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= 0179.0010.p
         (202 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ...   352   1e-98
gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38...   141   5e-35
gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ...    70   1e-13

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

 Score =  352 bits (902), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 169/172 (98%), Positives = 170/172 (98%)

Query: 1   VLARNVPAIKELQQKLIDLQARVVLPLPDLRGINKKMGAGEKKARMAKREMTEANLRLVI 60
           VL+RNVPAIKELQQKLIDLQARVVLPL DLR INKKMGAGEKKARMAKREMTEANLRLVI
Sbjct: 565 VLSRNVPAIKELQQKLIDLQARVVLPLQDLRAINKKMGAGEKKARMAKREMTEANLRLVI 624

Query: 61  SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 120
           SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR
Sbjct: 625 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 684

Query: 121 TIRIPVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKI 172
           TIRIPVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKI
Sbjct: 685 TIRIPVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKI 736


>gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38)
           factor protein [Herbaspirillum seropedicae SmR1]
          Length = 337

 Score =  141 bits (355), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 63/139 (45%), Positives = 97/139 (69%), Gaps = 2/139 (1%)

Query: 46  MAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 105
           +A+++M E NLRLV+SIAK Y NRG+  LDLI+EGN+GLM+A+DKFE  RG++FSTYATW
Sbjct: 96  VARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATW 155

Query: 106 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLAIKMEMPE 163
           WIRQ+I R+I +QART+R+PVHM+  +N++ R    +   Q  G +     +A  ++ P 
Sbjct: 156 WIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHLVDRPV 215

Query: 164 DKIRKIMKIXSSRTTTPWP 182
           ++++ ++ +     +   P
Sbjct: 216 EEVQDVLALSEHAASLDTP 234


>gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor
           protein [Herbaspirillum seropedicae SmR1]
          Length = 299

 Score = 70.1 bits (170), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/84 (42%), Positives = 51/84 (60%)

Query: 41  EKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 100
           EK    A ++M  ++LRLV+SIA+ Y   GL   DLIQEGNIGLMKAV +F+  +  +  
Sbjct: 56  EKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLV 115

Query: 101 TYATWWIRQAITRSIADQARTIRI 124
           +YA  WI+  I   I    R +++
Sbjct: 116 SYAMHWIKAEIHEYILKNWRLVKV 139


  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
   0.321    0.133    0.388 

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: 546,151
Number of extensions: 19237
Number of successful extensions: 68
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 69
Number of HSP's successfully gapped: 3
Length of query: 202
Length of database: 1,619,870
Length adjustment: 81
Effective length of query: 121
Effective length of database: 1,236,335
Effective search space: 149596535
Effective search space used: 149596535
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 (21.9 bits)
S2: 128 (53.9 bits)