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= 0476.0004.p
         (99 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

B3K6T1.1 B3K6T1_9BACI RNA chaperone Hfq                               152   1e-35
B1DG23.1 B1DG23_9BACL RNA chaperone Hfq                               143   4e-33
C0ZEY6.1 HFQ_BREBN Protein hfq                                        126   6e-28
C1PY91.1 C1PY91_ALIAC RNA-binding protein Hfq                         120   3e-26
B7DVJ0.1 B7DVJ0_9BACL RNA chaperone Hfq                               120   3e-26

>B3K6T1.1 B3K6T1_9BACI RNA chaperone Hfq
          Length = 79

 Score =  152 bits (383), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 73/78 (93%), Positives = 75/78 (96%)

Query: 1  MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAI 60
          MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRG IKAFDNFTIVIDSDGRQQMVYKHAI
Sbjct: 1  MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGTIKAFDNFTIVIDSDGRQQMVYKHAI 60

Query: 61 STFTPQRSVSLMQDSGSE 78
          STF PQR+VSLMQD+ SE
Sbjct: 61 STFMPQRNVSLMQDNNSE 78


>B1DG23.1 B1DG23_9BACL RNA chaperone Hfq
          Length = 80

 Score =  143 bits (361), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/79 (87%), Positives = 75/79 (94%), Gaps = 1/79 (1%)

Query: 1  MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAI 60
          MNKSINIQDTFLNQLRK+NIP TV+L NGFQIRG+IKAFDNFTI+IDS+GRQQMVYKHAI
Sbjct: 1  MNKSINIQDTFLNQLRKDNIPVTVFLMNGFQIRGVIKAFDNFTIIIDSEGRQQMVYKHAI 60

Query: 61 STFTPQRSVSLMQD-SGSE 78
          STFTPQR+VSLMQD S SE
Sbjct: 61 STFTPQRNVSLMQDNSASE 79


>C0ZEY6.1 HFQ_BREBN Protein hfq
          Length = 79

 Score =  126 bits (317), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 58/78 (74%), Positives = 67/78 (85%)

Query: 1  MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAI 60
          M ++INIQDTFLN LRKENI  T+YL NGFQ+RG IKAFDNFTIVIDS+G+QQ+VYKHAI
Sbjct: 1  MKQTINIQDTFLNHLRKENIAVTIYLVNGFQLRGYIKAFDNFTIVIDSEGKQQLVYKHAI 60

Query: 61 STFTPQRSVSLMQDSGSE 78
          STFTPQR VSLM    ++
Sbjct: 61 STFTPQRPVSLMSQENNQ 78


>C1PY91.1 C1PY91_ALIAC RNA-binding protein Hfq
          Length = 86

 Score =  120 bits (302), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 52/74 (70%), Positives = 64/74 (86%)

Query: 4  SINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAISTF 63
          S+NIQDTFLNQ+RKE IP  VYL NGFQIRG+++AFDNFTIV+++DG+QQ++YKHAISTF
Sbjct: 5  SVNIQDTFLNQVRKERIPVIVYLVNGFQIRGLVRAFDNFTIVVETDGKQQLIYKHAISTF 64

Query: 64 TPQRSVSLMQDSGS 77
           P R VSL+Q   S
Sbjct: 65 APMRPVSLVQPEPS 78


>B7DVJ0.1 B7DVJ0_9BACL RNA chaperone Hfq
          Length = 86

 Score =  120 bits (302), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 52/74 (70%), Positives = 64/74 (86%)

Query: 4  SINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAISTF 63
          S+NIQDTFLNQ+RKE IP  VYL NGFQIRG+++AFDNFTIV+++DG+QQ++YKHAISTF
Sbjct: 5  SVNIQDTFLNQVRKERIPVIVYLVNGFQIRGLVRAFDNFTIVVETDGKQQLIYKHAISTF 64

Query: 64 TPQRSVSLMQDSGS 77
           P R VSL+Q   S
Sbjct: 65 APMRPVSLVQPEPS 78


  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
   0.323    0.136    0.375 

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: 486,802,596
Number of extensions: 16036487
Number of successful extensions: 33198
Number of sequences better than 1.0e-05: 887
Number of HSP's gapped: 32750
Number of HSP's successfully gapped: 895
Length of query: 99
Length of database: 3,060,696,203
Length adjustment: 68
Effective length of query: 31
Effective length of database: 2,420,067,183
Effective search space: 75022082673
Effective search space used: 75022082673
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 125 (52.8 bits)