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= 0001.3657.p         (111 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_003776433.1| XRE family transcription regulator protein [...   170   6e-41
ref|YP_003776434.1| XRE family transcription regulator protein [...    86   1e-15
ref|ZP_07154650.1| helix-turn-helix protein [Escherichia coli MS...    80   8e-14
ref|YP_003774511.1| Cro/CI family transcription regulator [Herba...    77   1e-12
ref|YP_004111811.1| helix-turn-helix domain-containing protein [...    56   2e-06

>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 =  170 bits (431), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 87/108 (80%), Positives = 98/108 (90%)

Query: 1   MFSEEIGGRIKEIRLAHGLSQRELGQRLNTSTGHISWLEAGKAMPGGELLLQLYREFAVD 60
           MFSEEIGGRIKE+RLA+GLSQRELGQRL+TSTGHISWLEAGKAMPGGELLLQL+REF+VD
Sbjct: 1   MFSEEIGGRIKEVRLANGLSQRELGQRLDTSTGHISWLEAGKAMPGGELLLQLHREFSVD 60

Query: 61  LNWLLTGSEPDVLPQESDSDVRLLVDHYCRTDVQGREIIRTLASYAGR 108
           LNWLLTG E +    E+D +VR LVDHYCR D+QGREI+R+LASY GR
Sbjct: 61  LNWLLTGEEGEPGVMETDEEVRQLVDHYCRVDLQGREILRSLASYVGR 108


>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 = 86.3 bits (212), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/102 (46%), Positives = 61/102 (59%), Gaps = 1/102 (0%)

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

Query: 64  LLTGSEPDVLPQESDSDVRLLVDHYCRTDVQGREIIRTLASY 105
           LLTG EP  LP      VR LV  Y      GR +I  +ASY
Sbjct: 78  LLTGQEPS-LPPRYGLHVRSLVSDYGGASQAGRSLIMAVASY 118


>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 = 80.5 bits (197), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 38/69 (55%), Positives = 49/69 (71%)

Query: 3  SEEIGGRIKEIRLAHGLSQRELGQRLNTSTGHISWLEAGKAMPGGELLLQLYREFAVDLN 62
          S++IG R+  +R   GL+QRE   RL  S G IS +E GKAMPGGE LL++++EF VD+N
Sbjct: 2  SKDIGERVISVRKKAGLNQREFAARLGISNGGISQIENGKAMPGGEFLLKMHQEFNVDVN 61

Query: 63 WLLTGSEPD 71
          WLLTG   D
Sbjct: 62 WLLTGMSTD 70


>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 = 77.0 bits (188), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/98 (38%), Positives = 55/98 (56%)

Query: 6   IGGRIKEIRLAHGLSQRELGQRLNTSTGHISWLEAGKAMPGGELLLQLYREFAVDLNWLL 65
           +G RIK  RLA G SQR+    L T   HI  +E G+ MPG  LL  ++ +F +D+NWLL
Sbjct: 24  VGQRIKRARLAIGFSQRKFATVLGTLPNHICQIEQGRCMPGSRLLHGMHVQFNIDINWLL 83

Query: 66  TGSEPDVLPQESDSDVRLLVDHYCRTDVQGREIIRTLA 103
           TG          +  +R+L+ HY R D  G+ ++ + A
Sbjct: 84  TGQHQPFRLNSQEMGLRMLLHHYTRADETGKHLLCSAA 121


>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 = 56.2 bits (134), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/60 (43%), Positives = 40/60 (66%)

Query: 9  RIKEIRLAHGLSQRELGQRLNTSTGHISWLEAGKAMPGGELLLQLYREFAVDLNWLLTGS 68
          R++E+R   GL+Q E    + TS G++S  E GK +PGGE+L ++  +   ++NWLLTGS
Sbjct: 5  RLRELRKMLGLTQGEFAFHVGTSPGYVSEAEQGKKVPGGEILRRICEKLNANINWLLTGS 64