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= Rv1839c

Length=87
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

gi|15608976|ref|NP_216355.1|  hypothetical protein Rv1839c [Mycob...   167    5e-40
gi|289757943|ref|ZP_06517321.1|  LOW QUALITY PROTEIN: DNA-binding...   129    2e-28
gi|254550848|ref|ZP_05141295.1|  antitoxin [Mycobacterium tubercu...  90.5    8e-17
gi|342301106|emb|CCC68871.1|  hypothetical protein NCAS_0B07870 [...  37.4    0.69 
gi|310780659|ref|YP_003968990.1|  hypothetical protein Ilyop_2898...  35.4    2.7  
gi|334140991|ref|YP_004534197.1|  hypothetical protein PP1Y_AT147...  35.4    2.7  
gi|338820908|gb|EGP54879.1|  hydroxypyruvate reductase [Agrobacte...  34.7    5.0  
gi|225873268|ref|YP_002754727.1|  ribbon-helix-helix protein, cop...  34.7    5.2  
gi|333994855|ref|YP_004527468.1|  hypothetical protein TREAZ_0366...  34.3    5.7  


>gi|15608976|ref|NP_216355.1| hypothetical protein Rv1839c [Mycobacterium tuberculosis H37Rv]
 gi|15841307|ref|NP_336344.1| CopG family DNA-binding protein [Mycobacterium tuberculosis CDC1551]
 gi|31793029|ref|NP_855522.1| hypothetical protein Mb1870c [Mycobacterium bovis AF2122/97]
 72 more sequence titles
 Length=87

 Score =  167 bits (423),  Expect = 5e-40, Method: Compositional matrix adjust.
 Identities = 87/87 (100%), Positives = 87/87 (100%), Gaps = 0/87 (0%)

Query  1   MSKRLQVLLDPDEWEELREIARRHRTTVSEWVRRTLREAREREPRGDLDMKLRSVRAAAR  60
           MSKRLQVLLDPDEWEELREIARRHRTTVSEWVRRTLREAREREPRGDLDMKLRSVRAAAR
Sbjct  1   MSKRLQVLLDPDEWEELREIARRHRTTVSEWVRRTLREAREREPRGDLDMKLRSVRAAAR  60

Query  61  HEFPTADVEQMLEEIERGRGAEREGSR  87
           HEFPTADVEQMLEEIERGRGAEREGSR
Sbjct  61  HEFPTADVEQMLEEIERGRGAEREGSR  87


>gi|289757943|ref|ZP_06517321.1| LOW QUALITY PROTEIN: DNA-binding protein [Mycobacterium tuberculosis 
T85]
 gi|289713507|gb|EFD77519.1| LOW QUALITY PROTEIN: DNA-binding protein [Mycobacterium tuberculosis 
T85]
Length=73

 Score =  129 bits (323),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 69/73 (95%), Positives = 69/73 (95%), Gaps = 0/73 (0%)

Query  15  EELREIARRHRTTVSEWVRRTLREAREREPRGDLDMKLRSVRAAARHEFPTADVEQMLEE  74
           EE REIARR RTTVSEWV  TLREAREREPRGDLDMKLRSVRAAARHEFPTADVEQMLEE
Sbjct  1   EEFREIARRPRTTVSEWVPPTLREAREREPRGDLDMKLRSVRAAARHEFPTADVEQMLEE  60

Query  75  IERGRGAEREGSR  87
           IERGRGAEREGSR
Sbjct  61  IERGRGAEREGSR  73


>gi|254550848|ref|ZP_05141295.1| antitoxin [Mycobacterium tuberculosis '98-R604 INH-RIF-EM']
Length=45

 Score = 90.5 bits (223),  Expect = 8e-17, Method: Compositional matrix adjust.
 Identities = 45/45 (100%), Positives = 45/45 (100%), Gaps = 0/45 (0%)

Query  43  EPRGDLDMKLRSVRAAARHEFPTADVEQMLEEIERGRGAEREGSR  87
           EPRGDLDMKLRSVRAAARHEFPTADVEQMLEEIERGRGAEREGSR
Sbjct  1   EPRGDLDMKLRSVRAAARHEFPTADVEQMLEEIERGRGAEREGSR  45


>gi|342301106|emb|CCC68871.1| hypothetical protein NCAS_0B07870 [Naumovozyma castellii CBS 
4309]
Length=386

 Score = 37.4 bits (85),  Expect = 0.69, Method: Composition-based stats.
 Identities = 26/78 (34%), Positives = 35/78 (45%), Gaps = 16/78 (20%)

Query  18   REIARRHRTTVSEWVRRTLREAREREPRGDLDM-----------KLRSVRAAARH-----  61
            R+ AR HR      ++R L+EA+  +PR DLD+            L SV  AAR      
Sbjct  73   RDTARHHRNWCVRLIKRALKEAKINDPRLDLDVICFTKGPGMGAPLHSVVIAARTCSLLW  132

Query  62   EFPTADVEQMLEEIERGR  79
            + P   V   +  IE GR
Sbjct  133  DIPLVRVNHCVGHIEMGR  150


>gi|310780659|ref|YP_003968990.1| hypothetical protein Ilyop_2898 [Ilyobacter polytropus DSM 2926]
 gi|309749982|gb|ADO84642.1| conserved hypothetical protein [Ilyobacter polytropus DSM 2926]
Length=96

 Score = 35.4 bits (80),  Expect = 2.7, Method: Compositional matrix adjust.
 Identities = 22/81 (28%), Positives = 46/81 (57%), Gaps = 3/81 (3%)

Query  3   KRLQVLLDPDEWEELREIARRHRTTVSEWVRRTL-REAREREPRGDLDMKLRSVRAAARH  61
           KR  +L   +EWE + + A+  + +VSE++R+T+ +E +ERE +  L+   ++    +  
Sbjct  6   KRHNILFSDEEWELITDKAKELKISVSEFIRKTMAKEIQERENQDLLNYINQNCEFVSPE  65

Query  62  EFPTADVEQMLEEIERGRGAE  82
           E    D+  +LE+I+    ++
Sbjct  66  E--EKDIMLLLEDIDLNDDSD  84


>gi|334140991|ref|YP_004534197.1| hypothetical protein PP1Y_AT14788 [Novosphingobium sp. PP1Y]
 gi|333939021|emb|CCA92379.1| conserved hypothetical protein [Novosphingobium sp. PP1Y]
Length=110

 Score = 35.4 bits (80),  Expect = 2.7, Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 3/50 (6%)

Query  3   KRLQVLLDPDEWEELREIARRHRTTVSEWVRRTLREAREREPRGDLDMKL  52
           K LQV +  +  E +R  A+RH  +VSEW+R  L +A E +   DL  KL
Sbjct  5   KSLQVHVTVELAERVRAAAKRHDISVSEWIRSLLSQACEND---DLASKL  51


>gi|338820908|gb|EGP54879.1| hydroxypyruvate reductase [Agrobacterium tumefaciens F2]
Length=423

 Score = 34.7 bits (78),  Expect = 5.0, Method: Compositional matrix adjust.
 Identities = 16/48 (34%), Positives = 27/48 (57%), Gaps = 0/48 (0%)

Query  10   DPDEWEELREIARRHRTTVSEWVRRTLREAREREPRGDLDMKLRSVRA  57
            DP + + +REI  R+   + E VR+ L++  E    GD+D  +R + A
Sbjct  207  DPSDIKTVREIVSRYELDLPETVRKVLKKGEETPKAGDIDEDVRMIAA  254


>gi|225873268|ref|YP_002754727.1| ribbon-helix-helix protein, copG family [Acidobacterium capsulatum 
ATCC 51196]
 gi|225793698|gb|ACO33788.1| ribbon-helix-helix protein, copG family [Acidobacterium capsulatum 
ATCC 51196]
Length=84

 Score = 34.7 bits (78),  Expect = 5.2, Method: Compositional matrix adjust.
 Identities = 30/80 (38%), Positives = 42/80 (53%), Gaps = 9/80 (11%)

Query  3   KRLQVLLDPDEWEELREIARRHRTTVSEWVRRTLREAREREPRGDLD----MKLRSVRAA  58
           +R Q+ L+ D W  L   ARR +TT+SE VRR    ARE+   G  D    M   +   A
Sbjct  2   RRTQLYLEEDLWSALHARARREQTTISELVRRA---AREQYLHGVEDRQAVMAAFAGSRA  58

Query  59  ARHEFPTADVEQMLEEIERG  78
           A+H+  T D  + + E+ RG
Sbjct  59  AQHD--TQDSTEYVREMRRG  76


>gi|333994855|ref|YP_004527468.1| hypothetical protein TREAZ_0366 [Treponema azotonutricium ZAS-9]
 gi|333734607|gb|AEF80556.1| conserved hypothetical protein [Treponema azotonutricium ZAS-9]
Length=62

 Score = 34.3 bits (77),  Expect = 5.7, Method: Compositional matrix adjust.
 Identities = 16/45 (36%), Positives = 29/45 (65%), Gaps = 0/45 (0%)

Query  2   SKRLQVLLDPDEWEELREIARRHRTTVSEWVRRTLREAREREPRG  46
           +KRL +L+ P   E++++I+    T ++E V + LRE R++E R 
Sbjct  5   TKRLNLLIQPSLHEDIKKISVVKATNLNEIVNQALREYRDKEKRS  49



Lambda     K      H
   0.317    0.132    0.376 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 

Effective search space used: 130552747860


  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