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= 0541.0095.p
         (124 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

B3KB37.1 B3KB37_9BACI Cytochrome c oxidase subunit II                 127   3e-28
B1D7E3.1 B1D7E3_9BACL Cytochrome c oxidase subunit II                  69   1e-10
B1DLB1.1 B1DLB1_9BACL Cytochrome c oxidase subunit II                  69   1e-10
B1D7I0.1 B1D7I0_9BACL Cytochrome c oxidase subunit II                  65   2e-09
B5RYT6.1 B5RYT6_RALSO Cytochrome c oxidase subunit II protein          64   6e-09

>B3KB37.1 B3KB37_9BACI Cytochrome c oxidase subunit II
          Length = 128

 Score =  127 bits (319), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 53/96 (55%), Positives = 76/96 (79%)

Query: 29  GAAETGLTADEELIISATNYSFDQKEYHLKKGVPVNIVFKNESGNHGILVPELNLRLDGK 88
           G  +TG+  + EL+I  +N+ FDQ EYHLKKGVPV I ++NE GNHG+++P L L+LD K
Sbjct: 32  GITDTGVAPEAELVIKGSNFQFDQAEYHLKKGVPVKITYENEDGNHGVMIPALGLQLDRK 91

Query: 89  DSSQVIVPEEAGTFEMTCAIMCGSGHSSMSAKVIVE 124
           ++S V+ P++AG FE++C+IMCG+GHS M +K+IVE
Sbjct: 92  NNSTVVTPDKAGEFEVSCSIMCGAGHSKMISKLIVE 127


>B1D7E3.1 B1D7E3_9BACL Cytochrome c oxidase subunit II
          Length = 122

 Score = 68.9 bits (167), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 55/85 (64%), Gaps = 4/85 (4%)

Query: 40  ELIISATNYSFDQKEYHLKKGVPVNIVFKNESGNHGILVPELNLRLDGKDSSQVIVPEEA 99
           +++I A+++ FDQ EYH+KKG  + +   +  G HG+ + + N++L    +  + +  +A
Sbjct: 40  DVVIKASSWEFDQPEYHIKKGQTIKLELID--GVHGVEIEKTNVKLTQNKAKTITL--DA 95

Query: 100 GTFEMTCAIMCGSGHSSMSAKVIVE 124
           G +E+ C I CG GHS MSAK+IVE
Sbjct: 96  GEYEIKCNIPCGGGHSKMSAKLIVE 120


>B1DLB1.1 B1DLB1_9BACL Cytochrome c oxidase subunit II
          Length = 150

 Score = 68.9 bits (167), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 46/84 (54%)

Query: 41  LIISATNYSFDQKEYHLKKGVPVNIVFKNESGNHGILVPELNLRLDGKDSSQVIVPEEAG 100
           + I A N+ FDQ E  +K+G  V I   N  G HG  +P+ N+ +   +       ++ G
Sbjct: 67  ITIKAKNFEFDQPEIRVKQGDKVKITLSNTEGFHGFAIPDFNVDIKENNGVAEFTADKTG 126

Query: 101 TFEMTCAIMCGSGHSSMSAKVIVE 124
             E  C+++CG+GHS M  K+IVE
Sbjct: 127 EHEFHCSVVCGAGHSKMVGKIIVE 150


>B1D7I0.1 B1D7I0_9BACL Cytochrome c oxidase subunit II
          Length = 129

 Score = 65.5 bits (158), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 54/79 (68%)

Query: 46  TNYSFDQKEYHLKKGVPVNIVFKNESGNHGILVPELNLRLDGKDSSQVIVPEEAGTFEMT 105
           +++++ Q+EYH+K G  V +  +N+SG HG+ + +LN+ L+G +    +  ++ G + M 
Sbjct: 49  SDFTYGQEEYHVKVGDKVILKLQNKSGIHGLKIEDLNVDLEGDNLETNLEFDKPGEYVMH 108

Query: 106 CAIMCGSGHSSMSAKVIVE 124
           C++ CG+GH+ M AK+IV+
Sbjct: 109 CSVPCGAGHADMKAKLIVD 127


>B5RYT6.1 B5RYT6_RALSO Cytochrome c oxidase subunit II protein
          Length = 125

 Score = 63.5 bits (153), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 4/90 (4%)

Query: 38  DEELI-ISATNYSFDQKEYHLKKGVPVNIVFKNESGNHGILVPELNLRLD---GKDSSQV 93
           D ++I + A  ++F      LK+GVPV      +    G  +P+ N+R D   G+ +   
Sbjct: 35  DPQVIRVHARKFTFTPDHITLKRGVPVVFELTGQDILMGFSIPDFNVRADVVPGQTARLA 94

Query: 94  IVPEEAGTFEMTCAIMCGSGHSSMSAKVIV 123
           + P+ AGTFE  C I CG+GH +M+  ++V
Sbjct: 95  LTPDRAGTFEFLCDIFCGTGHETMNGTLVV 124


  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
   0.312    0.130    0.366 

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: 583,783,409
Number of extensions: 22028988
Number of successful extensions: 50800
Number of sequences better than 1.0e-05: 21
Number of HSP's gapped: 50935
Number of HSP's successfully gapped: 21
Length of query: 124
Length of database: 3,060,696,203
Length adjustment: 90
Effective length of query: 34
Effective length of database: 2,212,804,853
Effective search space: 75235365002
Effective search space used: 75235365002
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 (21.9 bits)
S2: 125 (52.8 bits)