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= 0005.0060.p
         (289 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38...   519   e-148
gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ...   186   3e-48
gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ...   117   1e-27

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

 Score =  519 bits (1336), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 250/289 (86%), Positives = 274/289 (94%)

Query: 1   VEELKKVLAAELSTDTTQHYLNQIGTRPLLTAPEELYFATLAKQGDFASRQKMIEHNLRL 60
           V+ELKKVLAAELSTDTTQHYLN+IG +PLLTA EEL+FAT AK G+F +RQKMIEHNLRL
Sbjct: 49  VDELKKVLAAELSTDTTQHYLNKIGAKPLLTAAEELHFATQAKAGEFVARQKMIEHNLRL 108

Query: 61  VVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQ 120
           VVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQ
Sbjct: 109 VVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQ 168

Query: 121 ARTVRLPVHMVRELNQILRAKYHLEAQHHDGRDATAEDIAHLVDRPVEDVQDVLALSEHA 180
           ARTVRLPVHMVRELNQILRAKYHLEAQ  DGRDA+AEDIAHLVDRPVE+VQDVLALSEHA
Sbjct: 169 ARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDVLALSEHA 228

Query: 181 ASLDTPLDNDPQASLIDLLPGSLDESPDSKAEYHEVSILIRDWLKNLPDKQRIVITRRFG 240
           ASLDTPLDNDPQASL+DLLP +++E PD++AE  E+++LIR+WLK+L +KQR+V+ RRFG
Sbjct: 229 ASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEKQRVVVARRFG 288

Query: 241 LDNDDPSTLEQLASEMGITRERVRQVQQEALIKLKRSLLARGVGKDALF 289
           LDNDDPSTLEQLASEMGITRERVRQVQQEALIKLKR L +RGVG+DALF
Sbjct: 289 LDNDDPSTLEQLASEMGITRERVRQVQQEALIKLKRLLTSRGVGRDALF 337


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

 Score =  186 bits (471), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 88/227 (38%), Positives = 150/227 (66%), Gaps = 2/227 (0%)

Query: 49  SRQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWW 108
           ++++M E NLRLV+SIAK Y NRG+  LDLI+EGN+GLM+A+DKFE  RG++FSTYATWW
Sbjct: 611 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 670

Query: 109 IRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQHHDGRDATAEDIAHLVDRPVE 168
           IRQ+I R+I +QART+R+PVHM+  +N++ R    +      G +     +A  ++ P +
Sbjct: 671 IRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLAIKMEMPED 728

Query: 169 DVQDVLALSEHAASLDTPLDNDPQASLIDLLPGSLDESPDSKAEYHEVSILIRDWLKNLP 228
            ++ ++ +++   S++TP+ +D  + L D +  +   +P   A +  +  +++D L +L 
Sbjct: 729 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLT 788

Query: 229 DKQRIVITRRFGLDNDDPSTLEQLASEMGITRERVRQVQQEALIKLK 275
            ++  V+  RFG++     TLE++  +  +TRER+RQ++ +AL KL+
Sbjct: 789 PREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835


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

 Score =  117 bits (293), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 94/275 (34%), Positives = 148/275 (53%), Gaps = 23/275 (8%)

Query: 20  YLNQIGTRPLLTAPEELYFA-TLAKQGDFASRQKMIEHNLRLVVSIAKHYINRGVALLDL 78
           Y++ +   P+LT  EE+  A  L ++ D  + QKM+  +LRLVVSIA+ Y+  G+   DL
Sbjct: 32  YISAVNRLPMLTHEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 91

Query: 79  IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMV-RELNQI 137
           I+EGN+GLM+A+ +F+P +  R  +YA  WI+  I   I+   R V++      R+L   
Sbjct: 92  IQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFN 151

Query: 138 LRAKYHLEAQHHDGRDATA----EDIAHLVDRPVEDVQDV-LALSEHAASLDTPLDN-DP 191
           LR+       H +G DA      E +A  +D   E+V ++   LS    +L++P D+ D 
Sbjct: 152 LRS-------HKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDEDD 204

Query: 192 QASLIDLLPGSLDESPDSKAEYHEVSIL----IRDWLKNLPDKQRIVITRRFGLDNDDPS 247
           + + I  L  S +  P    E  +   L    +   L  L ++ R ++  R+ L NDD S
Sbjct: 205 KFAPIAYL-SSDNSEPTRVIEAKQYDRLQSEGLEAALSKLDERSRRIVEARW-LANDDGS 262

Query: 248 --TLEQLASEMGITRERVRQVQQEALIKLKRSLLA 280
             TL +LA E G++ ER+RQ++  AL K+K SL A
Sbjct: 263 GATLHELADEFGVSAERIRQIEAVALKKMKTSLQA 297


  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
   0.319    0.135    0.381 

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: 882,051
Number of extensions: 36665
Number of successful extensions: 99
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 97
Number of HSP's successfully gapped: 3
Length of query: 289
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 205
Effective length of database: 1,222,130
Effective search space: 250536650
Effective search space used: 250536650
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 (21.8 bits)
S2: 130 (54.7 bits)