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= 0001.0564.p         (113 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_107188.1| putative DNA-binding protein [Burkholderia pseu...    86   2e-15
ref|YP_285454.1| helix-hairpin-helix DNA-binding motif-containin...    68   4e-10
ref|YP_285770.1| helix-hairpin-helix DNA-binding motif-containin...    66   1e-09
ref|YP_004845276.1| XRE family transcriptional regulator [Pseudo...    65   3e-09
ref|YP_003847246.1| helix-turn-helix domain-containing protein [...    64   1e-08

>ref|YP_107188.1| putative DNA-binding protein [Burkholderia pseudomallei K96243]
 ref|ZP_02409847.1| putative DNA-binding protein [Burkholderia pseudomallei 14]
 ref|ZP_02445867.1| putative DNA-binding protein [Burkholderia pseudomallei 91]
 emb|CAH34552.1| putative DNA-binding protein [Burkholderia pseudomallei K96243]
          Length = 125

 Score = 86.3 bits (212), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/108 (42%), Positives = 69/108 (63%)

Query: 1   MSNDIAVRIGRNIAARRRELGRTQADVAEMVGIDTVSLSRIERGVVTAGIPTLDKLADVL 60
           M   +A  IGRNIA+ R++ G TQA VAE + +D  ++SR ERG V  G+ TL++L  VL
Sbjct: 1   MPTSLASVIGRNIASVRKQRGLTQAAVAEQIDVDAETVSRFERGAVMPGVATLERLCAVL 60

Query: 61  GVPLGQLFDGASTNSAAMADAIIAQLAPLHDEDRIFLMEQLQIWAKKL 108
                 L +G+S ++  +A  I+  L PL  +DR+FL+EQ+++W  KL
Sbjct: 61  ECSWMDLLEGSSGDAQQVAHDIVRLLEPLAGDDRLFLLEQMKVWTSKL 108


>ref|YP_285454.1| helix-hairpin-helix DNA-binding motif-containing protein
           [Dechloromonas aromatica RCB]
 gb|AAZ46984.1| Helix-turn-helix motif protein [Dechloromonas aromatica RCB]
          Length = 119

 Score = 68.2 bits (165), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 40/97 (41%), Positives = 56/97 (57%)

Query: 2   SNDIAVRIGRNIAARRRELGRTQADVAEMVGIDTVSLSRIERGVVTAGIPTLDKLADVLG 61
           S  +A R+G N++ RR++LG TQ  VAE VG+D  ++SRIERG     +PTLD+LA  L 
Sbjct: 8   SARLAKRLGGNLSERRKQLGWTQEMVAERVGVDAETISRIERGAHLPSLPTLDRLAVALR 67

Query: 62  VPLGQLFDGASTNSAAMADAIIAQLAPLHDEDRIFLM 98
              G L        A+ A    A ++ L  +DR F+M
Sbjct: 68  CSAGDLLSNEGPEEASEAATFGAWISELGTDDRAFVM 104


>ref|YP_285770.1| helix-hairpin-helix DNA-binding motif-containing protein
           [Dechloromonas aromatica RCB]
 gb|AAZ47300.1| Helix-turn-helix motif protein [Dechloromonas aromatica RCB]
          Length = 120

 Score = 66.2 bits (160), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 41/112 (36%), Positives = 60/112 (53%)

Query: 2   SNDIAVRIGRNIAARRRELGRTQADVAEMVGIDTVSLSRIERGVVTAGIPTLDKLADVLG 61
           S  +A  +G N+  RR++LG TQ  VAE VG+D  ++SRIERG     +PTLD+LA  L 
Sbjct: 9   SAGLAKHLGGNLCERRKQLGWTQEIVAERVGVDVETVSRIERGAHLPSLPTLDRLAVALR 68

Query: 62  VPLGQLFDGASTNSAAMADAIIAQLAPLHDEDRIFLMEQLQIWAKKLAKSKK 113
              G L        A+ A    A ++ L  +DR F+M  ++   + L +  K
Sbjct: 69  CSAGDLLSKEGPAEASEAATFSAWISELGPDDRAFVMSVVRNCCEHLGQRSK 120


>ref|YP_004845276.1| XRE family transcriptional regulator [Pseudogulbenkiania sp. NH8B]
 dbj|BAK74862.1| transcriptional regulator, XRE family [Pseudogulbenkiania sp. NH8B]
          Length = 133

 Score = 65.1 bits (157), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 38/110 (34%), Positives = 63/110 (57%), Gaps = 3/110 (2%)

Query: 5   IAVRIGRNIAARRRELGRTQADVAEMVGIDTVSLSRIERGVVTAGIPTLDKLADVLGVPL 64
           ++V +GRN+  RR+ LG TQ+ +AEM+G++  ++SR ERG+V    P L+K+ DVL +  
Sbjct: 21  LSVIVGRNMQKRRQALGLTQSQLAEMLGVEMETVSRYERGIVAPSFPQLEKVCDVLQIQA 80

Query: 65  GQLF-DGASTNSAAMADAIIAQLAPLHDEDRIFLMEQLQIWAKKLAKSKK 113
             LF DG    +A     +   L  LH  DR F++  ++ + +     K+
Sbjct: 81  WTLFSDGTEVPNA--EGGVGELLQALHSRDREFVVSFVKSYVEHHGAKKR 128


>ref|YP_003847246.1| helix-turn-helix domain-containing protein [Gallionella
           capsiferriformans ES-2]
 gb|ADL55482.1| helix-turn-helix domain protein [Gallionella capsiferriformans
           ES-2]
          Length = 124

 Score = 63.5 bits (153), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 38/113 (33%), Positives = 64/113 (56%)

Query: 1   MSNDIAVRIGRNIAARRRELGRTQADVAEMVGIDTVSLSRIERGVVTAGIPTLDKLADVL 60
           + + + + +G NIA RR++L  TQA++AE +G+DT ++SR ERG     +  L+KLA+ L
Sbjct: 8   LGSSLGLILGANIAERRKKLNWTQAELAERIGVDTETVSRFERGSNLPSLHRLEKLAEAL 67

Query: 61  GVPLGQLFDGASTNSAAMADAIIAQLAPLHDEDRIFLMEQLQIWAKKLAKSKK 113
            +PL +L   +S      +  +   ++ L  +DR F M  L+     LA + K
Sbjct: 68  KIPLYKLVAASSPRHDDQSFILEEWMSELTPKDREFAMNTLKQLCAHLAGAAK 120