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= 0025.0078.p
         (181 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptid...   255   2e-69
gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptid...   146   1e-36
gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase ...   107   8e-25

>gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptide I
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 539

 Score =  255 bits (651), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 131/181 (72%), Positives = 142/181 (78%), Gaps = 17/181 (9%)

Query: 1   MTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQMQDTYYVVAHFHYVLVAGSLFALFA 60
           MTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQMQDTYYVVAHFHYVLVAGSLFALFA
Sbjct: 357 MTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQMQDTYYVVAHFHYVLVAGSLFALFA 416

Query: 61  GFYYWGPKWTGFMYNETRGKIHFWASLITFNVTFFPMHFLGLAGMPRRYADYPAQFTDFN 120
           G+YYWGPKWTGFMYNE RGK HFWASLITFN+TFFPMHFLGLAGMPRRYADYPAQFTDFN
Sbjct: 417 GYYYWGPKWTGFMYNEWRGKFHFWASLITFNITFFPMHFLGLAGMPRRYADYPAQFTDFN 476

Query: 121 MVASIGA--------RFRFVAGVLPVLRGDPVDQGRRQSRSQAMGRRRRSGVDRAEPGAV 172
           M+ASIGA         F F   V+P ++G          +++A       G++   P   
Sbjct: 477 MIASIGAFGFGLSQVYFLFFV-VIPSIKGG--------KQAEAKPWEGAEGLEWTVPSPA 527

Query: 173 P 173
           P
Sbjct: 528 P 528


>gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptide I
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 633

 Score =  146 bits (368), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 70/128 (54%), Positives = 90/128 (70%), Gaps = 2/128 (1%)

Query: 2   TFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQMQDTYYVVAHFHYVLVAGSLFALFAG 61
            F+TP+LF + F F+  MGG TGL+LA  P+D+Q+ DTY+VVAH HYVL+ G++F LF G
Sbjct: 351 VFKTPLLFVLAFFFILVMGGLTGLMLASVPLDLQLHDTYFVVAHLHYVLLGGAIFPLFGG 410

Query: 62  FYYWGPKWTGFMYNETRGKIHFWASLITFNVTFFPMHFLGLAGMPRRYADYPAQ--FTDF 119
           FYYW PK+TG M +E  G+ +FW   + FNV FFPMH LGL GM RR   Y AQ  +   
Sbjct: 411 FYYWFPKFTGRMLDERLGRWNFWLFFVGFNVCFFPMHVLGLQGMTRRVYTYAAQMGWEGL 470

Query: 120 NMVASIGA 127
           N+ A+IGA
Sbjct: 471 NLTATIGA 478


>gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase
           subunit I protein [Herbaspirillum seropedicae SmR1]
          Length = 667

 Score =  107 bits (266), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 56/127 (44%), Positives = 83/127 (65%), Gaps = 3/127 (2%)

Query: 3   FETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQMQDTYYVVAHFHYVLVAGSLFALFAGF 62
           FE PML+++GF+  F +GG TG++LAV P D  + ++ +++AHFH V++ G +F +FAG 
Sbjct: 387 FEVPMLWTIGFMVTFVIGGMTGVLLAVPPADFVLHNSLFLIAHFHNVIIGGVVFGMFAGI 446

Query: 63  YYWGPKWTGFMYNETRGKIHFWASLITFNVTFFPMHFLGLAGMPRRYA--DYPAQFTDFN 120
            +W PK  GF  NE  GK  FW  L+ F + F P++ LGL G+ RR +  D P+    F 
Sbjct: 447 NFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPLYVLGLMGVTRRMSHFDDPSLQIWF- 505

Query: 121 MVASIGA 127
           +VA+IGA
Sbjct: 506 VVAAIGA 512


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.331    0.144    0.463 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 616,017
Number of extensions: 26942
Number of successful extensions: 81
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 81
Number of HSP's successfully gapped: 3
Length of query: 181
Length of database: 1,619,870
Length adjustment: 79
Effective length of query: 102
Effective length of database: 1,245,805
Effective search space: 127072110
Effective search space used: 127072110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 127 (53.5 bits)