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= 0001.2420.p
         (202 letters)

Database: BlastDatabases/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134095261|ref|YP_001100336.1| RNA polymerase sigma factor Rpo...    74   5e-15
gi|134096429|ref|YP_001101504.1| putative RNA polymerase sigma f...    60   9e-11

>gi|134095261|ref|YP_001100336.1| RNA polymerase sigma factor RpoE
           [Herminiimonas arsenicoxydans]
          Length = 200

 Score = 73.9 bits (180), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 82/163 (50%), Gaps = 9/163 (5%)

Query: 36  LYTEHRSHLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIALNLAR 95
           L  +++  L+R V R V    +AEDVVQ  FI+A +   +F G S   TWL+ I +N A+
Sbjct: 26  LVIKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAK 85

Query: 96  N----QVRR----NIADRCDAVDENFMEQIVDTHADPAVLYEMRQMAEKVEGLLNELPVK 147
           N    Q RR      AD  +A   +  E + D +  P  L   +Q+A+ +   + ELP +
Sbjct: 86  NYLVTQGRRAPTSTEADIEEAETFDDGEHLRDINT-PESLLATKQIAQTLNLAMEELPEE 144

Query: 148 IRATFEAVLDGDATYEQAAEHLHIPIGTVRSRVSRVRATVRSK 190
           +R           +Y++ A  +  PIGTVRSR+ R R  +  K
Sbjct: 145 LRMAITLREIEGLSYDEIAVSMGCPIGTVRSRIFRAREAISEK 187


>gi|134096429|ref|YP_001101504.1| putative RNA polymerase sigma
           factor [Herminiimonas arsenicoxydans]
          Length = 168

 Score = 60.1 bits (144), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 47/154 (30%), Positives = 70/154 (45%), Gaps = 21/154 (13%)

Query: 43  HLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIALNLARNQVRRNI 102
            L R+ +  +G    A+D+VQ+T     K    +   S    WLFGI  NL  +QVRR  
Sbjct: 14  RLRRYARALIGERTGADDLVQDTMERGWKKLSSWQRGSDMRAWLFGIMHNLHIDQVRR-- 71

Query: 103 ADRCDAVDENFMEQIVD-------THADPAVLYEMRQMAEKVEGLLNELPVKIRATFEAV 155
                      M +++D       + A  A   EMR +    +  L  LP + R     V
Sbjct: 72  --------PGIMTEVLDDDTPLPTSKATQADGLEMRDL----QSALATLPPEQREILLLV 119

Query: 156 LDGDATYEQAAEHLHIPIGTVRSRVSRVRATVRS 189
              + +YE+ A  L +P+GTV SR+SR R  +R+
Sbjct: 120 ALEEMSYEEVATTLGLPLGTVMSRLSRARQKLRA 153


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
Lambda     K      H
   0.319    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: 3295
Number of Hits to DB: 355,145
Number of extensions: 12997
Number of successful extensions: 43
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 42
Number of HSP's successfully gapped: 2
Length of query: 202
Length of database: 1,000,347
Length adjustment: 77
Effective length of query: 125
Effective length of database: 746,632
Effective search space: 93329000
Effective search space used: 93329000
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: 126 (53.1 bits)