG      D+L+VP D LD++S+YVGG+ P L++LGGSDW N
Sbjct  521   TVAGATREYLLLEYGSSKRG---HPGDRLFVPTDQLDEVSKYVGGELPTLNKLGGSDWKN  577

Query  601   TKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEV  660
             TK +A++AV+EIA ELV LYA RQA+PGHAF PDTPWQ ELEDAF FTET DQL AI+EV
Sbjct  578   TKARAKKAVKEIAAELVQLYAARQAAPGHAFGPDTPWQGELEDAFPFTETNDQLAAIDEV  637

Query  661   KADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGER  720
             KADME+ +PMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLA QHL TF ER
Sbjct  638   KADMERGVPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAQQHLNTFHER  697

Query  721   MSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQ  780
             M  FPVTIKGLSRFT+  ES  +++ LA G VDIVIGTHRLLQTG+R+KDLGLV+VDEEQ
Sbjct  698   MRSFPVTIKGLSRFTNKTESDIILEQLASGEVDIVIGTHRLLQTGIRYKDLGLVIVDEEQ  757

Query  781   RFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGP  840
             RFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPE+R+P+LTYVG 
Sbjct  758   RFGVEHKEHIKALRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEDRHPILTYVGA  817

Query  841   HDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLET  900
             +DDKQ+ AA+RRELLRDGQ FYVHNRVSSI+ AA R+RELVPEARVV AHGQM ED LE 
Sbjct  818   YDDKQVGAAIRRELLRDGQVFYVHNRVSSIEKAARRIRELVPEARVVTAHGQMNEDKLEK  877

Query  901   TVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYA  960
              +Q FW  E+D+LVCTTIVETGLDISNANTL+VER D  GL+QLHQLRGRVGR RERGYA
Sbjct  878   IIQGFWENEYDVLVCTTIVETGLDISNANTLLVERGDLLGLAQLHQLRGRVGRGRERGYA  937

Query  961   YFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGF  1020
             YFLYPP+ PLTETA+DRLATIAQN ELGAGMAVA+KDLEIRGAGN+LG EQSGH+AGVGF
Sbjct  938   YFLYPPEAPLTETAHDRLATIAQNTELGAGMAVAMKDLEIRGAGNILGAEQSGHIAGVGF  997

Query  1021  DLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEG  1080
             DLYVRLVGEA++ +R    A          EE  DVR+DLP+DAH+P DY+  +RLRLE 
Sbjct  998   DLYVRLVGEAVDAFRRHAGAEP-----AEEEEMADVRVDLPIDAHIPHDYVPGERLRLEA  1052

Query  1081  YRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATV  1140
             YR++AAA     + AV +EL DRYG  P P  RL +VAR R  CR +G+T+V A    T+
Sbjct  1053  YRKIAAAPDTEGLDAVREELIDRYGQPPAPVNRLLSVARFRHTCREAGVTEV-AVQGNTI  1111

Query  1141  RLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPR---AGG-LGAPRIRDVELVQMVA  1196
             R +PL L DS  VRLKR+YP A ++A T TV VP P    AGG +GAP +RD EL++   
Sbjct  1112  RFAPLPLLDSQMVRLKRLYPKAVFKAVTNTVSVPKPTEGPAGGRIGAPTLRDEELLEWCT  1171

Query  1197  DLITALAGKP  1206
              L+  L  KP
Sbjct  1172  KLLVQLTKKP  1181


>gi|257057197|ref|YP_003135029.1| transcription-repair coupling factor Mfd [Saccharomonospora viridis 
DSM 43017]
 gi|256587069|gb|ACU98202.1| transcription-repair coupling factor Mfd [Saccharomonospora viridis 
DSM 43017]
Length=1199

 Score = 1377 bits (3564),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 746/1177 (64%), Positives = 893/1177 (76%), Gaps = 43/1177 (3%)

Query  46    ASARLLVASALARQG---PLLVVTATGREADDLAAELRGVFGDA-VALLPSWETLPHERL  101
             A+ +L+VA+  A +G   P+L VT TGR+A++L A LR + G+  VA  PSWETLPHERL
Sbjct  45    ATHQLVVAALAADRGAGRPVLAVTPTGRQAEELTAALRSLLGENLVADFPSWETLPHERL  104

Query  102   SPGVDTVGTRLMALRRLAHPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDE  161
             SP  DTVG RL  LRRLA PD   L     VVV +VRSL+QPM P LG + P+ L VG E
Sbjct  105   SPRADTVGKRLEVLRRLAQPDHGGLR----VVVATVRSLIQPMAPGLGGLHPVELRVGQE  160

Query  162   SPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMF  221
             S F+ V+ +LVELAYTRVDMV +RGEFAVRGGILDIF PTAEHP R+EFWGDE++E+R F
Sbjct  161   SDFEAVLDQLVELAYTRVDMVEKRGEFAVRGGILDIFGPTAEHPHRIEFWGDEVSEIRAF  220

Query  222   SVADQRSIPEIDIHTLVAFACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLA  281
             +V+DQRS+P  ++  ++A  CRE+LL+ DV+ARAA+LA  H           S+ML KLA
Sbjct  221   AVSDQRSLPG-EVTEVIAPPCREILLTPDVKARAAELARTHAD-----NAQLSEMLTKLA  274

Query  282   EGIAVDGMEAVLPVLWSDGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASW  341
             +G+  +GMEA++PVL      LLTD LP+GT V++ +PEK R RAADL+RTG+EFLEASW
Sbjct  275   DGVPCEGMEALIPVLCEGELQLLTDALPEGTHVVLIEPEKSRARAADLVRTGQEFLEASW  334

Query  342   SVAALGTAENQAPVDVEQLGGSGFVELDQVRAAAARTGHPWWTLSQLSDES-AIELDVRA  400
               AA G    +AP+D   LG S + +LD+VRA A  T   WWTLSQL+ ES A  + + +
Sbjct  335   MSAADG---GEAPLD---LGASAYRDLDEVRAHATETNRCWWTLSQLTSESGAHHVAIDS  388

Query  401   APSARGHQRDIDEIFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPG--  458
             AP+ RG   +++ +   LRAH A+GG A +V  G GTA R V++LS ++ PA +   G  
Sbjct  389   APAYRG---ELERVATDLRAHTASGGAAVVVVAGAGTAKRAVDQLSGAEVPATLATEGLT  445

Query  459   QAPKPGVVGVLQGPLRDGVIIPGANLVVITETDLTGSRVSAAEGK-----RLAAKRRNIV  513
             + PKPGVV V  G + DG + PG+ LVV++E D+TG   +A         ++ ++RRN V
Sbjct  446   EEPKPGVVTVTCGGISDGFVAPGSALVVLSEADITGRGATAGRSNVDLNTKMPSRRRNAV  505

Query  514   DPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPM  573
             DPLAL +GD VVHDQHGIGRFVEMV RTVGGA REYLV+EYA +KRG      D+L+VP 
Sbjct  506   DPLALKSGDYVVHDQHGIGRFVEMVRRTVGGATREYLVIEYAPSKRG---HPGDRLFVPT  562

Query  574   DSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSP  633
             D LD++SRYVGG+ P L+++GG+DW  TK +AR+AV+EIA ELV LYA RQA+PGHAFSP
Sbjct  563   DQLDEVSRYVGGETPTLNKMGGADWKKTKARARKAVKEIAAELVQLYAARQAAPGHAFSP  622

Query  634   DTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKA  693
             DTPWQ ELEDAF FTET DQL AI+EVK DME+ +PMDRVICGDVGYGKTEIAVRAAFKA
Sbjct  623   DTPWQRELEDAFPFTETADQLAAIDEVKRDMERDVPMDRVICGDVGYGKTEIAVRAAFKA  682

Query  694   VQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVD  753
             VQDGKQV VLVPTT+LA QHL TF ERM  FPVTIKGLSRFTD  E+  VI+GLADG VD
Sbjct  683   VQDGKQVVVLVPTTILAQQHLATFSERMRSFPVTIKGLSRFTDPHEAEQVINGLADGEVD  742

Query  754   IVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEM  813
             IVIGTHRLLQ+ VR+KDLGLV+VDEEQRFGVEHKEHIK+LRTHVDVLTMSATPIPRTLEM
Sbjct  743   IVIGTHRLLQSNVRYKDLGLVIVDEEQRFGVEHKEHIKALRTHVDVLTMSATPIPRTLEM  802

Query  814   SLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAA  873
             S+AGIREMSTILTPPE+R+P+LTYVG +DDKQ+AAA+RRELLRDGQ FYVHNRVSSI+ A
Sbjct  803   SMAGIREMSTILTPPEDRHPILTYVGAYDDKQVAAAIRRELLRDGQVFYVHNRVSSIERA  862

Query  874   AARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIV  933
             A R+RELVPEARVV AHGQM E  LE  +Q FW RE+D+LVCTTIVETGLDISNANTLIV
Sbjct  863   ARRLRELVPEARVVTAHGQMNEHRLEQIIQGFWEREYDVLVCTTIVETGLDISNANTLIV  922

Query  934   ERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAV  993
             E AD  GL+QLHQLRGRVGR RERGYAYFLYP   PLTETA+DRLATIAQN ELGAGMAV
Sbjct  923   EHADQLGLAQLHQLRGRVGRGRERGYAYFLYPADKPLTETAHDRLATIAQNTELGAGMAV  982

Query  994   ALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEP  1053
             A+KDLEIRGAGN+LG EQSGH+AGVGFDLYVRLVGEA+E +R   R A  G+        
Sbjct  983   AMKDLEIRGAGNILGAEQSGHIAGVGFDLYVRLVGEAVEAFR---RHAGAGEPEEEPTP-  1038

Query  1054  KDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARR  1113
              +VR+DLPVDAH+P DY+  +RLRLE YR++AAA     + AV +EL DRYG LP P  R
Sbjct  1039  TEVRVDLPVDAHIPHDYVPGERLRLEAYRKIAAAPDAEGLDAVREELVDRYGKLPAPVER  1098

Query  1114  LAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQV  1173
             L AVA  R +CR +G+T+VT      +R +PL L DS  VRLKR+YP A ++A T TV V
Sbjct  1099  LLAVAAFRQVCREAGVTEVT-LQGNNIRFTPLQLADSQLVRLKRLYPRAVFKAVTNTVSV  1157

Query  1174  PIPR---AGG-LGAPRIRDVELVQMVADLITALAGKP  1206
             P P    AGG +GAP +RD  L+     LI +L   P
Sbjct  1158  PRPTEGPAGGRIGAPVLRDEPLLDWCTTLIRSLTRTP  1194


>gi|25027590|ref|NP_737644.1| putative transcription-repair coupling factor [Corynebacterium 
efficiens YS-314]
 gi|23492872|dbj|BAC17844.1| putative transcription-repair coupling factor [Corynebacterium 
efficiens YS-314]
Length=1218

 Score = 1377 bits (3563),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 710/1213 (59%), Positives = 879/1213 (73%), Gaps = 50/1213 (4%)

Query  13    IAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTATGREA  72
             +AGL+++A + P  + ++   G R   L L     AR  V   LA   P+LVVTATGREA
Sbjct  5     LAGLLKVAATDPKLKGMISNVGAR--NLHLTGVDQARPWVIGTLAHHAPVLVVTATGREA  62

Query  73    DDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPPLGV  132
             +DL AELR + GD VA  PSWETLPHERLSPGVD VG R   L +L   DDA+      +
Sbjct  63    EDLTAELRAMMGDKVAWFPSWETLPHERLSPGVDIVGRRAQVLNKL---DDAK------I  113

Query  133   VVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRG  192
             +VT+ R+  QP+  +    +PL L  G E+ F  +   LV  AY  VDMV +RGEFA RG
Sbjct  114   IVTAARAFCQPVLKEAAGRQPLILREGAEADFSALGEELVFRAYKNVDMVAKRGEFATRG  173

Query  193   GILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSEDVR  252
             GILD+F  T ++PVR+EFWGDE++++R FSVADQR+IPE+ +  +  +  RELL++++V 
Sbjct  174   GILDVFPTTLDYPVRIEFWGDEVSDIRQFSVADQRTIPEMTLDEIEIYPARELLITDEVA  233

Query  253   ARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGT  312
             ARAA+L  +HP   + V     +ML+++++   VDGMEA++P L       L + +P+ T
Sbjct  234   ARAAELMVKHPGNPTLV-----EMLSRISDRTDVDGMEALIPALVDTPMVPLLELMPENT  288

Query  313   PVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE--QLGGSGFVELDQ  370
              ++V  PEKVRTR ADL  T  EF+ A W  AA+G      PV V+   L  S +   D 
Sbjct  289   HIMVIAPEKVRTRIADLEATDAEFMAAGWEAAAMGA---DGPVSVKGLDLEASSYRSYDS  345

Query  371   VRAAAARTGHPWWTLS-----QLSDESAIELDVRAAPSARGHQRDIDEIFAMLRAHIATG  425
             +  +A+ +  PWWT +     + SD   + LD    P+ RG    I+E+ A+L AH   G
Sbjct  346   LEVSASTSNLPWWTFAPTGMFEASDAETLPLDFEPGPTPRGDLEAINEMMALLLAHTKAG  405

Query  426   GYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGAN--  483
             G AA +AP  G   R+VER +E   P  +  PG  P PG V +       G++ P     
Sbjct  406   GRAAFIAPSEGAIRRMVERFAEQGIPTHVATPGWEPSPGQVTLYHALSHAGLVFPKVRKH  465

Query  484   -------LVVITETDLTGSRVSAAEG-KRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFV  535
                    LVVITETDLTG+RV    G KR  A+RRN VDPLALT GDLVVH+ HGIGRF+
Sbjct  466   RDADALPLVVITETDLTGNRVGDIAGAKRRPARRRNKVDPLALTPGDLVVHETHGIGRFI  525

Query  536   EMVERTVGG----ARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALS  591
             +M ERT+      +RREY+VLEYA +KRG   +  D+LYVPMDSLD LSRYVGG+ P LS
Sbjct  526   KMTERTISTGDETSRREYIVLEYAPSKRG---QPGDQLYVPMDSLDMLSRYVGGEKPTLS  582

Query  592   RLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETV  651
             ++GGSDW NTK KAR AVREIAGELV LYAKRQA+PGHAF PDTPWQ E+ED F + ET 
Sbjct  583   KMGGSDWKNTKKKARAAVREIAGELVELYAKRQAAPGHAFGPDTPWQKEMEDNFPYVETE  642

Query  652   DQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAD  711
             DQ+ AI+ VK DMEKP+PMDRVI GDVGYGKTE+AVRAAFKAVQDGKQVAVLVPTTLLA 
Sbjct  643   DQMLAIDAVKEDMEKPVPMDRVIVGDVGYGKTEVAVRAAFKAVQDGKQVAVLVPTTLLAQ  702

Query  712   QHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDL  771
             QH  TF ERM+GFPVTI GLSRFT  AES+  + GLA G VDIV+GTHRLLQTGV+WK+L
Sbjct  703   QHKSTFEERMAGFPVTIHGLSRFTSTAESKETLAGLASGEVDIVVGTHRLLQTGVQWKNL  762

Query  772   GLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEER  831
             GLV+VDEEQRFGVEHKEHIK+LR+HVDVLTMSATPIPRTLEMS+AGIREM+T+LTPPE+R
Sbjct  763   GLVIVDEEQRFGVEHKEHIKALRSHVDVLTMSATPIPRTLEMSMAGIREMTTMLTPPEDR  822

Query  832   YPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHG  891
             +P+LTYVGP++DKQ+AA++RRELLRDGQ F++HN+V+ I+  A  +R+LVPEARVVVAHG
Sbjct  823   HPILTYVGPYEDKQVAASIRRELLRDGQVFFIHNKVADIEKKARELRDLVPEARVVVAHG  882

Query  892   QMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRV  951
             QM E+LLE TVQ FW+RE+D+LVCTTIVETGLDI+NANTLIVE A   GLSQLHQLRGRV
Sbjct  883   QMSEELLEQTVQGFWDREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRV  942

Query  952   GRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQ  1011
             GRSRERGYAYFLYP    LTET+YDRLATIAQNN+LGAGMAVA+KDLE+RGAGNVLG EQ
Sbjct  943   GRSRERGYAYFLYPKGATLTETSYDRLATIAQNNDLGAGMAVAMKDLEMRGAGNVLGAEQ  1002

Query  1012  SGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVR-TAEEPKDVRIDLPVDAHLPPDY  1070
             SGH+AGVGFDLYVRLVGEA+E    AYRA ADG++V  T + P +VR+DLPVDAH+P +Y
Sbjct  1003  SGHIAGVGFDLYVRLVGEAVE----AYRALADGKSVDGTVKGPTEVRVDLPVDAHIPENY  1058

Query  1071  IASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGIT  1130
             I S+RLRLE YR+LA + S+ ++   V+E+ DRYG +PE   RL AVARLR   R +G+T
Sbjct  1059  INSERLRLEIYRKLATSESESDLQLAVEEMEDRYGPIPEEVSRLLAVARLRHQMRAAGLT  1118

Query  1131  DVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAG-GLGAPRIRDV  1189
             DV A     +++ P+ L DS QVRLKR++P A YRA    +QV  P+AG  +  P +RDV
Sbjct  1119  DV-AVQGTRIKIHPVELKDSQQVRLKRLFPSATYRAAAKAIQVSFPKAGRNVTDPLLRDV  1177

Query  1190  ELVQMVADLITAL  1202
             +L+Q V+D I  +
Sbjct  1178  DLLQWVSDFIAKM  1190


>gi|259507006|ref|ZP_05749906.1| transcription-repair coupling factor [Corynebacterium efficiens 
YS-314]
 gi|259165458|gb|EEW50012.1| transcription-repair coupling factor [Corynebacterium efficiens 
YS-314]
Length=1215

 Score = 1375 bits (3560),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 710/1213 (59%), Positives = 879/1213 (73%), Gaps = 50/1213 (4%)

Query  13    IAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTATGREA  72
             +AGL+++A + P  + ++   G R   L L     AR  V   LA   P+LVVTATGREA
Sbjct  2     LAGLLKVAATDPKLKGMISNVGAR--NLHLTGVDQARPWVIGTLAHHAPVLVVTATGREA  59

Query  73    DDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPPLGV  132
             +DL AELR + GD VA  PSWETLPHERLSPGVD VG R   L +L   DDA+      +
Sbjct  60    EDLTAELRAMMGDKVAWFPSWETLPHERLSPGVDIVGRRAQVLNKL---DDAK------I  110

Query  133   VVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRG  192
             +VT+ R+  QP+  +    +PL L  G E+ F  +   LV  AY  VDMV +RGEFA RG
Sbjct  111   IVTAARAFCQPVLKEAAGRQPLILREGAEADFSALGEELVFRAYKNVDMVAKRGEFATRG  170

Query  193   GILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSEDVR  252
             GILD+F  T ++PVR+EFWGDE++++R FSVADQR+IPE+ +  +  +  RELL++++V 
Sbjct  171   GILDVFPTTLDYPVRIEFWGDEVSDIRQFSVADQRTIPEMTLDEIEIYPARELLITDEVA  230

Query  253   ARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGT  312
             ARAA+L  +HP   + V     +ML+++++   VDGMEA++P L       L + +P+ T
Sbjct  231   ARAAELMVKHPGNPTLV-----EMLSRISDRTDVDGMEALIPALVDTPMVPLLELMPENT  285

Query  313   PVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVE--QLGGSGFVELDQ  370
              ++V  PEKVRTR ADL  T  EF+ A W  AA+G      PV V+   L  S +   D 
Sbjct  286   HIMVIAPEKVRTRIADLEATDAEFMAAGWEAAAMGA---DGPVSVKGLDLEASSYRSYDS  342

Query  371   VRAAAARTGHPWWTLS-----QLSDESAIELDVRAAPSARGHQRDIDEIFAMLRAHIATG  425
             +  +A+ +  PWWT +     + SD   + LD    P+ RG    I+E+ A+L AH   G
Sbjct  343   LEVSASTSNLPWWTFAPTGMFEASDAETLPLDFEPGPTPRGDLEAINEMMALLLAHTKAG  402

Query  426   GYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGAN--  483
             G AA +AP  G   R+VER +E   P  +  PG  P PG V +       G++ P     
Sbjct  403   GRAAFIAPSEGAIRRMVERFAEQGIPTHVATPGWEPSPGQVTLYHALSHAGLVFPKVRKH  462

Query  484   -------LVVITETDLTGSRVSAAEG-KRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFV  535
                    LVVITETDLTG+RV    G KR  A+RRN VDPLALT GDLVVH+ HGIGRF+
Sbjct  463   RDADALPLVVITETDLTGNRVGDIAGAKRRPARRRNKVDPLALTPGDLVVHETHGIGRFI  522

Query  536   EMVERTVGG----ARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALS  591
             +M ERT+      +RREY+VLEYA +KRG   +  D+LYVPMDSLD LSRYVGG+ P LS
Sbjct  523   KMTERTISTGDETSRREYIVLEYAPSKRG---QPGDQLYVPMDSLDMLSRYVGGEKPTLS  579

Query  592   RLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETV  651
             ++GGSDW NTK KAR AVREIAGELV LYAKRQA+PGHAF PDTPWQ E+ED F + ET 
Sbjct  580   KMGGSDWKNTKKKARAAVREIAGELVELYAKRQAAPGHAFGPDTPWQKEMEDNFPYVETE  639

Query  652   DQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLAD  711
             DQ+ AI+ VK DMEKP+PMDRVI GDVGYGKTE+AVRAAFKAVQDGKQVAVLVPTTLLA 
Sbjct  640   DQMLAIDAVKEDMEKPVPMDRVIVGDVGYGKTEVAVRAAFKAVQDGKQVAVLVPTTLLAQ  699

Query  712   QHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDL  771
             QH  TF ERM+GFPVTI GLSRFT  AES+  + GLA G VDIV+GTHRLLQTGV+WK+L
Sbjct  700   QHKSTFEERMAGFPVTIHGLSRFTSTAESKETLAGLASGEVDIVVGTHRLLQTGVQWKNL  759

Query  772   GLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEER  831
             GLV+VDEEQRFGVEHKEHIK+LR+HVDVLTMSATPIPRTLEMS+AGIREM+T+LTPPE+R
Sbjct  760   GLVIVDEEQRFGVEHKEHIKALRSHVDVLTMSATPIPRTLEMSMAGIREMTTMLTPPEDR  819

Query  832   YPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHG  891
             +P+LTYVGP++DKQ+AA++RRELLRDGQ F++HN+V+ I+  A  +R+LVPEARVVVAHG
Sbjct  820   HPILTYVGPYEDKQVAASIRRELLRDGQVFFIHNKVADIEKKARELRDLVPEARVVVAHG  879

Query  892   QMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRV  951
             QM E+LLE TVQ FW+RE+D+LVCTTIVETGLDI+NANTLIVE A   GLSQLHQLRGRV
Sbjct  880   QMSEELLEQTVQGFWDREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRV  939

Query  952   GRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQ  1011
             GRSRERGYAYFLYP    LTET+YDRLATIAQNN+LGAGMAVA+KDLE+RGAGNVLG EQ
Sbjct  940   GRSRERGYAYFLYPKGATLTETSYDRLATIAQNNDLGAGMAVAMKDLEMRGAGNVLGAEQ  999

Query  1012  SGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVR-TAEEPKDVRIDLPVDAHLPPDY  1070
             SGH+AGVGFDLYVRLVGEA+E    AYRA ADG++V  T + P +VR+DLPVDAH+P +Y
Sbjct  1000  SGHIAGVGFDLYVRLVGEAVE----AYRALADGKSVDGTVKGPTEVRVDLPVDAHIPENY  1055

Query  1071  IASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGIT  1130
             I S+RLRLE YR+LA + S+ ++   V+E+ DRYG +PE   RL AVARLR   R +G+T
Sbjct  1056  INSERLRLEIYRKLATSESESDLQLAVEEMEDRYGPIPEEVSRLLAVARLRHQMRAAGLT  1115

Query  1131  DVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAG-GLGAPRIRDV  1189
             DV A     +++ P+ L DS QVRLKR++P A YRA    +QV  P+AG  +  P +RDV
Sbjct  1116  DV-AVQGTRIKIHPVELKDSQQVRLKRLFPSATYRAAAKAIQVSFPKAGRNVTDPLLRDV  1174

Query  1190  ELVQMVADLITAL  1202
             +L+Q V+D I  +
Sbjct  1175  DLLQWVSDFIAKM  1187



Lambda     K      H
   0.318    0.135    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 

Effective search space used: 3143180842264


  Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF
excluding environmental samples from WGS projects
    Posted date:  Sep 5, 2011  4:36 AM
  Number of letters in database: 5,219,829,388
  Number of sequences in database:  15,229,318



Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40