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= 0016.0041.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...   504   e-144
gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ...    72   6e-14

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

 Score =  504 bits (1298), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 244/244 (100%), Positives = 244/244 (100%)

Query: 1   MYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETH 60
           MYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETH
Sbjct: 1   MYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETH 60

Query: 61  GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH 120
           GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH
Sbjct: 61  GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH 120

Query: 121 MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA 180
           MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA
Sbjct: 121 MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA 180

Query: 181 VVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLREHSW 240
           VVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLREHSW
Sbjct: 181 VVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLREHSW 240

Query: 241 SGVA 244
           SGVA
Sbjct: 241 SGVA 244


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

 Score = 71.6 bits (174), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 114/236 (48%), Gaps = 15/236 (6%)

Query: 5   KGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETHGAQF 64
           K +  K ++ E +  LV  +A +   +    ++  DLIQ G +GL+ AV+++E   G +F
Sbjct: 607 KARMAKREMTEANLRLVISIAKKYTNR---GLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 663

Query: 65  ETYAVQRIRGAML----DELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH 120
            TYA   IR A+     D+ R+   +P  + +   K+    + +LQ+ G +P  A LA  
Sbjct: 664 STYATWWIRQAITRSIADQARTIR-IPVHMIETINKMNRISRQILQETGAEPDPATLAIK 722

Query: 121 MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA 180
           M++  ED    + +     +       DDD    H  D  + +++  P    ++   R  
Sbjct: 723 MEMP-EDKIRKIMKIAKEPISMETPIGDDD--DSHLGDFIEDNNTLAPADAALHASMRNV 779

Query: 181 VVDSIKALPEREQILMALYYEQEMN----LKEIGAVMGVSESRVCQLHSQAISRMR 232
           V D + +L  RE  ++ + +  EM+    L+E+G    V+  R+ Q+ ++A+ ++R
Sbjct: 780 VKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 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
   0.317    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: 4735
Number of Hits to DB: 661,210
Number of extensions: 22740
Number of successful extensions: 116
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 117
Number of HSP's successfully gapped: 2
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 (21.6 bits)
S2: 129 (54.3 bits)