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= 0002.0536.p
         (144 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptid...   220   3e-59

>gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptide
           II precursor transmembrane protein [Herbaspirillum
           seropedicae SmR1]
          Length = 386

 Score =  220 bits (561), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 110/135 (81%), Positives = 119/135 (88%), Gaps = 4/135 (2%)

Query: 1   VPSWAWGDKVVDSQGGPAVLQTNFQPPVTQIAEQIYDLHHLMLIICLVIFVAVFGVMFYS 60
           +P+WA    VVDS GGPAVLQ NFQPPVT+IAEQIYDLH LMLIICLVIFVAVFGVMFYS
Sbjct: 21  LPAWA----VVDSPGGPAVLQMNFQPPVTKIAEQIYDLHILMLIICLVIFVAVFGVMFYS 76

Query: 61  ILKHRKSLGHKSASFHESTTVEIAWTVVPFLIVIGMALPATKTVVAMKDTSNADLTIKAT 120
           I+KHRKS+GHK+++FHEST VEIAWTVVPFLIVIGMALPATKTVVAMKDTSNADLTIK T
Sbjct: 77  IIKHRKSVGHKASTFHESTAVEIAWTVVPFLIVIGMALPATKTVVAMKDTSNADLTIKVT 136

Query: 121 GMQWKXADLTIKATG 135
           GMQWK     +K  G
Sbjct: 137 GMQWKWGYDYLKGEG 151


  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
   0.323    0.134    0.415 

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: 435,927
Number of extensions: 14518
Number of successful extensions: 54
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 54
Number of HSP's successfully gapped: 1
Length of query: 144
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 67
Effective length of database: 1,255,275
Effective search space: 84103425
Effective search space used: 84103425
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 126 (53.1 bits)