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= 0004.0003.p
         (92 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

B3K8Y9.1 B3K8Y9_9BACI RNA-binding S4 domain protein                   134   3e-30
B1DIG4.1 B1DIG4_9BACL RNA-binding S4 domain protein                   114   2e-24
A4IJD5.1 A4IJD5_GEOTN Heat shock protein 15                           106   8e-22
B4BS28.1 B4BS28_9BACI RNA-binding S4 domain protein                   106   8e-22
Q2B251.1 Q2B251_9BACI YabO                                            105   2e-21

>B3K8Y9.1 B3K8Y9_9BACI RNA-binding S4 domain protein
          Length = 92

 Score =  134 bits (337), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 65/92 (70%), Positives = 73/92 (79%)

Query: 1  MRLDKFLKVSRLIKRRTVAKDVSEQGRVLINGRESKPSSTVKIGDEITVQFGQXXXXXXX 60
          MR+DKFLKVSRLIKRRTVAKDVS+QGRVLINGRE+KPSSTVK+GDEITVQFGQ       
Sbjct: 1  MRVDKFLKVSRLIKRRTVAKDVSDQGRVLINGREAKPSSTVKVGDEITVQFGQKLVTVRV 60

Query: 61 XXXXXXXRKDEAAGMYTLLREEPVAKTSGLDW 92
                 RKDEA  +YTL++EEP+ K  GLDW
Sbjct: 61 ERLTETTRKDEATSLYTLVKEEPIVKDRGLDW 92


>B1DIG4.1 B1DIG4_9BACL RNA-binding S4 domain protein
          Length = 92

 Score =  114 bits (286), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/92 (63%), Positives = 66/92 (71%)

Query: 1  MRLDKFLKVSRLIKRRTVAKDVSEQGRVLINGRESKPSSTVKIGDEITVQFGQXXXXXXX 60
          MRLDKFLKVSRLIKRRTVAKDVSEQGRV INGRE+K SSTVK GDE+T+Q+GQ       
Sbjct: 1  MRLDKFLKVSRLIKRRTVAKDVSEQGRVWINGREAKASSTVKAGDELTIQYGQKTVTVRV 60

Query: 61 XXXXXXXRKDEAAGMYTLLREEPVAKTSGLDW 92
                 RKDEA  +YTL++EE   +   L W
Sbjct: 61 ERIAETTRKDEAGELYTLIKEEQRPREDNLGW 92


>A4IJD5.1 A4IJD5_GEOTN Heat shock protein 15
          Length = 93

 Score =  106 bits (264), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 53/91 (58%), Positives = 65/91 (71%)

Query: 1  MRLDKFLKVSRLIKRRTVAKDVSEQGRVLINGRESKPSSTVKIGDEITVQFGQXXXXXXX 60
          MRLDKFLKVSRLIKRRT+AK+V++QGRV ING  +K SS VKIGDE+T+QFGQ       
Sbjct: 1  MRLDKFLKVSRLIKRRTLAKEVADQGRVWINGHVAKASSNVKIGDELTIQFGQKRVTVKV 60

Query: 61 XXXXXXXRKDEAAGMYTLLREEPVAKTSGLD 91
                 +K+EA G+Y L+REE +A  S  D
Sbjct: 61 ADLKETTKKEEATGLYELIREERIASASEQD 91


>B4BS28.1 B4BS28_9BACI RNA-binding S4 domain protein
          Length = 93

 Score =  106 bits (264), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 53/91 (58%), Positives = 65/91 (71%)

Query: 1  MRLDKFLKVSRLIKRRTVAKDVSEQGRVLINGRESKPSSTVKIGDEITVQFGQXXXXXXX 60
          MRLDKFLKVSRLIKRRT+AK+V++QGRV ING  +K SS VKIGDE+T+QFGQ       
Sbjct: 1  MRLDKFLKVSRLIKRRTLAKEVADQGRVWINGHVAKASSNVKIGDELTIQFGQKRVTVKV 60

Query: 61 XXXXXXXRKDEAAGMYTLLREEPVAKTSGLD 91
                 +K+EA G+Y L+REE +A  S  D
Sbjct: 61 ADLKETTKKEEATGLYELIREERIASASEQD 91


>Q2B251.1 Q2B251_9BACI YabO
          Length = 89

 Score =  105 bits (261), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/82 (62%), Positives = 64/82 (78%)

Query: 1  MRLDKFLKVSRLIKRRTVAKDVSEQGRVLINGRESKPSSTVKIGDEITVQFGQXXXXXXX 60
          MRLDKFLKVSRLIKRRT+AK+V++QGR+LING++ K SSTVK+GDE+TV+ GQ       
Sbjct: 1  MRLDKFLKVSRLIKRRTLAKEVADQGRILINGQQGKASSTVKVGDELTVRLGQRIVTAKI 60

Query: 61 XXXXXXXRKDEAAGMYTLLREE 82
                 RK+EAA MYT+L+EE
Sbjct: 61 ERLQETSRKEEAAEMYTILKEE 82


  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
   0.315    0.133    0.363 

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: 385,699,096
Number of extensions: 9662652
Number of successful extensions: 25177
Number of sequences better than 1.0e-05: 381
Number of HSP's gapped: 25187
Number of HSP's successfully gapped: 381
Length of query: 92
Length of database: 3,060,696,203
Length adjustment: 61
Effective length of query: 31
Effective length of database: 2,486,014,288
Effective search space: 77066442928
Effective search space used: 77066442928
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: 126 (53.1 bits)