BLASTP 2.2.21 [Jun-14-2009]

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 compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 0035.0227.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 [...   251   3e-65
ref|YP_003776433.1| XRE family transcription regulator protein [...    87   8e-16
ref|ZP_07154650.1| helix-turn-helix protein [Escherichia coli MS...    85   3e-15
ref|YP_003774511.1| Cro/CI family transcription regulator [Herba...    81   5e-14

>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 =  251 bits (640), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 123/124 (99%), Positives = 123/124 (99%)

Query: 1   MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG 60
           MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG
Sbjct: 1   MGKHIGKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPG 60

Query: 61  GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120
           GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV
Sbjct: 61  GRFLRSLHHEFDVNVNWLLTGQEPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120

Query: 121 RQGA 124
            QGA
Sbjct: 121 GQGA 124


>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 = 87.0 bits (214), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 47/107 (43%), Positives = 65/107 (60%), Gaps = 3/107 (2%)

Query: 18  DAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPGGRFLRSLHHEFDVNVNW 77
           + IG R+K VRL  G++QR+   RL TS  +IS +E G +MPGG  L  LH EF V++NW
Sbjct: 4   EEIGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVDLNW 63

Query: 78  LLTGQ--EPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLVRQ 122
           LLTG+  EP +       VR LV  Y      GR ++ ++ASY+ R+
Sbjct: 64  LLTGEEGEPGV-METDEEVRQLVDHYCRVDLQGREILRSLASYVGRE 109


>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 = 85.1 bits (209), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 42/67 (62%), Positives = 51/67 (76%), Gaps = 1/67 (1%)

Query: 15 ISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPGGRFLRSLHHEFDVN 74
          +SKD IGER+ SVR  AG+NQR+FAARL  S   IS +E G +MPGG FL  +H EF+V+
Sbjct: 1  MSKD-IGERVISVRKKAGLNQREFAARLGISNGGISQIENGKAMPGGEFLLKMHQEFNVD 59

Query: 75 VNWLLTG 81
          VNWLLTG
Sbjct: 60 VNWLLTG 66


>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 = 81.3 bits (199), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 43/116 (37%), Positives = 64/116 (55%), Gaps = 1/116 (0%)

Query: 6   GKSDTSGMRISKDAIGERLKSVRLLAGMNQRDFAARLKTSGAYISCVELGHSMPGGRFLR 65
           G +    M  SK A+G+R+K  RL  G +QR FA  L T   +I  +E G  MPG R L 
Sbjct: 10  GITSQPAMNASKKAVGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLH 69

Query: 66  SLHHEFDVNVNWLLTGQ-EPSLPPRYGLHVRSLVSDYGGASQAGRSLIMAVASYLV 120
            +H +F++++NWLLTGQ +P       + +R L+  Y  A + G+ L+ + A  L 
Sbjct: 70  GMHVQFNIDINWLLTGQHQPFRLNSQEMGLRMLLHHYTRADETGKHLLCSAACLLA 125