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= 0001.3161.p
         (475 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312501|ref|YP_003776593.1| cbb3-type cytochrome c oxidase ...   923   0.0  

>gi|300312501|ref|YP_003776593.1| cbb3-type cytochrome c oxidase
           subunit I transmembrane protein [Herbaspirillum
           seropedicae SmR1]
          Length = 475

 Score =  923 bits (2386), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 463/475 (97%), Positives = 473/475 (99%)

Query: 1   VNKENSYNYTVVRQFTVATILWGVVGMLVGVIIAAQLAWPELNMGIPWLSFGRLRPLHTN 60
           ++KENSYNYTVVRQFTVATILWGVVGMLVGVIIAAQLAWPELNMG+PWLSFGRLRPLHTN
Sbjct: 1   MSKENSYNYTVVRQFTVATILWGVVGMLVGVIIAAQLAWPELNMGVPWLSFGRLRPLHTN 60

Query: 61  AVIFAFGGCALMATSYYVVQRTCQVRLFSDFLAAFTFWGWQLVIVGAAITLPMGLTRGKE 120
           AVIFAFGGCALMATSYYVVQRTCQVRLFSDFLAAFTFWGWQLVIVGAAI+LP+GLTRGKE
Sbjct: 61  AVIFAFGGCALMATSYYVVQRTCQVRLFSDFLAAFTFWGWQLVIVGAAISLPLGLTRGKE 120

Query: 121 YAELEWPITILIAVVWVAYAVVFFGTLIKRKVKHIYVANWFYGAFIIAVAILHIVNGMTM 180
           YAELEWP+TILIAVVWVAYAVVFFGTLIKRKV+HIYVANWFYGAFIIAVAILHIVNGMTM
Sbjct: 121 YAELEWPLTILIAVVWVAYAVVFFGTLIKRKVQHIYVANWFYGAFIIAVAILHIVNGMTM 180

Query: 181 PATLTKSYSMYSGAQDAMIQWWYGHNAVGFFLTAGFLGMMYYFIPKQVNRPVYSYRLSIV 240
           PATLTKSYSMYSGAQDAMIQWWYGHNAVGFFLTAGFLGMMYYFIPKQVNRPVYSYRLSIV
Sbjct: 181 PATLTKSYSMYSGAQDAMIQWWYGHNAVGFFLTAGFLGMMYYFIPKQVNRPVYSYRLSIV 240

Query: 241 HFWALIFTYMWAGPHHLHYTALPDWTQSLGMVFSLILLAPSWGGMINGMMTMSGAWHQLR 300
           HFWALIFTYMWAGPHHLHYTALPDWTQSLGMVFSLILLAPSWGGMINGMMT+SGAWHQLR
Sbjct: 241 HFWALIFTYMWAGPHHLHYTALPDWTQSLGMVFSLILLAPSWGGMINGMMTLSGAWHQLR 300

Query: 301 TDPILKFLVVSLSFYGMSTFEGPMMAIKTVNALSHYTDWTIGHVHSGALGWVGFVTMGAM 360
           TDPILKFLVVSLSFYGMSTFEGPMMAIKTVNALSHYTDWTIGHVHSGALGWVGFVTMGAM
Sbjct: 301 TDPILKFLVVSLSFYGMSTFEGPMMAIKTVNALSHYTDWTIGHVHSGALGWVGFVTMGAM 360

Query: 361 YYLIPRLSGKTQMWSKDLIEIHFWVATIGIVLYIAAMWIAGVMQGLMWRAVNDDGTLTYS 420
           YYLIPRLSGKTQMWSKDLIEIHFWVATIGIVLYIAAMWIAGVMQGLMWRAVN DGTLTY+
Sbjct: 361 YYLIPRLSGKTQMWSKDLIEIHFWVATIGIVLYIAAMWIAGVMQGLMWRAVNADGTLTYT 420

Query: 421 FVEGVKATYPYYVIRLVGGLMYLSGMLVMAYNTWRTMRGTELAVAPIPAVTNAAH 475
           FVE VKATYPYYVIRL+GGLMYLSGMLVMAYNTWRTMRGTELAVAPIPAVTNAAH
Sbjct: 421 FVESVKATYPYYVIRLMGGLMYLSGMLVMAYNTWRTMRGTELAVAPIPAVTNAAH 475


  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    0.139    0.465 

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: 1,519,667
Number of extensions: 64566
Number of successful extensions: 253
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 253
Number of HSP's successfully gapped: 3
Length of query: 475
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 386
Effective length of database: 1,198,455
Effective search space: 462603630
Effective search space used: 462603630
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: 132 (55.5 bits)