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= 0231.0018.p
         (95 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|NP_845612.1| RNA polymerase sigma-70 factor, ECF subfamily [...    96   2e-19
ref|NP_657186.1| Sigma70_ECF, Sigma-70 factor (ECF subfamily) [B...    96   2e-19
ref|NP_388833.1| similar to RNA polymerase ECF-type sigma factor...    92   3e-18
gb|AAP68417.1| SigM [Bacillus subtilis subsp. spizizenii]              92   4e-18
ref|NP_655022.1| Sigma70_ECF, Sigma-70 factor (ECF subfamily) [B...    86   2e-16

>ref|NP_845612.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
          str. Ames]
 gb|AAP27098.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
          str. Ames]
          Length = 166

 Score = 96.3 bits (238), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 62/90 (68%), Gaps = 3/90 (3%)

Query: 6  LDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFRVAYNA 65
          ++E+Y+IY+ D+Y YL SL   H+ AEDLMQETFYRAYLYLE+    K+K WLF+VAY+ 
Sbjct: 3  IEEIYKIYINDVYRYLFSLSRSHHAAEDLMQETFYRAYLYLEDYENQKVKSWLFKVAYHT 62

Query: 66 FVDHTRKAKRRITAAYTCFSPLQIVQLSEN 95
          F+D  RK K+    ++     L+ +Q  E+
Sbjct: 63 FIDFVRKEKK---VSFVGTEELEAIQAGES 89


>ref|NP_657186.1| Sigma70_ECF, Sigma-70 factor (ECF subfamily) [Bacillus anthracis
          A2012]
          Length = 166

 Score = 96.3 bits (238), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 62/90 (68%), Gaps = 3/90 (3%)

Query: 6  LDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFRVAYNA 65
          ++E+Y+IY+ D+Y YL SL   H+ AEDLMQETFYRAYLYLE+    K+K WLF+VAY+ 
Sbjct: 3  IEEIYKIYINDVYRYLFSLSRSHHAAEDLMQETFYRAYLYLEDYENQKVKSWLFKVAYHT 62

Query: 66 FVDHTRKAKRRITAAYTCFSPLQIVQLSEN 95
          F+D  RK K+    ++     L+ +Q  E+
Sbjct: 63 FIDFVRKEKK---VSFVGTEELEAIQAGES 89


>ref|NP_388833.1| similar to RNA polymerase ECF-type sigma factor [Bacillus
          subtilis]
 pir||C69826 RNA polymerase ECF-type sigma factor homolog yhdM - Bacillus
          subtilis
 emb|CAA74497.1| hypothetical protein [Bacillus subtilis]
 emb|CAB12791.1| RNA polymerase ECF(extracytoplasmic function)-type sigma factor
          (sigma-M) [Bacillus subtilis subsp. subtilis str. 168]
          Length = 163

 Score = 92.0 bits (227), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 39/83 (46%), Positives = 60/83 (72%)

Query: 5  SLDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFRVAYN 64
          ++DE+YQ+Y+ D+Y +L S+  D +LAEDL+QETF RAY+++ +    K+KPWLF+VA N
Sbjct: 2  TIDEIYQMYMNDVYRFLLSMTKDKHLAEDLLQETFMRAYIHIHSYDHSKVKPWLFQVARN 61

Query: 65 AFVDHTRKAKRRITAAYTCFSPL 87
          AF+D+ RK K+ +T +      L
Sbjct: 62 AFIDYVRKHKKEVTISDDLIGSL 84


>gb|AAP68417.1| SigM [Bacillus subtilis subsp. spizizenii]
          Length = 163

 Score = 92.0 bits (227), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 39/83 (46%), Positives = 60/83 (72%)

Query: 5  SLDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFRVAYN 64
          ++DE+YQ+Y+ D+Y +L S+  D +LAEDL+QETF RAY+++ +    K+KPWLF+VA N
Sbjct: 2  TIDEIYQMYMNDVYRFLLSMTKDKHLAEDLLQETFMRAYIHIHSYDHSKVKPWLFQVARN 61

Query: 65 AFVDHTRKAKRRITAAYTCFSPL 87
          AF+D+ RK K+ +T +      L
Sbjct: 62 AFIDYVRKHKKEVTISDDLIGSL 84


>ref|NP_655022.1| Sigma70_ECF, Sigma-70 factor (ECF subfamily) [Bacillus anthracis
          A2012]
 ref|NP_843600.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
          str. Ames]
 gb|AAP25086.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
          str. Ames]
          Length = 161

 Score = 86.3 bits (212), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 58/83 (69%)

Query: 2  KPNSLDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFRV 61
          +  SL+E+Y  ++QD++ YL SL  D + AEDLMQETFYR  ++++  + ++I+PWLF +
Sbjct: 3  RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTI 62

Query: 62 AYNAFVDHTRKAKRRITAAYTCF 84
          AYNAF+D  RK KR  T   T F
Sbjct: 63 AYNAFIDWYRKEKRYKTTTITEF 85


  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
   0.326    0.138    0.428 

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: 132,763,017
Number of extensions: 4374518
Number of successful extensions: 11975
Number of sequences better than 1.0e-05: 15
Number of HSP's gapped: 12127
Number of HSP's successfully gapped: 15
Length of query: 95
Length of database: 757,237,578
Length adjustment: 63
Effective length of query: 32
Effective length of database: 586,186,341
Effective search space: 18757962912
Effective search space used: 18757962912
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 120 (50.8 bits)