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= 0002.0521.p
         (296 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 ...   563   e-162
gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38...   114   1e-26
gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ...    90   2e-19

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

 Score =  563 bits (1450), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 275/299 (91%), Positives = 288/299 (96%), Gaps = 3/299 (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 WIKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKTGLDAMTPAQVDALAKTLDVKREE 177
           WIKAE+HEYILKNWRLVKVATTKAQRKLFFNLRSHK GLDAMTPAQV+ALAKTLDVKREE
Sbjct: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180

Query: 178 VIEMETRLSGRDVALEAPTDDDDDKFAPIAYLSSDNNEPTRVMEAKQYDRLQSEGLEAAL 237
           VIEMETRLSGRD+ALE+PTDD+DDKFAPIAYLSSDN+EPTRV+EAKQYDRLQSEGLEAAL
Sbjct: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAAL 240

Query: 238 SKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKGSLQAFA 296
           SKLD+RSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMK SLQA++
Sbjct: 241 SKLDERSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQAYS 299


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

 Score =  114 bits (284), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 141/265 (53%), Gaps = 13/265 (4%)

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 LRSHKTGLDAMT----PAQVDALAKTLDVKREEVIEMETRLSGRDVALEAPTDDDDDKFA 204
           LR+ K  L+A       A  + +A  +D   EEV ++   LS    +L+ P D+D     
Sbjct: 186 LRA-KYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDV-LALSEHAASLDTPLDNDPQASL 243

Query: 205 PIAYLSSDNNEPTRVMEAKQYDRLQSEGLEAALSKLDDRSRRIVEARWLANDDGSGATLH 264
                S+    P    E+++   L  E L++   K     +R+V AR    D+   +TL 
Sbjct: 244 MDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEK-----QRVVVARRFGLDNDDPSTLE 298

Query: 265 ELADEFGVSAERIRQIEAVALKKMK 289
           +LA E G++ ER+RQ++  AL K+K
Sbjct: 299 QLASEMGITRERVRQVQQEALIKLK 323


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

 Score = 89.7 bits (221), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 123/239 (51%), Gaps = 10/239 (4%)

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

Query: 113 SYAMHWIKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKTGLDAMTPAQVDALAKTLD 172
           +YA  WI+  +   I    R +++     +     N  S +   +         LA  ++
Sbjct: 665 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAIKME 724

Query: 173 VKREEVIEMETRLSGRDVALEAPTDDDDDKFAPIAYLSSDNNE--PTRVMEAKQYDRLQS 230
           +  +++ ++  +++   +++E P  DDDD    +     DNN   P    +A  +  +++
Sbjct: 725 MPEDKIRKI-MKIAKEPISMETPIGDDDDSH--LGDFIEDNNTLAPA---DAALHASMRN 778

Query: 231 EGLEAALSKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMK 289
             ++  L  L  R  +++  R+   +  +  TL E+  +F V+ ERIRQIEA AL+K++
Sbjct: 779 -VVKDILDSLTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 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    0.131    0.363 

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: 866,412
Number of extensions: 34766
Number of successful extensions: 132
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 128
Number of HSP's successfully gapped: 3
Length of query: 296
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 211
Effective length of database: 1,217,395
Effective search space: 256870345
Effective search space used: 256870345
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: 130 (54.7 bits)