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= 0028.0111.p
         (418 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...   707   0.0  

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

 Score =  707 bits (1824), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/402 (89%), Positives = 367/402 (91%), Gaps = 21/402 (5%)

Query: 1   MQYQANRPGAGALLGASPLVQASADGVPDLQAIERSHQRSSSYGITRGQRPDLDSLSRAD 60
           MQYQANRP AGALLG SPLVQAS DGVPDLQAIERSHQRSSSYGI RGQRPDLDSLSRAD
Sbjct: 1   MQYQANRPSAGALLGTSPLVQASTDGVPDLQAIERSHQRSSSYGIMRGQRPDLDSLSRAD 60

Query: 61  LAQTLEANQALSGHARPVMETLYDQIRNTHSMVLLSDAEGTILHTLGDSDFLAKADRVAL 120
           LAQTLEANQ LSGHARPVMETLYDQIRNTHSMV+LSDAEGTILHTLGDSDFLAKADRVAL
Sbjct: 61  LAQTLEANQTLSGHARPVMETLYDQIRNTHSMVILSDAEGTILHTLGDSDFLAKADRVAL 120

Query: 121 GPGGRWSEQLRGTNAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD 180
           GPGGRWSEQLRGTNAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD
Sbjct: 121 GPGGRWSEQLRGTNAIGTALFEQKPTTVHAQQHYLDANRFLTCSAAPIFDHRGQVLGVLD 180

Query: 181 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPG 240
           VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPG
Sbjct: 181 VSGECGSFHKHTMALVRMSAQMIENHLLAGSFPDCITLHFHSRAEFVGTLVEGIVSFTPG 240

Query: 241 GRFLAANRSAQFQLGLTLSALQSHTFASLFGVPLSLLFEHHRKAASGLLELCLHNGIRIH 300
           GRFLAANRSAQFQLGLTL+ALQSHTFASLFGVPLSLLFEHHRKAA GLLELCLHNGIRIH
Sbjct: 241 GRFLAANRSAQFQLGLTLAALQSHTFASLFGVPLSLLFEHHRKAAPGLLELCLHNGIRIH 300

Query: 301 GRAELRLRDQHFQNAREAVIEAPEVLPASPA------------ARHAPPARPHPGQPRGG 348
           GRAELRLRDQHFQ AREAVI+AP +LP +P             ARH         Q R  
Sbjct: 301 GRAELRLRDQHFQAAREAVIDAPGLLPPAPNTTTPPPSPPQQRARH---------QRRPD 351

Query: 349 LQALDTGDARMSAVIAKLRKVIDRDIPVLITGETGTGKEWLA 390
           LQALDTGD RMSA+IAKLR+VIDRDIP+LITGETGTGKEWLA
Sbjct: 352 LQALDTGDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLA 393


  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
   0.320    0.135    0.399 

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: 1,268,470
Number of extensions: 50564
Number of successful extensions: 171
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 170
Number of HSP's successfully gapped: 1
Length of query: 418
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 330
Effective length of database: 1,203,190
Effective search space: 397052700
Effective search space used: 397052700
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 (21.8 bits)
S2: 132 (55.5 bits)