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= 0012.0136.p
         (539 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase ...    62   8e-11
gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptid...    58   2e-09

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

 Score = 62.4 bits (150), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 101/468 (21%), Positives = 187/468 (39%), Gaps = 73/468 (15%)

Query: 43  PEHYYRSVTLHGTVMAYVLPTLVAMGI-GYAI-TEIALRQ---PLLGLRWAWLGFWLVIG 97
           P HY +  T HG +M + +   +  G+  Y +  +I  R    P L        FW+   
Sbjct: 106 PHHYDQVFTAHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNN----FSFWMTTF 161

Query: 98  GTVMAGATTAAGK------------SSVLYTFYPPMIGSPFYYLGVVLVVVGSWIWVALM 145
           G ++  A+   G+            S +LY+   P +G  +Y   + +  VG+ +    +
Sbjct: 162 GALLVMASLFVGEFARTGWLAYPPLSGILYS---PDVGVDYYIWALQVAGVGTLLSGINL 218

Query: 146 VINLLAWKRVHPGQVVPLAMYGNVAGACLWAWTSMGASSEI---------------LLQI 190
           V+ ++  K   PG         N+    ++ WTS+  +  I               L ++
Sbjct: 219 VVTIV--KMRAPGM--------NMMKMPVFTWTSLCTNVLIVAAFPVLTAVLAMLSLDRV 268

Query: 191 LPASLGWTDTINAGLARVLFSWTL-HAIVYFWLVPAYLVFYTIFPRAIGGRLYSDTMARV 249
              +    D     +  V   W   H  VY  ++PA+ +F  I     G RL+  T    
Sbjct: 269 FGTNFFTNDMGGNAMMYVNLIWIWGHPEVYILVLPAFGIFSEIVSTFSGKRLFGYTSMVY 328

Query: 250 SFALFLVFSMPIGIHHLFADPQVGAGFKFVHAAMTAMVSIPTFLTVFTIVASAEIVGRLR 309
           +  +  + S  + +HH F     GA         T ++SIPT   +F  + +    GR+R
Sbjct: 329 ATVVITILSYLVWLHHFFTMGS-GASVNSFFGITTMIISIPTGAKIFNWLFTMY-RGRIR 386

Query: 310 GGKGPFGWVRALPWDQPMMLAVTYAFIMLGFGGAGGLINMNYQVNETVHNTQWVTGHFHL 369
                        ++ PM+  + +  +    GG  G++      +  +HN+ ++  HFH 
Sbjct: 387 -------------FEVPMLWTIGF-MVTFVIGGMTGVLLAVPPADFVLHNSLFLIAHFHN 432

Query: 370 IFAGAIVIMYFMAAYELWPQLRHNATPSPRLIKLQIALWFAGMMILTMPWHLVGLLGAPR 429
           +  G +V   F A    W         +    K     W  G  +  MP +++GL+G  R
Sbjct: 433 VIIGGVVFGMF-AGINFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPLYVLGLMGVTR 491

Query: 430 RMAYYDYTHPALQPHGLLVLISVVGGMVLVVSAGLFLYILA-SARTQS 476
           RM+++D   P+LQ   +  +++ +G  ++ +  G F+  +A S R + 
Sbjct: 492 RMSHFD--DPSLQ---IWFVVAAIGAGLIALGIGSFIIQIAVSIRDRK 534


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

 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 93/204 (45%), Gaps = 21/204 (10%)

Query: 263 IHHLFADPQVGAGFKFVHAAMTAMVSIPTFLTVFTIVASAEIVGRLRGGKGPFGWVRALP 322
           +HH+FA     AG K    A + ++++PT L +F  +++               W+    
Sbjct: 307 VHHMFATTLPEAG-KLFFTAASLLIALPTALQIFCWISTI--------------WLGRPV 351

Query: 323 WDQPMMLAVTYAFIMLGFGGAGGLINMNYQVNETVHNTQWVTGHFHLIFAGAIVIMYFMA 382
           +  P++  + + FI++  GG  GL+  +  ++  +H+T +V  H H +  G  +   F  
Sbjct: 352 FKTPLLFVLAFFFILV-MGGLTGLMLASVPLDLQLHDTYFVVAHLHYVLLGGAIFPLFGG 410

Query: 383 AYELWPQLRHNATPSPRLIKLQIALWFAGMMILTMPWHLVGLLGAPRRMAYYDYTHPALQ 442
            Y  +P+         RL +    L+F G  +   P H++GL G  RR+    YT+ A  
Sbjct: 411 FYYWFPKFTGRML-DERLGRWNFWLFFVGFNVCFFPMHVLGLQGMTRRV----YTYAAQM 465

Query: 443 PHGLLVLISVVGGMVLVVSAGLFL 466
               L L + +G  ++ +S  LFL
Sbjct: 466 GWEGLNLTATIGAFLIGLSVLLFL 489


  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
   0.329    0.142    0.471 

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: 1,813,256
Number of extensions: 78711
Number of successful extensions: 326
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 320
Number of HSP's successfully gapped: 3
Length of query: 539
Length of database: 1,619,870
Length adjustment: 90
Effective length of query: 449
Effective length of database: 1,193,720
Effective search space: 535980280
Effective search space used: 535980280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 133 (55.8 bits)