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= 0031.0015.p
         (482 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313260|ref|YP_003777352.1| RNA polymerase sigma-N (sigma-5...   979   0.0  

>gi|300313260|ref|YP_003777352.1| RNA polymerase sigma-N (sigma-54)
           factor transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 496

 Score =  979 bits (2530), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 482/482 (100%), Positives = 482/482 (100%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV
Sbjct: 15  LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 74

Query: 61  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 120
           SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL
Sbjct: 75  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 134

Query: 121 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 180
           EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL
Sbjct: 135 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 194

Query: 181 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 240
           EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD
Sbjct: 195 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 254

Query: 241 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 300
           FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH
Sbjct: 255 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 314

Query: 301 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 360
           EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF
Sbjct: 315 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 374

Query: 361 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 420
           FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE
Sbjct: 375 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 434

Query: 421 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 480
           ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK
Sbjct: 435 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 494

Query: 481 SL 482
           SL
Sbjct: 495 SL 496


  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
   0.316    0.132    0.365 

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: 1,250,600
Number of extensions: 46614
Number of successful extensions: 184
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 182
Number of HSP's successfully gapped: 1
Length of query: 482
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 393
Effective length of database: 1,198,455
Effective search space: 470992815
Effective search space used: 470992815
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: 132 (55.5 bits)