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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

B3K4E0.1 B3K4E0_9BACI RNA polymerase sigma factor, SigM family        112   1e-23
C0GD66.1 C0GD66_9FIRM RNA polymerase, sigma-24 subunit, ECF subf...   111   2e-23
C3A8A7.1 C3A8A7_BACMY RNA polymerase sigma-70 factor, ECF subfamily    99   2e-19
C2XWF3.1 C2XWF3_BACCE RNA polymerase sigma-70 factor, ECF subfamily    98   2e-19
Q638V8.1 Q638V8_BACCZ RNA polymerase sigma-70 factor                   97   4e-19

>B3K4E0.1 B3K4E0_9BACI RNA polymerase sigma factor, SigM family
          Length = 166

 Score =  112 bits (279), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 53/87 (60%), Positives = 67/87 (77%)

Query: 1  MKPNSLDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFR 60
          MK NSL  +YQ YV+D+Y YL SL +DH+ AEDL+QETFYRAYLYLE+ +E++IKPWLFR
Sbjct: 1  MKLNSLGSIYQYYVKDVYRYLYSLSYDHHTAEDLVQETFYRAYLYLEDWKEERIKPWLFR 60

Query: 61 VAYNAFVDHTRKAKRRITAAYTCFSPL 87
          VA+NA+VD+ RKA R I      F  +
Sbjct: 61 VAHNAYVDYQRKASRSIVRDAEFFDQM 87


>C0GD66.1 C0GD66_9FIRM RNA polymerase, sigma-24 subunit, ECF subfamily
          Length = 162

 Score =  111 bits (278), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/87 (59%), Positives = 68/87 (78%)

Query: 1  MKPNSLDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFR 60
          MK ++LDE+Y+ Y+ ++Y YL  LC +HYLAED+MQETFYRAYL+LE+C E+++KPWLFR
Sbjct: 1  MKRDTLDEIYKSYMDEVYRYLLFLCRNHYLAEDVMQETFYRAYLHLEDCPEERVKPWLFR 60

Query: 61 VAYNAFVDHTRKAKRRITAAYTCFSPL 87
          VA+NAFVD  RK  R  T A+  F  L
Sbjct: 61 VAHNAFVDIQRKDTRNYTKAHDYFERL 87


>C3A8A7.1 C3A8A7_BACMY RNA polymerase sigma-70 factor, ECF subfamily
          Length = 203

 Score = 98.6 bits (244), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 63/90 (70%), Gaps = 3/90 (3%)

Query: 6   LDELYQIYVQDIYAYLRSLCHDHYLAEDLMQETFYRAYLYLENCREDKIKPWLFRVAYNA 65
           ++E+Y++Y+ D+Y YL SL   H++AEDLMQETFYRAYLYLE+    K+K WLF+VAY+ 
Sbjct: 40  IEEIYKVYINDVYRYLFSLSRSHHVAEDLMQETFYRAYLYLEDYENQKVKSWLFKVAYHT 99

Query: 66  FVDHTRKAKRRITAAYTCFSPLQIVQLSEN 95
           F+D  RK K+    A+     L+ +Q  E+
Sbjct: 100 FIDFVRKEKK---VAFVGTEELETIQAGES 126


>C2XWF3.1 C2XWF3_BACCE RNA polymerase sigma-70 factor, ECF subfamily
          Length = 166

 Score = 98.2 bits (243), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 63/90 (70%), Gaps = 3/90 (3%)

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

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


>Q638V8.1 Q638V8_BACCZ RNA polymerase sigma-70 factor
          Length = 166

 Score = 97.4 bits (241), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 63/90 (70%), Gaps = 3/90 (3%)

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

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


  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
   0.326    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: 9421015
Number of Hits to DB: 529,053,350
Number of extensions: 17468831
Number of successful extensions: 50490
Number of sequences better than 1.0e-05: 181
Number of HSP's gapped: 51732
Number of HSP's successfully gapped: 181
Length of query: 95
Length of database: 3,060,696,203
Length adjustment: 64
Effective length of query: 31
Effective length of database: 2,457,751,243
Effective search space: 76190288533
Effective search space used: 76190288533
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: 126 (53.1 bits)