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/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134096264|ref|YP_001101339.1| RNA polymerase factor sigma-54 ...   776   0.0  

>gi|134096264|ref|YP_001101339.1| RNA polymerase factor sigma-54
           [Herminiimonas arsenicoxydans]
          Length = 489

 Score =  776 bits (2004), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/496 (78%), Positives = 434/496 (87%), Gaps = 7/496 (1%)

Query: 1   MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60
           MKQSLQLR SQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNPLLER DD LD+++RL
Sbjct: 1   MKQSLQLRVSQHLALTPQLQQSIRLLQLSTLELHQELEQILADNPLLERTDDPLDHAIRL 60

Query: 61  LADGAVSASPSSGVADTGGDNSGDTAPAAADGESSFEYQDNSPDTGVTGESDWSFDDVAR 120
           LADGA+    S+G    G     +    A   ES    +   P     G+++WSFDDVAR
Sbjct: 61  LADGAIG---SAGTTPEGASVEAN----AQTPESDTSVEAPEPAEASNGDAEWSFDDVAR 113

Query: 121 SGKSPEDEDARPQLEAHELTLREHLLEQIRVTARTQRDRALLELLTDALDESGYLEEPLE 180
           + K+P+D+DARPQLEAHE TLREHLLEQ+RVT R +RDRALLEL+ DAL+++GYLEE LE
Sbjct: 114 TSKAPDDDDARPQLEAHETTLREHLLEQMRVTVRERRDRALLELIIDALNDNGYLEETLE 173

Query: 181 EILARLPEELGIDLEELSISLKLLQSLDPAGVGARNAGECLALQIRRLPKIAFVTRKLAL 240
           EI ARLPEEL I+ EEL I+L LLQS DPAGVGARNA ECLALQI+R+PK+A VTR++AL
Sbjct: 174 EIHARLPEELEIEPEELQIALNLLQSFDPAGVGARNASECLALQIKRMPKVAMVTRRMAL 233

Query: 241 RIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDVSDYVVPDVI 300
            IVE +L LFAQRDFNK++KALDCDDEDLREAQ VI+QC PHPG+ FA D SDYVVPDVI
Sbjct: 234 AIVEHHLGLFAQRDFNKLRKALDCDDEDLREAQVVIKQCNPHPGSIFATDTSDYVVPDVI 293

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

Query: 361 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 420
           LRV+QAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK
Sbjct: 354 LRVSQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 413

Query: 421 YFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAK 480
           YFFGSHVATETGGEASSTAIRALIKQLIGAEN +TP SDSKIA+MLAEQGMVVARRTVAK
Sbjct: 414 YFFGSHVATETGGEASSTAIRALIKQLIGAENQKTPFSDSKIAEMLAEQGMVVARRTVAK 473

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


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
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: 3295
Number of Hits to DB: 827,768
Number of extensions: 31533
Number of successful extensions: 99
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 98
Number of HSP's successfully gapped: 1
Length of query: 496
Length of database: 1,000,347
Length adjustment: 86
Effective length of query: 410
Effective length of database: 716,977
Effective search space: 293960570
Effective search space used: 293960570
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)