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= 0001.4635.p
         (382 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcriptio...    89   9e-19

>gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription
           activator protein [Herbaspirillum seropedicae SmR1]
          Length = 675

 Score = 88.6 bits (218), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 101/232 (43%), Gaps = 14/232 (6%)

Query: 78  CLSMLHQTVREADYCVMLTNAGGTTIDYRVDRERRQDFKRAGLYLGSCWSESEEGTCGVA 137
            +  L+  +R     V+L++A GT +    D +      R  L  G  WSE   GT  + 
Sbjct: 78  VMETLYDQIRNTHSMVILSDAEGTILHTLGDSDFLAKADRVALGPGGRWSEQLRGTNAIG 137

Query: 138 AVLQDALPITVHKSDHFRAAFTTLTCSAAPIFSPAGELIGVLDASAIRSPDERDSQNLVN 197
             L +  P TVH   H+  A   LTCSAAPIF   G+++GVLD S       + +  L  
Sbjct: 138 TALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLDVSGECGSFHKHTMAL-- 195

Query: 198 RIVQQSATLIEDGYFLNAMACAWVLLVHRSRHYVEAQPEILIAFDALGNIIAANRRAREC 257
             V+ SA +IE+     +      L  H    +V    E +++F   G  +AANR A+  
Sbjct: 196 --VRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPGGRFLAANRSAQFQ 253

Query: 258 IDGL-------HCLPRPLGEVFDLHFERLLDSRALQGLHLLRLHGGATLYGR 302
           + GL       H      G    L FE     +A  GL  L LH G  ++GR
Sbjct: 254 L-GLTLAALQSHTFASLFGVPLSLLFEH--HRKAAPGLLELCLHNGIRIHGR 302


  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
   0.322    0.135    0.404 

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: 1,032,986
Number of extensions: 37659
Number of successful extensions: 153
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 153
Number of HSP's successfully gapped: 1
Length of query: 382
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 295
Effective length of database: 1,207,925
Effective search space: 356337875
Effective search space used: 356337875
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 (22.0 bits)
S2: 131 (55.1 bits)