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= 0025.0068.p
         (333 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ...   510   e-146
gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38...    90   2e-19
gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ...    70   3e-13

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

 Score =  510 bits (1314), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 249/272 (91%), Positives = 260/272 (95%), Gaps = 3/272 (1%)

Query: 1   MKSA---TALMPVETNALALGFSGSLGNIDAYISAVNRLPMLTQAEEVSLARALREKNDL 57
           MK+A   TALMP E+NALALGFSGSLGNIDAYISAVNRLPMLT  EEV LAR LREKNDL
Sbjct: 1   MKTASAQTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDL 60

Query: 58  GAAQKLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQNVRLVSYAMH 117
           GAAQK+VLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDP QNVRLVSYAMH
Sbjct: 61  GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH 120

Query: 118 WIKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKSGLDAMTPAQVDALAKTLDVKREE 177
           WIKAE+HEYILKNWRLVKVATTKAQRKLFFNLRSHK GLDAMTPAQV+ALAKTLDVKREE
Sbjct: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180

Query: 178 VIEMETRLSGRDVALEAPTDDEDDKFAPIAYLSSDSSEPTRVMEAKQYDRLQSEGLEAAL 237
           VIEMETRLSGRD+ALE+PTDDEDDKFAPIAYLSSD+SEPTRV+EAKQYDRLQSEGLEAAL
Sbjct: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAAL 240

Query: 238 SKLDDRSRRIVEARWLANDDGSGATLHEXSTE 269
           SKLD+RSRRIVEARWLANDDGSGATLHE + E
Sbjct: 241 SKLDERSRRIVEARWLANDDGSGATLHELADE 272


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

 Score = 90.1 bits (222), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 130/246 (52%), Gaps = 15/246 (6%)

Query: 29  YISAVNRLPMLTQAEEVSLARALREKNDLGAAQKLVLSHLRLVVSIARGYLGYGLPHADL 88
           Y++ +   P+LT AEE+  A   +   +  A QK++  +LRLVVSIA+ Y+  G+   DL
Sbjct: 68  YLNKIGAKPLLTAAEELHFATQAK-AGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDL 126

Query: 89  IQEGNIGLMKAVKRFDPDQNVRLVSYAMHWIKAEMHEYILKNWRLVKVATTKAQRKLFFN 148
           I+EGN+GLM+A+ +F+P++  R  +YA  WI+  +   I+   R V++      R+L   
Sbjct: 127 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMV-RELNQI 185

Query: 149 LRSHKSGLDAMT----PAQVDALAKTLDVKREEVIEMETRLSGRDVALEAPTDDEDDKFA 204
           LR+ K  L+A       A  + +A  +D   EEV ++   LS    +L+ P D+ D + +
Sbjct: 186 LRA-KYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDV-LALSEHAASLDTPLDN-DPQAS 242

Query: 205 PIAYLSSDSSE-PTRVMEAKQYDRLQSEGLEAALSKLDDRSRRIVEARWLANDDGSGATL 263
            +  L S   E P    E+++   L  E L++   K     +R+V AR    D+   +TL
Sbjct: 243 LMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEK-----QRVVVARRFGLDNDDPSTL 297

Query: 264 HEXSTE 269
            + ++E
Sbjct: 298 EQLASE 303


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

 Score = 69.7 bits (169), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 49/152 (32%), Positives = 79/152 (51%), Gaps = 7/152 (4%)

Query: 53  EKNDLGAAQKLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQNVRLV 112
           EK    A +++  ++LRLV+SIA+ Y   GL   DLIQEGNIGLMKAV +F+  +  +  
Sbjct: 605 EKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 664

Query: 113 SYAMHWIKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKSGLDAMTPAQVDALAKTLD 172
           +YA  WI+  +   I    R +++     +     N  S +  +   T A+ D    TL 
Sbjct: 665 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ--ILQETGAEPD--PATLA 720

Query: 173 VKR---EEVIEMETRLSGRDVALEAPTDDEDD 201
           +K    E+ I    +++   +++E P  D+DD
Sbjct: 721 IKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 752


  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    0.131    0.384 

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: 952,806
Number of extensions: 36178
Number of successful extensions: 121
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 119
Number of HSP's successfully gapped: 3
Length of query: 333
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 247
Effective length of database: 1,212,660
Effective search space: 299527020
Effective search space used: 299527020
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: 131 (55.1 bits)