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= 0402.0034.p
         (76 letters)

Database: pfamseq 
           9,421,015 sequences; 3,060,696,203 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

B1IFI7.1 B1IFI7_CLOBK DNA-binding response regulator                  122   9e-27
C3KUW6.1 C3KUW6_CLOB6 DNA-binding response regulator                  122   1e-26
C1FM18.1 C1FM18_CLOBJ DNA-binding response regulator                  122   1e-26
B1QI03.1 B1QI03_CLOBO DNA-binding response regulator                  122   1e-26
B1Q9N0.1 B1Q9N0_CLOBO DNA-binding response regulator                  122   1e-26

>B1IFI7.1 B1IFI7_CLOBK DNA-binding response regulator
          Length = 230

 Score =  122 bits (307), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 55/76 (72%), Positives = 66/76 (86%)

Query: 1   MTPKEYGILLLLARNKGRVFTSRDIYELVWEDTYLESDNTVLTHIRNLREKLGDTVKNSK 60
           +TPKE+ IL LLARNKGR+F S +IYE VW   +LE+DN++LTHIRNLREKL DTVKNSK
Sbjct: 155 LTPKEFDILFLLARNKGRIFPSSEIYERVWGQEFLENDNSLLTHIRNLREKLSDTVKNSK 214

Query: 61  YIRTVWGVGYKVDKEV 76
           YI+TVWGVGYK++KE 
Sbjct: 215 YIKTVWGVGYKIEKEA 230


>C3KUW6.1 C3KUW6_CLOB6 DNA-binding response regulator
          Length = 230

 Score =  122 bits (306), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/76 (72%), Positives = 66/76 (86%)

Query: 1   MTPKEYGILLLLARNKGRVFTSRDIYELVWEDTYLESDNTVLTHIRNLREKLGDTVKNSK 60
           +TPKE+ IL LLARNKGR+F S +IYE VW   +LE+DN++LTHIRNLREKL DTVKNSK
Sbjct: 155 LTPKEFDILFLLARNKGRIFPSSEIYERVWGQEFLENDNSLLTHIRNLREKLSDTVKNSK 214

Query: 61  YIRTVWGVGYKVDKEV 76
           YI+TVWGVGYK++KE 
Sbjct: 215 YIKTVWGVGYKIEKEA 230


>C1FM18.1 C1FM18_CLOBJ DNA-binding response regulator
          Length = 230

 Score =  122 bits (306), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/76 (72%), Positives = 66/76 (86%)

Query: 1   MTPKEYGILLLLARNKGRVFTSRDIYELVWEDTYLESDNTVLTHIRNLREKLGDTVKNSK 60
           +TPKE+ IL LLARNKGR+F S +IYE VW   +LE+DN++LTHIRNLREKL DTVKNSK
Sbjct: 155 LTPKEFDILFLLARNKGRIFPSSEIYERVWGQEFLENDNSLLTHIRNLREKLSDTVKNSK 214

Query: 61  YIRTVWGVGYKVDKEV 76
           YI+TVWGVGYK++KE 
Sbjct: 215 YIKTVWGVGYKIEKEA 230


>B1QI03.1 B1QI03_CLOBO DNA-binding response regulator
          Length = 230

 Score =  122 bits (306), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/76 (72%), Positives = 66/76 (86%)

Query: 1   MTPKEYGILLLLARNKGRVFTSRDIYELVWEDTYLESDNTVLTHIRNLREKLGDTVKNSK 60
           +TPKE+ IL LLARNKGR+F S +IYE VW   +LE+DN++LTHIRNLREKL DTVKNSK
Sbjct: 155 LTPKEFDILFLLARNKGRIFPSSEIYERVWGQEFLENDNSLLTHIRNLREKLSDTVKNSK 214

Query: 61  YIRTVWGVGYKVDKEV 76
           YI+TVWGVGYK++KE 
Sbjct: 215 YIKTVWGVGYKIEKEA 230


>B1Q9N0.1 B1Q9N0_CLOBO DNA-binding response regulator
          Length = 230

 Score =  122 bits (306), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/76 (72%), Positives = 66/76 (86%)

Query: 1   MTPKEYGILLLLARNKGRVFTSRDIYELVWEDTYLESDNTVLTHIRNLREKLGDTVKNSK 60
           +TPKE+ IL LLARNKGR+F S +IYE VW   +LE+DN++LTHIRNLREKL DTVKNSK
Sbjct: 155 LTPKEFDILFLLARNKGRIFPSSEIYERVWGQEFLENDNSLLTHIRNLREKLSDTVKNSK 214

Query: 61  YIRTVWGVGYKVDKEV 76
           YI+TVWGVGYK++KE 
Sbjct: 215 YIKTVWGVGYKIEKEA 230


  Database: pfamseq
    Posted date:  Aug 5, 2010  3:22 PM
  Number of letters in database: 3,060,696,203
  Number of sequences in database:  9,421,015
  
Lambda     K      H
   0.318    0.137    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9421015
Number of Hits to DB: 473,341,831
Number of extensions: 15538048
Number of successful extensions: 58823
Number of sequences better than 1.0e-05: 3773
Number of HSP's gapped: 60675
Number of HSP's successfully gapped: 3773
Length of query: 76
Length of database: 3,060,696,203
Length adjustment: 47
Effective length of query: 29
Effective length of database: 2,617,908,498
Effective search space: 75919346442
Effective search space used: 75919346442
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 (21.7 bits)
S2: 125 (52.8 bits)