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= 0001.1495.p
         (117 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310946|ref|YP_003775038.1| periplasmic cytochrome c553 pro...   198   1e-52
gi|300309495|ref|YP_003773587.1| cytochrome c553 protein [Herbas...    65   1e-12
gi|300310945|ref|YP_003775037.1| periplasmic cytochrome c553 pro...    53   6e-09

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

 Score =  198 bits (503), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 96/117 (82%), Positives = 102/117 (87%)

Query: 1   MKNNLIAFALLAATALLAQAAGAADLANGRAQLEKYNCASCHGKDYNSPTDPGTPKLAGQ 60
           MK NLI   LLAA  L  QAA AAD+ANGRA  EKYNCASCHGKDYNSPT+P  PKLAGQ
Sbjct: 1   MKKNLITLCLLAAATLCTQAANAADVANGRALTEKYNCASCHGKDYNSPTEPAYPKLAGQ 60

Query: 61  HADYLKHALTAYRRGDSAMNGRNNAVMSPNAKPLSDRDINDIAAYLHSLPGTLVVRK 117
           HADYLKHALTAYRRG++AMNGRNNA+MS  AKPLSDRDINDIAAYLHSLPG+LVVRK
Sbjct: 61  HADYLKHALTAYRRGNTAMNGRNNAIMSAQAKPLSDRDINDIAAYLHSLPGSLVVRK 117


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

 Score = 65.1 bits (157), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 41/87 (47%), Positives = 48/87 (55%), Gaps = 6/87 (6%)

Query: 20  AAGAADLANGRAQLEKYNCASCHGKDYNSPTDPGTPKLAGQHADYLKHALTAYRRGDSAM 79
           A G A   NG +      C SCHG   NS T    PKLAGQH  Y+   L  +R  D   
Sbjct: 38  AKGEALYTNGDSARNIVACVSCHGAAGNS-TITQNPKLAGQHEAYIAKQLLNFRTPD--- 93

Query: 80  NGRNNAVMSPNAKPLSDRDINDIAAYL 106
             RNN VMSP AK LSD DI+++AA+L
Sbjct: 94  --RNNPVMSPMAKALSDEDIHNVAAFL 118


>gi|300310945|ref|YP_003775037.1| periplasmic cytochrome c553
           protein [Herbaspirillum seropedicae SmR1]
          Length = 106

 Score = 53.1 bits (126), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 57/110 (51%), Gaps = 14/110 (12%)

Query: 1   MKNNLIAFALLAATALLAQAAGAADLA-NGRAQLEKYN-CASCHG-KDYNS--PTDPGTP 55
           MK +L+  AL+        +A AAD+  N +A   K + C  CHG   Y +  P     P
Sbjct: 1   MKKHLVFLALVGVVG----SASAADIVGNAKAAENKVSMCIGCHGIPGYKASYPEVYQVP 56

Query: 56  KLAGQHADYLKHALTAYRRGDSAMNGRNNAVMSPNAKPLSDRDINDIAAY 105
            L GQ A Y++ AL AY++G+     R +  M   A  LSD+DI D+AAY
Sbjct: 57  MLGGQSAAYIESALRAYQKGE-----RKHPSMMGVAASLSDQDIADLAAY 101


  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
   0.315    0.129    0.376 

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: 330,353
Number of extensions: 12332
Number of successful extensions: 59
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 57
Number of HSP's successfully gapped: 3
Length of query: 117
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 43
Effective length of database: 1,269,480
Effective search space: 54587640
Effective search space used: 54587640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 124 (52.4 bits)