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= 0001.3855.p
         (496 letters)

Database: BlastDatabases/707/707 
           3697 sequences; 1,221,021 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152980475|ref|YP_001355042.1| RNA polymerase factor sigma-54 ...   786   0.0  

>gi|152980475|ref|YP_001355042.1| RNA polymerase factor sigma-54
           [Janthinobacterium sp. Marseille]
          Length = 489

 Score =  786 bits (2030), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/496 (80%), Positives = 441/496 (88%), Gaps = 7/496 (1%)

Query: 1   MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60
           MKQSLQLR SQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNP+LER DD LD++VRL
Sbjct: 1   MKQSLQLRVSQHLALTPQLQQSIRLLQLSTLELHQELEQILADNPMLERTDDPLDHAVRL 60

Query: 61  LADGAVSASPSSGVADTGGDNSGDTAPAAADGESSFEYQDNSPDTGVTGESDWSFDDVAR 120
           LADGA+ AS   G    G     +T     + E+SFE  D  P+    G+S+WSFDDVAR
Sbjct: 61  LADGAIGAS---GTTPEGASVEANTQ--TPESETSFEAPD-LPEAS-NGDSEWSFDDVAR 113

Query: 121 SGKSPEDEDARPQLEAHELTLREHLLEQIRVTARTQRDRALLELLTDALDESGYLEEPLE 180
           + K+PED+DARPQLEAHE TLREHLLEQ+RVT R  RDRALLEL+ DAL+++GYLEE LE
Sbjct: 114 TSKAPEDDDARPQLEAHETTLREHLLEQMRVTVREHRDRALLELIIDALNDNGYLEEELE 173

Query: 181 EILARLPEELGIDLEELSISLKLLQSLDPAGVGARNAGECLALQIRRLPKIAFVTRKLAL 240
           EI ARLPEEL I+LEEL ISLK+LQS DP GVGAR+A ECLALQI+R+PK+A VTR++AL
Sbjct: 174 EIHARLPEELEIELEELQISLKMLQSFDPPGVGARDAAECLALQIKRMPKVAMVTRRMAL 233

Query: 241 RIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDVSDYVVPDVI 300
            IVE++LPLFAQRDFNK++KALDCDDEDLREAQA+I+QC PHPG+ FA D SDYVVPDVI
Sbjct: 234 AIVENHLPLFAQRDFNKLRKALDCDDEDLREAQAIIKQCNPHPGSIFATDASDYVVPDVI 293

Query: 301 VKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTI 360
           VK+T+NGWQVMLNH+VMP+LRVN+MYA+ LKQ+KGEGSL SQLQEAKWLIKNMRQRFDTI
Sbjct: 294 VKRTRNGWQVMLNHDVMPRLRVNSMYANILKQSKGEGSLGSQLQEAKWLIKNMRQRFDTI 353

Query: 361 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 420
           LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK
Sbjct: 354 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 413

Query: 421 YFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAK 480
           YFFGSHVATE GGEASSTAIRALIKQLIGAE+P+ P SDSKIADMLAEQGMVVARRTVAK
Sbjct: 414 YFFGSHVATEAGGEASSTAIRALIKQLIGAEDPKIPFSDSKIADMLAEQGMVVARRTVAK 473

Query: 481 YREVLKIPPVNLRKSL 496
           YRE LKIPPVNLRKSL
Sbjct: 474 YREALKIPPVNLRKSL 489


  Database: BlastDatabases/707/707
    Posted date:  Apr 13, 2011 12:58 PM
  Number of letters in database: 1,221,021
  Number of sequences in database:  3697
  
Lambda     K      H
   0.316    0.132    0.366 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3697
Number of Hits to DB: 1,011,379
Number of extensions: 38686
Number of successful extensions: 130
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 129
Number of HSP's successfully gapped: 1
Length of query: 496
Length of database: 1,221,021
Length adjustment: 87
Effective length of query: 409
Effective length of database: 899,382
Effective search space: 367847238
Effective search space used: 367847238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 131 (55.1 bits)