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= 0001.0159.p
         (319 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309492|ref|YP_003773584.1| RNA polymerase sigma-24 factor ...   516   e-147

>gi|300309492|ref|YP_003773584.1| RNA polymerase sigma-24 factor
           protein [Herbaspirillum seropedicae SmR1]
          Length = 324

 Score =  516 bits (1328), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 263/319 (82%), Positives = 276/319 (86%), Gaps = 4/319 (1%)

Query: 1   MTDDLDGDLFLQLRPRLFGVAYRMLSSRSDAQDVLQDAWLRWQAQDRQALASTEAWLVTV 60
           MTDDL   LF Q RPRLFGVAYRML+SRS+A DVLQDAWLRW AQD+  L S EAWLVTV
Sbjct: 1   MTDDLALALFTQHRPRLFGVAYRMLASRSEADDVLQDAWLRWHAQDKAVLDSAEAWLVTV 60

Query: 61  VTRLCIDRLRQLQQERQHYVGHWLPEPLVGLTEPGA--DIDLYGQAQLAPSPEALLEQQS 118
           VTRLCIDRLRQLQQERQHYVGHWLPEPLV L EPG   DIDLYGQA+LAPSPE LLEQ S
Sbjct: 61  VTRLCIDRLRQLQQERQHYVGHWLPEPLVDLAEPGPGPDIDLYGQARLAPSPEQLLEQHS 120

Query: 119 DVSFAYLLLLEHLKPEERAAFLLREVFDNDYPDIAAILQKSEANCRQLVHRARARLARQ- 177
           D+SFAYLLLLEHLKPEERAAFLLREVFDNDYPDIAAILQKSEA+CRQLVHRAR RLARQ 
Sbjct: 121 DLSFAYLLLLEHLKPEERAAFLLREVFDNDYPDIAAILQKSEASCRQLVHRARERLARQE 180

Query: 178 -HTDARRKPVRAATGPVTRETHALLLEKFLHAVQSGQREAMLGLLAEDARLIGDGGGKVA 236
              D R   VRAA+ PVTRETHALLLEKF+ A+QSGQREAMLGLLAEDARLIGDGGGKVA
Sbjct: 181 HQADPRSPAVRAASSPVTRETHALLLEKFMQALQSGQREAMLGLLAEDARLIGDGGGKVA 240

Query: 237 SFPHPLAGGERISWLYYANVRRLAQRIVYRAAWINGSPGLLRYVDGALESAQVLETDGTH 296
           SFPHPL G ERISWLYYANVRR   RIVYRAAWING+ GLLRYVDG LESAQ L+     
Sbjct: 241 SFPHPLEGAERISWLYYANVRRFGTRIVYRAAWINGAAGLLRYVDGVLESAQALQWQAGR 300

Query: 297 IHAIYVVRNPDKLAAIAQQ 315
           + AIYVVRNPDKLAAIA+Q
Sbjct: 301 VSAIYVVRNPDKLAAIARQ 319


  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    0.136    0.406 

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: 1,108,547
Number of extensions: 48268
Number of successful extensions: 165
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 163
Number of HSP's successfully gapped: 1
Length of query: 319
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 234
Effective length of database: 1,217,395
Effective search space: 284870430
Effective search space used: 284870430
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: 130 (54.7 bits)