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= 0012.0135.p
         (195 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309495|ref|YP_003773587.1| cytochrome c553 protein [Herbas...    89   2e-19
gi|300310720|ref|YP_003774812.1| cytochrome c553 protein [Herbas...    85   5e-18
gi|300310946|ref|YP_003775038.1| periplasmic cytochrome c553 pro...    57   9e-10

>gi|300309495|ref|YP_003773587.1| cytochrome c553 protein
           [Herbaspirillum seropedicae SmR1]
          Length = 220

 Score = 89.4 bits (220), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 63/188 (33%), Positives = 95/188 (50%), Gaps = 10/188 (5%)

Query: 9   PAMSRPATPQAV---GRGATLALACTMCHGVQGHSR-SDAPGLAGQFPEVIIKQLADYRS 64
           P  + PA  +A+   G  A   +AC  CHG  G+S  +  P LAGQ    I KQL ++R+
Sbjct: 32  PVKADPAKGEALYTNGDSARNIVACVSCHGAAGNSTITQNPKLAGQHEAYIAKQLLNFRT 91

Query: 65  GKRSNAVMGALARTLSERDAADLAAYFAS-LPRPAQAGGLADSAVPRLV-QVGDPLRNIA 122
             R+N VM  +A+ LS+ D  ++AA+ A+  P+P  A       + + + + G   +N+ 
Sbjct: 92  PDRNNPVMSPMAKALSDEDIHNVAAFLAAQAPKPGAAKNKDTIDLGKHIWRAGIAAKNVP 151

Query: 123 PCISCH--GGADRKIGAPWLDGLPRHYLAEQLALFKRGERANDAMLQMRNVAHAMREDEI 180
            C  CH   GA      P L G  + Y   QL  F+ G R N   +QM  ++  + + EI
Sbjct: 152 ACAGCHSPNGAGIPAQYPRLAGQHQDYTVAQLTNFRGGARTNS--VQMTTISERLSDKEI 209

Query: 181 SAIADYYA 188
            A+ADY A
Sbjct: 210 KAVADYIA 217


>gi|300310720|ref|YP_003774812.1| cytochrome c553 protein
           [Herbaspirillum seropedicae SmR1]
          Length = 252

 Score = 84.7 bits (208), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 61/176 (34%), Positives = 88/176 (50%), Gaps = 14/176 (7%)

Query: 29  ACTMCHGVQGHSRSDA--PGLAGQFPEVIIKQLADYRSGKRSNAVMGALARTLSERDAAD 86
           ACT CHG QG + +D   P +AG+    ++ QL  +R G+R   +M  L   LS+     
Sbjct: 51  ACTACHGKQGRATADGYYPRIAGKPEAYLLNQLQSFRDGQRRYPMMNYLLANLSDDYLQQ 110

Query: 87  LAAYFASL--PRPAQAGGLADSAV----PRLVQVGDPLRNIAPCISCH----GGADRKIG 136
           +A +FA    P P  A   A + V     RLV  GDP R +  C +CH    GG   + G
Sbjct: 111 IARFFADQHPPYPPPASNEASATVLERGRRLVTEGDPQRRLPACAACHAPSLGGV--QPG 168

Query: 137 APWLDGLPRHYLAEQLALFKRGERANDAMLQMRNVAHAMREDEISAIADYYARAAL 192
            P L GLPR Y+  QL  ++ G+R       M  VA A+  +EI+A + + +  A+
Sbjct: 169 IPGLLGLPRDYINAQLGAWRNGDRTAKTPDCMAAVARALSPEEINAASSWLSAQAV 224


>gi|300310946|ref|YP_003775038.1| periplasmic cytochrome c553
           protein [Herbaspirillum seropedicae SmR1]
          Length = 117

 Score = 57.0 bits (136), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 45/84 (53%), Gaps = 7/84 (8%)

Query: 19  AVGRGATLALACTMCHGVQGHSRSD--APGLAGQFPEVIIKQLADYRSGK-----RSNAV 71
           A GR  T    C  CHG   +S ++   P LAGQ  + +   L  YR G      R+NA+
Sbjct: 27  ANGRALTEKYNCASCHGKDYNSPTEPAYPKLAGQHADYLKHALTAYRRGNTAMNGRNNAI 86

Query: 72  MGALARTLSERDAADLAAYFASLP 95
           M A A+ LS+RD  D+AAY  SLP
Sbjct: 87  MSAQAKPLSDRDINDIAAYLHSLP 110


  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
   0.321    0.134    0.399 

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: 669,394
Number of extensions: 29124
Number of successful extensions: 113
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 3
Length of query: 195
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 115
Effective length of database: 1,241,070
Effective search space: 142723050
Effective search space used: 142723050
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 (21.9 bits)
S2: 128 (53.9 bits)