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/707/707 
           3697 sequences; 1,221,021 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152980473|ref|YP_001353052.1| RNA polymerase sigma factor Rpo...    76   2e-15
gi|152980264|ref|YP_001355194.1| ECF subfamily RNA polymerase si...    61   5e-11

>gi|152980473|ref|YP_001353052.1| RNA polymerase sigma factor RpoE
           [Janthinobacterium sp. Marseille]
          Length = 200

 Score = 75.9 bits (185), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 83/163 (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   +  + + D +  P  L   +Q+A+ +   + ELP +
Sbjct: 86  NYLVTQGRRAPTSTEADVEEAETFDDGDHLRDINT-PESLLATKQIAQTLNLAMEELPEE 144

Query: 148 IRATFEAVLDGDATYEQAAEHLHIPIGTVRSRVSRVRATVRSK 190
           +R           +Y++ AE +  PIGTVRSR+ R R  +  K
Sbjct: 145 LRMAITLREIEGLSYDEIAESMGCPIGTVRSRIFRAREAISEK 187


>gi|152980264|ref|YP_001355194.1| ECF subfamily RNA polymerase sigma
           factor [Janthinobacterium sp. Marseille]
          Length = 168

 Score = 60.8 bits (146), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 46/149 (30%), Positives = 70/149 (46%), Gaps = 7/149 (4%)

Query: 43  HLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIALNLARNQVRRNI 102
            L R+ +  +G    A+D+VQ+T     K    +   S    WLFGI  NL  +QVR+  
Sbjct: 14  RLRRYARALLGDRTGADDLVQDTMERGWKKLSSWQRGSDMRAWLFGIMHNLHVDQVRKPS 73

Query: 103 ADRCDAVDENFMEQIVDTHADPAVLYEMRQMAEKVEGLLNELPVKIRATFEAVLDGDATY 162
               +  D+     I   H   +   EMR +    E  L+ LP + R     V   + +Y
Sbjct: 74  LPTEELDDDT---PIPAAHTSVSDGLEMRDL----ESALHSLPTEQREILLLVALEEMSY 126

Query: 163 EQAAEHLHIPIGTVRSRVSRVRATVRSKY 191
           E+ A  L +P+GTV SR+SR R  +R++ 
Sbjct: 127 EEVAATLGLPLGTVMSRLSRARQKLRTQM 155


  Database: BlastDatabases/707/707
    Posted date:  Apr 13, 2011 12:58 PM
  Number of letters in database: 1,221,021
  Number of sequences in database:  3697
  
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: 3697
Number of Hits to DB: 430,081
Number of extensions: 15617
Number of successful extensions: 73
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 75
Number of HSP's successfully gapped: 2
Length of query: 202
Length of database: 1,221,021
Length adjustment: 79
Effective length of query: 123
Effective length of database: 928,958
Effective search space: 114261834
Effective search space used: 114261834
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: 127 (53.5 bits)