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= 0058.0008.p
         (376 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...   566   e-162

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

 Score =  566 bits (1459), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 288/371 (77%), Positives = 322/371 (86%), Gaps = 7/371 (1%)

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

Query: 61  LADGAISSPPSAQADPVENTAASAAPA----EGEAG-DPQDSVVGDDHAGGDTDWSFDDV 115
           LADGA+S+ PS+       + AS+  A    +GE+  + QD+    +   GD+DWSFDDV
Sbjct: 61  LADGAVSAAPSSGVSETTGSEASSEAAPAAADGESSFEYQDT--APEGVSGDSDWSFDDV 118

Query: 116 ARTGKTPDDEDSRPQLEAHDITLREHLQEQTRLTVRSLRDRALIELIVDAIDDHGYLEES 175
           AR+GK+PDDED+RPQLEAH+ITLREHL EQ R+T R+ RDRAL+EL+ DA+DD GYLEE 
Sbjct: 119 ARSGKSPDDEDARPQLEAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEP 178

Query: 176 LEEIHARLPEELEIELDELTIALKLLQSFDPAGIGARSASECLALQIRRLPKVAFVTRRL 235
           LE+I ARLPEEL ++L+EL+I+LKLLQS DPAG+GARSA ECLALQIRRLPKV FVTRRL
Sbjct: 179 LEDILARLPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRL 238

Query: 236 ALTIVEDYLALFAQRDFNKIKKALGCDDEDLREAQAVIRQCHPHPGAVFASGRSDYVVPD 295
           AL IVEDYL LFAQRDFNKIKKAL CDDEDLREAQAVIRQC PHPGA FA   SDYVVPD
Sbjct: 239 ALKIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPD 298

Query: 296 VIVKAAKDGWQVLLNHDVMPRLRVNAMYANALKQTKGDGSLGSQLQEAKWLIKNMRQRFD 355
           VIVK  K+GWQV+LNH+VMP+LRVNAMYA+ALKQ KG+GSL SQLQEAKWLIKNMRQRFD
Sbjct: 299 VIVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFD 358

Query: 356 TILRVAQAIVE 366
           TILRVAQAIVE
Sbjct: 359 TILRVAQAIVE 369


  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    0.133    0.374 

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: 1,034,913
Number of extensions: 38854
Number of successful extensions: 159
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 157
Number of HSP's successfully gapped: 1
Length of query: 376
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 289
Effective length of database: 1,207,925
Effective search space: 349090325
Effective search space used: 349090325
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: 131 (55.1 bits)