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= 0002.0005.p
         (146 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    50   1e-06
ML1076 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    49   4e-06

>lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigma
          subunit, sigma24 homolog
          Length = 301

 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 0/45 (0%), Positives = 8/45 (17%)

Query: 1  LKSREEAEDAVQDIFVKVYRELERYRKVESFSAWLYKVAYHHCLD 45
           ++       +          ++           + ++       
Sbjct: 40 AQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASS 84


>ML1076 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 263

 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/112 (26%), Positives = 54/112 (48%), Gaps = 9/112 (8%)

Query: 6   EAEDAVQDIFVKVYRELERYRKVESFSAWLYKVAYHHCLDQIXXXXXXXXXX-------X 58
           +AED  Q+ F++V+R ++ Y+   +F  WL+++  +  LD +                  
Sbjct: 112 DAEDLTQETFIRVFRSVQNYQP-GTFEGWLHRITTNLFLDMVRRRARIRMDALPDDYDRV 170

Query: 59  XYKEQHPKAYYEPNGEGP-VQLLMDSLSAEESNLLILKVVEQYSFEEIGQIM 109
              E +P+  Y  +  GP +Q  +DSL  E    ++L  +E  S+EEIG  +
Sbjct: 171 PADEPNPEQIYHDSRLGPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIGATL 222


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.314    0.132    0.379 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 8,380,460
Number of extensions: 248077
Number of successful extensions: 308
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 318
Number of HSP's successfully gapped: 4
Length of query: 146
Length of database: 38,378,431
Length adjustment: 96
Effective length of query: 50
Effective length of database: 27,306,367
Effective search space: 1365318350
Effective search space used: 1365318350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 110 (47.0 bits)