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= 0009.0264.p
         (300 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription...   162   2e-41

>gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 437

 Score =  162 bits (411), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 87/130 (66%), Positives = 95/130 (73%), Gaps = 5/130 (3%)

Query: 167 NLRQMHAVIRYCCAVMNGDRIEAGDLPEELMETFAPSTSHAIHYEGPAISPASNVRSIVP 226
           NLRQMHAVIRY CAVMNG RIE  DLPEELM+ F P+T   +H     I+  + +R    
Sbjct: 309 NLRQMHAVIRYSCAVMNGGRIEVRDLPEELMQ-FQPATLAEVH----PITRTAQIRPFTS 363

Query: 227 QAGAADILPRPSGGPLGDERTRVIDALVGSRWNISAASRQLGMCRASLYRKLRQLDIPHV 286
           +A       R SG P  DERTRVIDAL GSRWNISAASRQLGMCRASLYRKLRQLDIPHV
Sbjct: 364 RAEGEAGRERSSGDPYRDERTRVIDALNGSRWNISAASRQLGMCRASLYRKLRQLDIPHV 423

Query: 287 RDQAMPTHFA 296
           RDQAMP + A
Sbjct: 424 RDQAMPAYPA 433


  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
   0.323    0.135    0.422 

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: 1,053,964
Number of extensions: 47286
Number of successful extensions: 202
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 201
Number of HSP's successfully gapped: 1
Length of query: 300
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 215
Effective length of database: 1,217,395
Effective search space: 261739925
Effective search space used: 261739925
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 130 (54.7 bits)