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= 0001.3855.p
         (496 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...   939   0.0  

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

 Score =  939 bits (2427), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 466/497 (93%), Positives = 484/497 (97%), Gaps = 2/497 (0%)

Query: 1   MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60
           MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNPLLERLDDALDNSVRL
Sbjct: 1   MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRL 60

Query: 61  LADGAVSASPSSGVADTGGDNSGDTAPAAA-DGESSFEYQDNSPDTGVTGESDWSFDDVA 119
           LADGAVSA+PSSGV++T G  +   A  AA DGESSFEYQD +P+ GV+G+SDWSFDDVA
Sbjct: 61  LADGAVSAAPSSGVSETTGSEASSEAAPAAADGESSFEYQDTAPE-GVSGDSDWSFDDVA 119

Query: 120 RSGKSPEDEDARPQLEAHELTLREHLLEQIRVTARTQRDRALLELLTDALDESGYLEEPL 179
           RSGKSP+DEDARPQLEAHE+TLREHLLEQIRVTARTQRDRALLELLTDALD+SGYLEEPL
Sbjct: 120 RSGKSPDDEDARPQLEAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPL 179

Query: 180 EEILARLPEELGIDLEELSISLKLLQSLDPAGVGARNAGECLALQIRRLPKIAFVTRKLA 239
           E+ILARLPEELG+DLEELSISLKLLQSLDPAGVGAR+AGECLALQIRRLPK+ FVTR+LA
Sbjct: 180 EDILARLPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLA 239

Query: 240 LRIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDVSDYVVPDV 299
           L+IVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARD SDYVVPDV
Sbjct: 240 LKIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDV 299

Query: 300 IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDT 359
           IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDT
Sbjct: 300 IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDT 359

Query: 360 ILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL 419
           ILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL
Sbjct: 360 ILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL 419

Query: 420 KYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVA 479
           KYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVA
Sbjct: 420 KYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVA 479

Query: 480 KYREVLKIPPVNLRKSL 496
           KYREVLKIPPVNLRKSL
Sbjct: 480 KYREVLKIPPVNLRKSL 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    0.366 

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: 1,366,932
Number of extensions: 53616
Number of successful extensions: 218
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 215
Number of HSP's successfully gapped: 1
Length of query: 496
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 407
Effective length of database: 1,198,455
Effective search space: 487771185
Effective search space used: 487771185
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)