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= 0020.0081.p
         (244 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase...   440   e-125
gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ...    68   8e-13

>gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase
           sigma factor [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score =  440 bits (1131), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 206/244 (84%), Positives = 227/244 (93%)

Query: 1   MYNVKGKTAKNDLLQLHAALVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVNRYEETH 60
           MYNVKGK  KNDLL+ HA LVKKLAHQ+KAKLPPSVEVDDLIQAGM+GLLDAVNRYEETH
Sbjct: 1   MYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETH 60

Query: 61  GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNTRKIEEAIHVLLQQLGRPPQEAEVATQ 120
           GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQN RK+EEA+  LLQQLGR P+EAE+A  
Sbjct: 61  GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH 120

Query: 121 LKLSLPEYQDMLTECGGHQLIYYEDFHDADGGHEHFLDRYQTRDTDDPLQNLINGGFRDA 180
           +++SL +YQ +L+ECGGHQLIYYEDFHD DGGHEHFLDR+QT D+DDPLQNLINGGFR+A
Sbjct: 121 MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA 180

Query: 181 VIDSIKALPEREKILMGLYYEQEMNLKEIGAVMGVSESRVCQLHSQAIARMRSTLREQAW 240
           V+DSIKALPERE+ILM LYYEQEMNLKEIGAVMGVSESRVCQLHSQAI+RMRS LRE +W
Sbjct: 181 VVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLREHSW 240

Query: 241 TGVA 244
           +GVA
Sbjct: 241 SGVA 244


>gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor
           transcription regulator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 850

 Score = 67.8 bits (164), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 111/245 (45%), Gaps = 33/245 (13%)

Query: 5   KGKTAKNDLLQLHAALVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVNRYEETHGAQF 64
           K + AK ++ + +  LV  +A +   +    ++  DLIQ G IGL+ AV+++E   G +F
Sbjct: 607 KARMAKREMTEANLRLVISIAKKYTNR---GLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 663

Query: 65  ETYAVQRIRGAMLDELRSSDWLPRSIRQNTRKIEEAIHV-------------LLQQLGRP 111
            TYA   IR A          + RSI    R I   +H+             +LQ+ G  
Sbjct: 664 STYATWWIRQA----------ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAE 713

Query: 112 PQEAEVATQLKLSLPEYQDMLTECGGHQLIYYEDFHDADGGHEHFLDRYQTRDTDDPLQN 171
           P  A +A  +K+ +PE +         + I  E     D    H  D  +  +T  P   
Sbjct: 714 PDPATLA--IKMEMPEDKIRKIMKIAKEPISMET-PIGDDDDSHLGDFIEDNNTLAPADA 770

Query: 172 LINGGFRDAVIDSIKALPEREKILMGLYYEQEMN----LKEIGAVMGVSESRVCQLHSQA 227
            ++   R+ V D + +L  RE  ++ + +  EM+    L+E+G    V+  R+ Q+ ++A
Sbjct: 771 ALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 830

Query: 228 IARMR 232
           + ++R
Sbjct: 831 LRKLR 835


  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
   0.318    0.134    0.386 

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: 759,234
Number of extensions: 31267
Number of successful extensions: 111
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 112
Number of HSP's successfully gapped: 3
Length of query: 244
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 161
Effective length of database: 1,226,865
Effective search space: 197525265
Effective search space used: 197525265
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 129 (54.3 bits)