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= 0001.3039.p
         (195 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312377|ref|YP_003776469.1| RNA polymerase sigma-70 factor,...   373   e-105

>gi|300312377|ref|YP_003776469.1| RNA polymerase sigma-70 factor,
           ECF subfamily (sigma-24) transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 195

 Score =  373 bits (957), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 187/195 (95%), Positives = 190/195 (97%)

Query: 1   MQPISTLSPMSDQDREITATVMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLP 60
           MQPIS  SPMSDQDREITATVMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLP
Sbjct: 1   MQPISLSSPMSDQDREITATVMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLP 60

Query: 61  EPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQVDGAEDAWRLDLVLPASADGPE 120
           EPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQVDGA+DAWRLDL LPASADGPE
Sbjct: 61  EPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQVDGADDAWRLDLALPASADGPE 120

Query: 121 AAYARAALIEALQEALDELPEAQREVFIAHELDGLSFKAMAASSGTSLNTLLARKRYAVL 180
           AAYARAALI+ALQEAL ELPEAQREVFIAHELDGLSFK MAA+SGTSLNTLLARKRYAVL
Sbjct: 121 AAYARAALIDALQEALGELPEAQREVFIAHELDGLSFKEMAAASGTSLNTLLARKRYAVL 180

Query: 181 HLRERLQAVYDELEM 195
           HLRERLQAVYDELEM
Sbjct: 181 HLRERLQAVYDELEM 195


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.319    0.134    0.373 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 562,028
Number of extensions: 21023
Number of successful extensions: 100
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 103
Number of HSP's successfully gapped: 4
Length of query: 195
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 115
Effective length of database: 1,241,070
Effective search space: 142723050
Effective search space used: 142723050
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: 128 (53.9 bits)