BLASTP 2.2.17 [Aug-26-2007]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
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:
Schaffer, Alejandro A., 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.

Query= 0001.3095.p         (110 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects 
           15,459,386 sequences; 5,307,515,862 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|YP_003774867.1| transcription regulator protein [Herbaspiril...   162   2e-38
ref|YP_785831.1| phage DNA-binding protein [Bordetella avium 197...   120   6e-26
ref|ZP_01287748.1| Helix-turn-helix motif [delta proteobacterium...   119   2e-25
ref|ZP_01287754.1| Helix-turn-helix motif [delta proteobacterium...   117   5e-25
ref|ZP_01289121.1| Helix-turn-helix motif [delta proteobacterium...   117   5e-25

>ref|YP_003774867.1| transcription regulator protein [Herbaspirillum seropedicae SmR1]
 gb|ADJ62959.1| transcription regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 110

 Score =  162 bits (409), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 81/110 (73%), Positives = 96/110 (87%)

Query: 1   MTARTNTQIIHGADGRPAFVVIPYADYVREHPQEDEPYVPHEVVSMMVDHQWTAIRSWRE 60
           M A TN QIIH  DG+PAFVVIPYADY++E P+ +  YVPHEVV++MVDHQWTAIRSWRE
Sbjct: 1   MNAPTNIQIIHDPDGKPAFVVIPYADYLKEQPRVEGQYVPHEVVALMVDHQWTAIRSWRE 60

Query: 61  HLNLTQQEVAARIGISQSAYAQQESSKRLRPMSLERIAAALGLSVEQLDF 110
           HLNLTQQE+A+R+GISQSAYAQQE+S  LRP SL++IA ALG+ +EQLDF
Sbjct: 61  HLNLTQQEMASRLGISQSAYAQQENSGSLRPSSLKKIAIALGVGIEQLDF 110


>ref|YP_785831.1| phage DNA-binding protein [Bordetella avium 197N]
 emb|CAJ48918.1| Putative phage DNA-binding protein [Bordetella avium 197N]
          Length = 108

 Score =  120 bits (302), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 66/110 (60%), Positives = 83/110 (75%), Gaps = 2/110 (1%)

Query: 1   MTARTNTQIIHGADGRPAFVVIPYADYVREHPQEDEPYVPHEVVSMMVDHQWTAIRSWRE 60
           M A TN QII+G +GRPAFVVIPY DY+     E +  +PH+VVS  VD   T +R+WRE
Sbjct: 1   MNAPTNIQIINGPEGRPAFVVIPYEDYIASRNAEKD-LIPHDVVSRTVDGA-TPVRAWRE 58

Query: 61  HLNLTQQEVAARIGISQSAYAQQESSKRLRPMSLERIAAALGLSVEQLDF 110
           HL +TQ E+A ++GISQSAYAQQE+S+RLR  S E+IAAALG++  QLDF
Sbjct: 59  HLGVTQSEIADKLGISQSAYAQQENSERLRKSSREKIAAALGITAAQLDF 108


>ref|ZP_01287748.1| Helix-turn-helix motif [delta proteobacterium MLMS-1]
 gb|EAT05800.1| Helix-turn-helix motif [delta proteobacterium MLMS-1]
          Length = 109

 Score =  119 bits (298), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 63/110 (57%), Positives = 86/110 (78%), Gaps = 1/110 (0%)

Query: 1   MTARTNTQIIHGADGRPAFVVIPYADYVREHPQEDEPYVPHEVVSMMVDHQWTAIRSWRE 60
           M   TN QII+GADG PAFVV+PYA+++ +    D+  VPHEVV+++ DH WT +R+WRE
Sbjct: 1   MNVHTNIQIINGADGSPAFVVLPYAEWIAQR-DRDQAGVPHEVVNLVFDHNWTPVRAWRE 59

Query: 61  HLNLTQQEVAARIGISQSAYAQQESSKRLRPMSLERIAAALGLSVEQLDF 110
           HLNLTQ EVA RIGISQ+AYAQ E++ + R  +L++IA A+ +++EQLDF
Sbjct: 60  HLNLTQAEVAKRIGISQAAYAQSEAAAKPRKSTLKKIATAMNITLEQLDF 109


>ref|ZP_01287754.1| Helix-turn-helix motif [delta proteobacterium MLMS-1]
 gb|EAT05806.1| Helix-turn-helix motif [delta proteobacterium MLMS-1]
          Length = 125

 Score =  117 bits (293), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 85/106 (80%), Gaps = 1/106 (0%)

Query: 5   TNTQIIHGADGRPAFVVIPYADYVREHPQEDEPYVPHEVVSMMVDHQWTAIRSWREHLNL 64
           TN QII+GADG PAFVV+PYA+++ +    D+  VPHEVV+++ DH WT +R+WRE+LNL
Sbjct: 21  TNIQIINGADGSPAFVVLPYAEWIAQR-DRDQAGVPHEVVNLIFDHNWTPVRAWREYLNL 79

Query: 65  TQQEVAARIGISQSAYAQQESSKRLRPMSLERIAAALGLSVEQLDF 110
           TQ EVA RIGISQ+AYAQ E++ + R  +L++IA A+ +++EQLDF
Sbjct: 80  TQAEVAKRIGISQAAYAQSEAAAKPRKSTLKKIATAMNITLEQLDF 125


>ref|ZP_01289121.1| Helix-turn-helix motif [delta proteobacterium MLMS-1]
 gb|EAT04449.1| Helix-turn-helix motif [delta proteobacterium MLMS-1]
          Length = 109

 Score =  117 bits (293), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 62/110 (56%), Positives = 86/110 (78%), Gaps = 1/110 (0%)

Query: 1   MTARTNTQIIHGADGRPAFVVIPYADYVREHPQEDEPYVPHEVVSMMVDHQWTAIRSWRE 60
           M   TN QII+GADG PAFVV+PYA+++ +    D+  VPHEVV+++ DH WT +R+WRE
Sbjct: 1   MNVHTNIQIINGADGSPAFVVLPYAEWIAQR-DRDQAGVPHEVVNLVFDHNWTPVRAWRE 59

Query: 61  HLNLTQQEVAARIGISQSAYAQQESSKRLRPMSLERIAAALGLSVEQLDF 110
           +LNLTQ EVA RIGISQ+AYAQ E++ + R  +L++IA A+ +++EQLDF
Sbjct: 60  YLNLTQAEVAKRIGISQAAYAQSEAAAKPRKSTLKKIATAMNITLEQLDF 109