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= 0165.0012.p
         (128 letters)

Database: pfamseq 
           9,421,015 sequences; 3,060,696,203 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family     95   3e-18
B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family     91   3e-17
C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor             82   1e-14
A3I711.1 A3I711_9BACI RNA polymerase sigma factor SigW                 82   1e-14
C0Z4U4.1 C0Z4U4_BREBN RNA polymerase ECF-type sigma factor             77   5e-13

>B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family
          Length = 193

 Score = 94.7 bits (234), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 41/80 (51%), Positives = 61/80 (76%)

Query: 4  IESIETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVR 63
          ++SIE  + R++AGEV  F  I++TY+ +IY YC R+L  +++A+DAVQDI +K F K+ 
Sbjct: 1  MDSIEEYVGRVKAGEVDCFEPIVETYKKQIYLYCCRMLGCKQDAQDAVQDIFIKAFTKLY 60

Query: 64 YYQPKGSFTSWLYKVAYNHC 83
           Y+ K SF+SWLYK+AY+HC
Sbjct: 61 TYEAKVSFSSWLYKIAYHHC 80


>B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family
          Length = 204

 Score = 90.9 bits (224), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 37/78 (47%), Positives = 58/78 (74%)

Query: 6  SIETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVRYY 65
           IE  I R+  G+   F  I++ +Q +I+ YC RLL+ R++AEDAVQ+IM+K ++K+  Y
Sbjct: 14 DIEVTIERVLNGDRQAFVHIVEAFQQQIFMYCWRLLNQRQDAEDAVQEIMVKAYQKLETY 73

Query: 66 QPKGSFTSWLYKVAYNHC 83
          +P+ SF++WLYK+AY+HC
Sbjct: 74 KPETSFSAWLYKMAYHHC 91


>C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor
          Length = 189

 Score = 82.4 bits (202), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 55/77 (71%)

Query: 7  IETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVRYYQ 66
          +E  +  ++AG++  F  IID  Q +++ YC  +L +R+EAEDAVQ++ LK FE++  Y+
Sbjct: 1  MEQVLKEVRAGDIEQFGLIIDAMQKQLFVYCYHMLGHRQEAEDAVQEVFLKAFEQLDSYR 60

Query: 67 PKGSFTSWLYKVAYNHC 83
             SF++W+YK+AY+HC
Sbjct: 61 HNVSFSAWMYKIAYHHC 77


>A3I711.1 A3I711_9BACI RNA polymerase sigma factor SigW
          Length = 132

 Score = 82.4 bits (202), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/77 (45%), Positives = 54/77 (70%)

Query: 7  IETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVRYYQ 66
          I+  + ++QAG+ Y + +II  +Q +IY YC  LL N+EEAEDA QD+ +K  E +R + 
Sbjct: 13 IKEVVKQVQAGDTYAYTEIIRCFQKQIYLYCYYLLGNKEEAEDASQDVFIKGLENIRQFT 72

Query: 67 PKGSFTSWLYKVAYNHC 83
             SF++WLYK+A++HC
Sbjct: 73 YSVSFSAWLYKIAHHHC 89


>C0Z4U4.1 C0Z4U4_BREBN RNA polymerase ECF-type sigma factor
          Length = 190

 Score = 77.0 bits (188), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 52/77 (67%)

Query: 7  IETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVRYYQ 66
          IE  +  I+AG +  +  IID YQ  I+ YC  +L +R++AEDAVQ+++ + +E +  Y 
Sbjct: 6  IERLLIEIKAGSLEQYELIIDYYQQPIFTYCYHMLGHRQDAEDAVQEVLFRAYEHLDQYT 65

Query: 67 PKGSFTSWLYKVAYNHC 83
             SF++WLY++AYNHC
Sbjct: 66 YSLSFSAWLYRIAYNHC 82


  Database: pfamseq
    Posted date:  Aug 5, 2010  3:22 PM
  Number of letters in database: 3,060,696,203
  Number of sequences in database:  9,421,015
  
Lambda     K      H
   0.324    0.135    0.408 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9421015
Number of Hits to DB: 628,797,108
Number of extensions: 19464916
Number of successful extensions: 67739
Number of sequences better than 1.0e-05: 285
Number of HSP's gapped: 68324
Number of HSP's successfully gapped: 285
Length of query: 128
Length of database: 3,060,696,203
Length adjustment: 93
Effective length of query: 35
Effective length of database: 2,184,541,808
Effective search space: 76458963280
Effective search space used: 76458963280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 126 (53.1 bits)