BLASTP 2.2.18 [Mar-02-2008]


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= 0574.0006.p
         (66 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           2,715,099 sequences; 757,237,578 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|ZP_00097440.1| COG1476: Predicted transcriptional regulators...    92   3e-18
ref|NP_635257.1| HTH DNA-binding protein [Methanosarcina mazei G...    86   2e-16
ref|NP_463945.1| similar to putative transcription regulator [Li...    81   9e-15
ref|NP_126319.1| repressor protein, putative [Pyrococcus abyssi]...    81   1e-14
ref|NP_349109.1| Predicted transcriptional regulator [Clostridiu...    79   3e-14

>ref|ZP_00097440.1| COG1476: Predicted transcriptional regulators [Desulfitobacterium
          hafniense]
          Length = 70

 Score = 92.0 bits (227), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 44/55 (80%), Positives = 50/55 (90%)

Query: 1  MKNKLEAIRKQQGIKQEELAEALEVSRQTICSLENGRYNPSIILAFKLARYFKLS 55
          MKN+LE IRKQ+GI+QEELA AL VSRQTI SLENGRYNPSIILAFK+AR+F +S
Sbjct: 1  MKNRLEEIRKQRGIRQEELAAALAVSRQTIGSLENGRYNPSIILAFKIARFFGMS 55


>ref|NP_635257.1| HTH DNA-binding protein [Methanosarcina mazei Goe1]
 gb|AAM32929.1| HTH DNA-binding protein [Methanosarcina mazei Goe1]
          Length = 96

 Score = 86.3 bits (212), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/55 (76%), Positives = 48/55 (87%)

Query: 11 QQGIKQEELAEALEVSRQTICSLENGRYNPSIILAFKLARYFKLSIEDIFEYEEE 65
           +GIKQEELAEAL VSRQT  SLENGRYNPSIILAFK+A YF ++IE++F YEEE
Sbjct: 37 NKGIKQEELAEALGVSRQTTGSLENGRYNPSIILAFKIAGYFNITIEEVFIYEEE 91


>ref|NP_463945.1| similar to putative transcription regulator [Listeria
          monocytogenes EGD-e]
 pir||AI1126 probable transcription regulator homolog lmo0416 [imported] -
          Listeria monocytogenes (strain EGD-e)
 emb|CAC98495.1| lmo0416 [Listeria monocytogenes]
          Length = 67

 Score = 80.9 bits (198), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 55/64 (85%)

Query: 1  MKNKLEAIRKQQGIKQEELAEALEVSRQTICSLENGRYNPSIILAFKLARYFKLSIEDIF 60
          ++NK++ +R+++GI Q ELA ALEVSRQTI ++E G+YNPS+ L+ K+ARYF+L+IE+IF
Sbjct: 3  VRNKVKQLREERGIGQNELALALEVSRQTIHAIEKGKYNPSLELSLKMARYFRLTIEEIF 62

Query: 61 EYEE 64
          + EE
Sbjct: 63 QLEE 66


>ref|NP_126319.1| repressor protein, putative [Pyrococcus abyssi]
 pir||G75183 probable repressor protein PAB7155 - Pyrococcus abyssi  (strain
          Orsay)
 emb|CAB49550.1| Helix-turn-helix repressor protein family [Pyrococcus abyssi]
          Length = 73

 Score = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 51/65 (78%)

Query: 1  MKNKLEAIRKQQGIKQEELAEALEVSRQTICSLENGRYNPSIILAFKLARYFKLSIEDIF 60
          MKN+L   R++ G+ QEELA  L V+RQTI ++E G+Y+PS+ LAFK+AR+F + IEDIF
Sbjct: 1  MKNRLREFREKYGLTQEELARILGVTRQTIIAIEKGKYDPSLRLAFKIARFFGVRIEDIF 60

Query: 61 EYEEE 65
           YEEE
Sbjct: 61 IYEEE 65


>ref|NP_349109.1| Predicted transcriptional regulator [Clostridium acetobutylicum]
 pir||F97207 probable transcription regulator [imported] - Clostridium
          acetobutylicum
 gb|AAK80449.1| Predicted transcriptional regulator [Clostridium acetobutylicum]
          Length = 64

 Score = 79.0 bits (193), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 51/64 (79%)

Query: 1  MKNKLEAIRKQQGIKQEELAEALEVSRQTICSLENGRYNPSIILAFKLARYFKLSIEDIF 60
          MKN +  +R+Q G+ Q+ELAE + VSRQTI SLEN RYNPSI LA K+A+ F+L+IE++F
Sbjct: 1  MKNNIRKLREQFGLTQQELAERVSVSRQTIISLENERYNPSIFLAHKIAKSFELTIENVF 60

Query: 61 EYEE 64
           +E+
Sbjct: 61 IFED 64


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Mar 24, 2004  1:53 AM
  Number of letters in database: 757,237,578
  Number of sequences in database:  2,715,099
  
Lambda     K      H
   0.315    0.134    0.355 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 2715099
Number of Hits to DB: 84,447,813
Number of extensions: 2386767
Number of successful extensions: 9552
Number of sequences better than 1.0e-05: 145
Number of HSP's gapped: 9566
Number of HSP's successfully gapped: 145
Length of query: 66
Length of database: 757,237,578
Length adjustment: 37
Effective length of query: 29
Effective length of database: 656,778,915
Effective search space: 19046588535
Effective search space used: 19046588535
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 120 (50.8 bits)