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= 0011.0340.p
         (344 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptid...   616   e-178
gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptid...    88   1e-18

>gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptide
           II precursor transmembrane protein [Herbaspirillum
           seropedicae SmR1]
          Length = 344

 Score =  616 bits (1589), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 336/344 (97%), Positives = 338/344 (98%)

Query: 1   MAAMPTTSSLLLRLLAASTCCAVPVAQARQQWQDVLQPAGPQAATIASLWHVTLGLCTVV 60
           MAAMPTTSSLLLRLLAAS CCAVPVAQAR QWQDV QPAGPQAATIASLWHVTLGLCTVV
Sbjct: 1   MAAMPTTSSLLLRLLAASACCAVPVAQARAQWQDVQQPAGPQAATIASLWHVTLGLCTVV 60

Query: 61  FLLTLLACAVALFRRRRYSAEAAAATPRLTWAIGWALGLSATGLLALFAADVVASRALDQ 120
           FLLTLLACAVALFRRRRYSAEAAAATPRLTWAIGWALGLSATGLLALFAADVVASRALDQ
Sbjct: 61  FLLTLLACAVALFRRRRYSAEAAAATPRLTWAIGWALGLSATGLLALFAADVVASRALDQ 120

Query: 121 LPTAGALQVKLTARQWWWQAQYHDPLTGQGFTTANELHLPVGRAVIIDLDSEDVIHSLWL 180
           LPTAGALQVKLTARQWWWQAQYHDPLTGQGFTTANELHLPVGRAVIIDLDSEDVIHSLWL
Sbjct: 121 LPTAGALQVKLTARQWWWQAQYHDPLTGQGFTTANELHLPVGRAVIIDLDSEDVIHSLWL 180

Query: 181 PNLHGKLDLIPGKPAQLRLRADQTGTYRGQCAEFCGLEHARMALLVNAESPADYARWASG 240
           PNLHGKLDLIPGKPAQLRLRADQ GTYRGQCAEFCGLEHARMALLV AESPADYARWASG
Sbjct: 181 PNLHGKLDLIPGKPAQLRLRADQAGTYRGQCAEFCGLEHARMALLVTAESPADYARWASG 240

Query: 241 QARAAAPVADAAATVAQLRAVFMERGCAQCHAIRGTDAAGQSGPDLTHLASRSTLAAGIF 300
           QARAAAPVADAAATVA+ RAVFMERGCAQCHAIRGTDAAGQ+GPDLTHLASRSTLAAGIF
Sbjct: 241 QARAAAPVADAAATVARGRAVFMERGCAQCHAIRGTDAAGQNGPDLTHLASRSTLAAGIF 300

Query: 301 PNQRGFLAGWITDARSLKTGVIMPPAQLPPDELNALLDYLETLQ 344
           PNQRGFLAGWITDARSLKTGVIMPPAQLPPDELNALLDYLETLQ
Sbjct: 301 PNQRGFLAGWITDARSLKTGVIMPPAQLPPDELNALLDYLETLQ 344


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

 Score = 87.8 bits (216), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/284 (27%), Positives = 109/284 (38%), Gaps = 52/284 (18%)

Query: 38  PAGPQAATIASLWHVTLGLCTVVFLLTLLACAVALFRRRRYSAEAAAATPRLT-WAIGWA 96
           P    A  I  L  + L +C V+F+        ++ + R+     A+     T   I W 
Sbjct: 43  PVTKIAEQIYDLHILMLIICLVIFVAVFGVMFYSIIKHRKSVGHKASTFHESTAVEIAWT 102

Query: 97  L--GLSATGLLALFAADVVASRALDQLPTAGALQVKLTARQWWWQAQYHDPLTGQGFTTA 154
           +   L   G+       VVA +      +   L +K+T  QW W   Y   L G+G   +
Sbjct: 103 VVPFLIVIGMALPATKTVVAMKDT----SNADLTIKVTGMQWKWGYDY---LKGEGEGIS 155

Query: 155 NELHLPVGRAVIID----------------------------LDSEDVIHSLWLPNLHGK 186
              +L   R  + D                              + DVIHS  +P    K
Sbjct: 156 FLSNLATPREQVTDPSLKKNDNYLIEVDNPVVVPVNKKVRIVTTANDVIHSWTIPAFGVK 215

Query: 187 LDLIPGKPAQLRLRADQTGTYRGQCAEFCGLEHARMALLVNAESPADYARWASGQARAAA 246
            D IPG       RA++ GTYRGQC E CG +HA M ++VN  S  DY +W  G+ +  A
Sbjct: 216 QDAIPGFVRDTWFRAEKIGTYRGQCVELCGKDHAFMPIVVNVVSEDDYKQWVDGKKKEMA 275

Query: 247 PVADAAA---TVAQLRAVFMERG-------CAQCHAIRGTDAAG 280
             AD      TV +L+    +RG       C  CH   G    G
Sbjct: 276 AKADDPNKTWTVDELK----QRGEKVYAANCVTCHQANGKGVPG 315


  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
   0.322    0.132    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: 909,907
Number of extensions: 34007
Number of successful extensions: 122
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 3
Length of query: 344
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 258
Effective length of database: 1,212,660
Effective search space: 312866280
Effective search space used: 312866280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 131 (55.1 bits)