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= 0001.3658.p         (124 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_003776434.1| XRE family transcription regulator protein [...   159   9e-38
ref|YP_003774511.1| Cro/CI family transcription regulator [Herba...    83   2e-14
ref|ZP_07154650.1| helix-turn-helix protein [Escherichia coli MS...    82   3e-14
ref|YP_003776433.1| XRE family transcription regulator protein [...    79   3e-13
ref|YP_004111811.1| helix-turn-helix domain-containing protein [...    62   2e-08

>ref|YP_003776434.1| XRE family transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
 gb|ADJ64526.1| XRE family transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 124

 Score =  159 bits (403), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 79/122 (64%), Positives = 96/122 (78%)

Query: 1   MDAPIDNAPSQAALAAKQAIGERLKATRQLSGLNQRDFASRLGTSGAYISCVELGHSMPG 60
           M   I  + +     +K AIGERLK+ R L+G+NQRDFA+RL TSGAYISCVELGHSMPG
Sbjct: 1   MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG 60

Query: 61  GRFLRSLHREFDVNINWLLTGLEQELPPRHGFHIKVLIGDYVRASERGKSLVMAVASFLV 120
           GRFLRSLH EFDVN+NWLLTG E  LPPR+G H++ L+ DY  AS+ G+SL+MAVAS+LV
Sbjct: 61  GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120

Query: 121 SR 122
            +
Sbjct: 121 GQ 122


>ref|YP_003774511.1| Cro/CI family transcription regulator [Herbaspirillum seropedicae
           SmR1]
 gb|ADJ62603.1| Cro/CI family transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 152

 Score = 82.8 bits (203), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 48/116 (41%), Positives = 70/116 (60%), Gaps = 6/116 (5%)

Query: 10  SQAAL-AAKQAIGERLKATRQLSGLNQRDFASRLGTSGAYISCVELGHSMPGGRFLRSLH 68
           SQ A+ A+K+A+G+R+K  R   G +QR FA+ LGT   +I  +E G  MPG R L  +H
Sbjct: 13  SQPAMNASKKAVGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLHGMH 72

Query: 69  REFDVNINWLLTGLEQELPPR---HGFHIKVLIGDYVRASERGKSLVMAVASFLVS 121
            +F+++INWLLTG  Q  P R       +++L+  Y RA E GK L+ + A  L +
Sbjct: 73  VQFNIDINWLLTG--QHQPFRLNSQEMGLRMLLHHYTRADETGKHLLCSAACLLAT 126


>ref|ZP_07154650.1| helix-turn-helix protein [Escherichia coli MS 21-1]
 gb|EFK18619.1| helix-turn-helix protein [Escherichia coli MS 21-1]
          Length = 118

 Score = 82.0 bits (201), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 36/66 (54%), Positives = 51/66 (77%)

Query: 20 IGERLKATRQLSGLNQRDFASRLGTSGAYISCVELGHSMPGGRFLRSLHREFDVNINWLL 79
          IGER+ + R+ +GLNQR+FA+RLG S   IS +E G +MPGG FL  +H+EF+V++NWLL
Sbjct: 5  IGERVISVRKKAGLNQREFAARLGISNGGISQIENGKAMPGGEFLLKMHQEFNVDVNWLL 64

Query: 80 TGLEQE 85
          TG+  +
Sbjct: 65 TGMSTD 70


>ref|YP_003776433.1| XRE family transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
 gb|ADJ64525.1| XRE family transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 115

 Score = 78.6 bits (192), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 42/103 (40%), Positives = 63/103 (61%), Gaps = 1/103 (0%)

Query: 18  QAIGERLKATRQLSGLNQRDFASRLGTSGAYISCVELGHSMPGGRFLRSLHREFDVNINW 77
           + IG R+K  R  +GL+QR+   RL TS  +IS +E G +MPGG  L  LHREF V++NW
Sbjct: 4   EEIGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVDLNW 63

Query: 78  LLTGLEQELPPRH-GFHIKVLIGDYVRASERGKSLVMAVASFL 119
           LLTG E E         ++ L+  Y R   +G+ ++ ++AS++
Sbjct: 64  LLTGEEGEPGVMETDEEVRQLVDHYCRVDLQGREILRSLASYV 106


>ref|YP_004111811.1| helix-turn-helix domain-containing protein [Desulfurispirillum
          indicum S5]
 gb|ADU65255.1| helix-turn-helix domain protein [Desulfurispirillum indicum S5]
          Length = 224

 Score = 62.4 bits (150), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/62 (45%), Positives = 40/62 (64%)

Query: 20 IGERLKATRQLSGLNQRDFASRLGTSGAYISCVELGHSMPGGRFLRSLHREFDVNINWLL 79
          + +RL+  R++ GL Q +FA  +GTS  Y+S  E G  +PGG  LR +  + + NINWLL
Sbjct: 2  LNQRLRELRKMLGLTQGEFAFHVGTSPGYVSEAEQGKKVPGGEILRRICEKLNANINWLL 61

Query: 80 TG 81
          TG
Sbjct: 62 TG 63