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= 0004.0002.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             112   2e-25
BH1309 [L] COG0776 Bacterial nucleoid DNA-binding protein             110   6e-25
BH3356 [L] COG0776 Bacterial nucleoid DNA-binding protein             107   3e-24
L102317 [L] COG0776 Bacterial nucleoid DNA-binding protein            106   1e-23
BU032 [L] COG0776 Bacterial nucleoid DNA-binding protein               96   2e-20

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

 Score =  112 bits (279), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 54/89 (60%), Positives = 64/89 (71%)

Query: 1  MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60
          MNKT+L+N ++E S L+KKD    ++ V   I DAL  GDK+QLIGFG FE R+RS R G
Sbjct: 1  MNKTELINAVAEASELSKKDATKAVDSVFDTILDALKNGDKIQLIGFGNFEVRERSARKG 60

Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89
          RNPQTG  IEIP S VPAFK G  LK+AV
Sbjct: 61 RNPQTGEEIEIPASKVPAFKPGKALKDAV 89


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

 Score =  110 bits (275), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 52/90 (57%), Positives = 67/90 (74%)

Query: 1  MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60
          MNKTDL+N ++E++ L+KKD    ++ V   IT AL +G KVQL+GFG+FE R+RS R G
Sbjct: 1  MNKTDLINAVAEQAELSKKDASKAVDAVFESITGALKEGGKVQLVGFGSFEVRERSARKG 60

Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAVN 90
          RNPQTG  IEIP +  PAFK G +LK+AVN
Sbjct: 61 RNPQTGEEIEIPATKNPAFKPGKQLKDAVN 90


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

 Score =  107 bits (268), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 49/89 (55%), Positives = 67/89 (75%)

Query: 1  MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60
          MNKT+L++ ++E++ ++KKD   V+N V   I ++LAQGD VQLIGFG FE R+R+ R G
Sbjct: 1  MNKTELIHQVAERTQMSKKDAGEVVNTVFDVIAESLAQGDSVQLIGFGNFEVRERAARKG 60

Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89
          RNPQTG  I+I  +  PAFKAG +LK+AV
Sbjct: 61 RNPQTGEEIDIAATKTPAFKAGKQLKDAV 89


>L102317 [L] COG0776 Bacterial nucleoid DNA-binding protein
          Length = 91

 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 51/88 (57%), Positives = 65/88 (73%)

Query: 2  NKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSGR 61
          NK DL+  ++ K+GL KKD E  +N     +T+ LA+G+KVQLIGFGTFETR+R+ R GR
Sbjct: 3  NKQDLIAEVAAKTGLTKKDSEKAVNAFGEVVTEFLAKGEKVQLIGFGTFETRERAAREGR 62

Query: 62 NPQTGTPIEIPESTVPAFKAGNKLKEAV 89
          NPQTG  I+I  + VPAFKAG  LK+AV
Sbjct: 63 NPQTGEAIKIAATVVPAFKAGKALKDAV 90


>BU032 [L] COG0776 Bacterial nucleoid DNA-binding protein
          Length = 92

 Score = 95.5 bits (236), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 61/89 (68%)

Query: 1  MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60
          MNKT L+N IS+KS L+K   +  L   L  I D+L +G+ VQ++GFGTF+   RS R+G
Sbjct: 1  MNKTQLINVISKKSNLSKIQAKLTLETTLSTIIDSLKKGESVQIVGFGTFKVNLRSSRTG 60

Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89
          RNPQTG  I+IP + VP+F +G  LK A+
Sbjct: 61 RNPQTGKEIQIPATKVPSFTSGKTLKNAI 89


  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
   0.308    0.130    0.351 

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: 7,189,939
Number of extensions: 287264
Number of successful extensions: 1480
Number of sequences better than 1.0e-05: 86
Number of HSP's gapped: 1480
Number of HSP's successfully gapped: 86
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 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 109 (46.6 bits)