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= 0006.0015.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|300311223|ref|YP_003775315.1| sigma-54 dependent transcriptio...    88   7e-19

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

 Score = 88.2 bits (217), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 83/289 (28%), Positives = 119/289 (41%), Gaps = 27/289 (9%)

Query: 18  DGQPDPAASPYLQRLSSSYLRSLDQHHLDPADMRGPR----VLSSGELRQVQQGEEDFLR 73
           DG PD  A     + SSSY             MRG R     LS  +L Q  +  +    
Sbjct: 25  DGVPDLQAIERSHQRSSSY-----------GIMRGQRPDLDSLSRADLAQTLEANQTLSG 73

Query: 74  ASGQCLSVLHQTVREADYCVMLTNAGGTTIDYRVDRERRHDFKRAGLYLGSCWSESEEGT 133
            +   +  L+  +R     V+L++A GT +    D +      R  L  G  WSE   GT
Sbjct: 74  HARPVMETLYDQIRNTHSMVILSDAEGTILHTLGDSDFLAKADRVALGPGGRWSEQLRGT 133

Query: 134 CGVAAVLQDALPITVHKSDHFRAAFTTLTCSAAPIFSPSGELIGVLDASAIRSPDARDSQ 193
             +   L +  P TVH   H+  A   LTCSAAPIF   G+++GVLD S     +     
Sbjct: 134 NAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLDVSG----ECGSFH 189

Query: 194 NLVNRIVQQSATLIEDGYFLNAMACAWVLLVHRSRHYVEAQPEILIAFDALGNIIAANRR 253
                +V+ SA +IE+     +      L  H    +V    E +++F   G  +AANR 
Sbjct: 190 KHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPGGRFLAANRS 249

Query: 254 ARE----CIAGLQQLPRPMGEIFDLQFERLLDS--RALQGLHLLRLHGG 296
           A+      +A LQ        +F +    L +   +A  GL  L LH G
Sbjct: 250 AQFQLGLTLAALQS--HTFASLFGVPLSLLFEHHRKAAPGLLELCLHNG 296


  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    0.136    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: 871,116
Number of extensions: 34148
Number of successful extensions: 111
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 111
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 130 (54.7 bits)