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= 0002.0531.p
         (266 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313443|ref|YP_003777535.1| cytochrome c oxidase subunit II...   434   e-123
gi|300311777|ref|YP_003775869.1| cytochrome o ubiquinol oxidase ...    87   1e-18

>gi|300313443|ref|YP_003777535.1| cytochrome c oxidase subunit III
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 286

 Score =  434 bits (1117), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 225/266 (84%), Positives = 243/266 (91%)

Query: 1   VLAGIAMLATMAGASAWVNSYSWGMPLNLIGIVAVLVVLYKWFGQAIGESESGQYSARID 60
           ++AGI+ML TM GASAWVN  SW   +N++GI+ VLVVLY WFG AI ESESG YS RID
Sbjct: 21  MMAGISMLITMIGASAWVNGVSWAPYVNILGILMVLVVLYYWFGDAIRESESGLYSERID 80

Query: 61  ASFRWSMGWFIFSEVMFFAAFFGALFYARSITMPWLADLDHKVIWPDFAAHWGNIGPART 120
            S+RWSM WFIFSEVMFFAAFFGALFYARSITMPWLADLDHK+IWPDFA  WGN+GPA T
Sbjct: 81  LSYRWSMSWFIFSEVMFFAAFFGALFYARSITMPWLADLDHKLIWPDFAGQWGNVGPAGT 140

Query: 121 IESFQTMGPFPIPTINTALLLTSGVTLTISHHALRAGHRAQTAIWLFATVLLGAIFMGFQ 180
           +E+F TMGPFPIPTINT LLLTSGVTLTISHHA+RAGHR QTA+WLF T+LLGA+FMGFQ
Sbjct: 141 VENFTTMGPFPIPTINTLLLLTSGVTLTISHHAMRAGHRTQTAVWLFLTILLGAVFMGFQ 200

Query: 181 AYEYMHAYSELNLKLTSGIYGSTFFMLTGFHGFHVTMGAIMLSVVLYRVLRGHFTPEHHF 240
           AYEY+HAYSELNLKL+SGIYGSTFFMLTGFHGFHVTMGAIMLSVVLYRVLRGHFTP HHF
Sbjct: 201 AYEYIHAYSELNLKLSSGIYGSTFFMLTGFHGFHVTMGAIMLSVVLYRVLRGHFTPTHHF 260

Query: 241 AFEGAAWYWHFVDVVWLGLYVVVYWL 266
           AFEGAAWYWHFVDVVWLGLYVVVYWL
Sbjct: 261 AFEGAAWYWHFVDVVWLGLYVVVYWL 286


>gi|300311777|ref|YP_003775869.1| cytochrome o ubiquinol oxidase
           subunit III protein [Herbaspirillum seropedicae SmR1]
          Length = 208

 Score = 87.4 bits (215), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 52/136 (38%), Positives = 79/136 (58%), Gaps = 1/136 (0%)

Query: 131 PIPTINTALLLTSGVTLTISHHALRAGHRAQTAIWLFATVLLGAIFMGFQAYEYMHAYSE 190
           P+  +NTALLL S +T   +  A++A  +  T  WL  T LLGA F+ F+ YE++H   E
Sbjct: 70  PLVALNTALLLLSSITYGFAMLAMQAKKQQNTIFWLIITGLLGAGFIYFELYEFLHLIHE 129

Query: 191 LNLKLTSGIYGSTFFMLTGFHGFHVTMGAIMLSVVLYRVLRGHFTPEHHFAFEGAAWYWH 250
                 SG + ++FF L G HG HVT G I L V+L+++ +   T  +       + +WH
Sbjct: 130 GAGPTRSG-FLTSFFALVGTHGLHVTFGIIWLVVLLFQINKHGLTEANGRRLMCLSMFWH 188

Query: 251 FVDVVWLGLYVVVYWL 266
           F+DVVW+G++  VY +
Sbjct: 189 FLDVVWIGVFTFVYLM 204


  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
   0.330    0.140    0.474 

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: 803,465
Number of extensions: 31674
Number of successful extensions: 138
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 138
Number of HSP's successfully gapped: 3
Length of query: 266
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 182
Effective length of database: 1,222,130
Effective search space: 222427660
Effective search space used: 222427660
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 (21.9 bits)
S2: 130 (54.7 bits)