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= 0256.0047.p
         (90 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BS_hbs [L] COG0776 Bacterial nucleoid DNA-binding protein             152   1e-37
BH1309 [L] COG0776 Bacterial nucleoid DNA-binding protein             145   1e-35
BH3356 [L] COG0776 Bacterial nucleoid DNA-binding protein             122   1e-28
HI0430 [L] COG0776 Bacterial nucleoid DNA-binding protein             114   3e-26
BS_yonN [L] COG0776 Bacterial nucleoid DNA-binding protein            113   7e-26

>BS_hbs [L] COG0776 Bacterial nucleoid DNA-binding protein
          Length = 92

 Score =  152 bits (385), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 72/89 (80%), Positives = 82/89 (92%)

Query: 1  MNKSDLINVVTEATELPKKDATKAVDAVFEAITGALQNGDKVQLVGFGNFEVRERSARKG 60
          MNK++LIN V EA+EL KKDATKAVD+VF+ I  AL+NGDK+QL+GFGNFEVRERSARKG
Sbjct: 1  MNKTELINAVAEASELSKKDATKAVDSVFDTILDALKNGDKIQLIGFGNFEVRERSARKG 60

Query: 61 RNPQTGEEIEIPSSKVPAFKPGKALKDGI 89
          RNPQTGEEIEIP+SKVPAFKPGKALKD +
Sbjct: 61 RNPQTGEEIEIPASKVPAFKPGKALKDAV 89


>BH1309 [L] COG0776 Bacterial nucleoid DNA-binding protein
          Length = 90

 Score =  145 bits (367), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/89 (79%), Positives = 79/89 (88%)

Query: 1  MNKSDLINVVTEATELPKKDATKAVDAVFEAITGALQNGDKVQLVGFGNFEVRERSARKG 60
          MNK+DLIN V E  EL KKDA+KAVDAVFE+ITGAL+ G KVQLVGFG+FEVRERSARKG
Sbjct: 1  MNKTDLINAVAEQAELSKKDASKAVDAVFESITGALKEGGKVQLVGFGSFEVRERSARKG 60

Query: 61 RNPQTGEEIEIPSSKVPAFKPGKALKDGI 89
          RNPQTGEEIEIP++K PAFKPGK LKD +
Sbjct: 61 RNPQTGEEIEIPATKNPAFKPGKQLKDAV 89


>BH3356 [L] COG0776 Bacterial nucleoid DNA-binding protein
          Length = 90

 Score =  122 bits (306), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 57/90 (63%), Positives = 72/90 (80%)

Query: 1  MNKSDLINVVTEATELPKKDATKAVDAVFEAITGALQNGDKVQLVGFGNFEVRERSARKG 60
          MNK++LI+ V E T++ KKDA + V+ VF+ I  +L  GD VQL+GFGNFEVRER+ARKG
Sbjct: 1  MNKTELIHQVAERTQMSKKDAGEVVNTVFDVIAESLAQGDSVQLIGFGNFEVRERAARKG 60

Query: 61 RNPQTGEEIEIPSSKVPAFKPGKALKDGIK 90
          RNPQTGEEI+I ++K PAFK GK LKD +K
Sbjct: 61 RNPQTGEEIDIAATKTPAFKAGKQLKDAVK 90


>HI0430 [L] COG0776 Bacterial nucleoid DNA-binding protein
          Length = 136

 Score =  114 bits (285), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 55/90 (61%), Positives = 69/90 (76%)

Query: 1   MNKSDLINVVTEATELPKKDATKAVDAVFEAITGALQNGDKVQLVGFGNFEVRERSARKG 60
           MNK+DLI+ +  A EL KK A  A++A  +AIT +L+ G+ VQL+GFG F+V ER+AR G
Sbjct: 47  MNKTDLIDAIANAAELNKKQAKAALEATLDAITASLKEGEPVQLIGFGTFKVNERAARTG 106

Query: 61  RNPQTGEEIEIPSSKVPAFKPGKALKDGIK 90
           RNPQTG EI+I +SKVPAF  GKALKD IK
Sbjct: 107 RNPQTGAEIQIAASKVPAFVSGKALKDAIK 136


>BS_yonN [L] COG0776 Bacterial nucleoid DNA-binding protein
          Length = 92

 Score =  113 bits (282), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 54/90 (60%), Positives = 71/90 (78%)

Query: 1  MNKSDLINVVTEATELPKKDATKAVDAVFEAITGALQNGDKVQLVGFGNFEVRERSARKG 60
          MNK++LI  V E   + KK+   +V+ VF+ I+ AL++G+KV + GFG FEVRER+ARKG
Sbjct: 1  MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKG 60

Query: 61 RNPQTGEEIEIPSSKVPAFKPGKALKDGIK 90
          RNPQTGEEI+IP++K PAFKP KALKD +K
Sbjct: 61 RNPQTGEEIDIPATKAPAFKPAKALKDAVK 90


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.310    0.130    0.353 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 6,500,747
Number of extensions: 216458
Number of successful extensions: 1451
Number of sequences better than 1.0e-05: 87
Number of HSP's gapped: 1450
Number of HSP's successfully gapped: 87
Length of query: 90
Length of database: 38,378,431
Length adjustment: 60
Effective length of query: 30
Effective length of database: 31,458,391
Effective search space: 943751730
Effective search space used: 943751730
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 109 (46.6 bits)