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= 0249.0001.p
         (98 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           2,715,099 sequences; 757,237,578 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|ZP_00100726.1| COG1595: DNA-directed RNA polymerase speciali...    75   4e-13
ref|ZP_00100114.1| COG1595: DNA-directed RNA polymerase speciali...    58   8e-08
ref|ZP_00098468.1| COG1595: DNA-directed RNA polymerase speciali...    55   7e-07

>ref|ZP_00100726.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit,
          sigma24 homolog [Desulfitobacterium hafniense]
          Length = 75

 Score = 75.1 bits (183), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 32/65 (49%), Positives = 49/65 (75%)

Query: 29 KLIDQAEALNVHKVLHALNEPFKEVFMLRVFGELSFDHISQIFGRTESWARVTYHRARLK 88
          +++++  A  +H++LH ++EP+KEVF LRVFGEL F+ I  IF +  SWARVT++RA+ K
Sbjct: 4  QIMNEDTAFVIHQILHDMDEPYKEVFSLRVFGELPFEKIGLIFNKNASWARVTFYRAKNK 63

Query: 89 IQKLL 93
          + K L
Sbjct: 64 LLKTL 68


>ref|ZP_00100114.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog [Desulfitobacterium hafniense]
          Length = 174

 Score = 57.8 bits (138), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 47/67 (70%)

Query: 28  QKLIDQAEALNVHKVLHALNEPFKEVFMLRVFGELSFDHISQIFGRTESWARVTYHRARL 87
           ++L+ + ++  + + ++ L E ++ V +LR F ELS+  I++I G+TE+W RVT+ RA+ 
Sbjct: 98  EQLLQKEQSQTMQRAIYCLPETYRTVIILREFEELSYGEIAKILGKTENWVRVTFFRAKQ 157

Query: 88  KIQKLLM 94
           K+++ ++
Sbjct: 158 KLKETIL 164


>ref|ZP_00098468.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog [Desulfitobacterium hafniense]
          Length = 166

 Score = 54.7 bits (130), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 41  KVLHALNEPFKEVFMLRVFGELSFDHISQIFGRTESWARVTYHRARLKIQKLLMEDE 97
           KVL  L E ++EVF LR + EL+++ I+ I G++  W +VT HRARL+ +K   E E
Sbjct: 107 KVLQELPENYREVFWLREWHELAYEQIAVIIGKSVPWVKVTLHRARLQFRKNYAEKE 163


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Mar 24, 2004  1:53 AM
  Number of letters in database: 757,237,578
  Number of sequences in database:  2,715,099
  
Lambda     K      H
   0.321    0.136    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 2715099
Number of Hits to DB: 135,294,257
Number of extensions: 4380757
Number of successful extensions: 12910
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 12911
Number of HSP's successfully gapped: 3
Length of query: 98
Length of database: 757,237,578
Length adjustment: 66
Effective length of query: 32
Effective length of database: 578,041,044
Effective search space: 18497313408
Effective search space used: 18497313408
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: 120 (50.8 bits)