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= 0001.4016.p
         (299 letters)

Database: BlastDatabases/707/707 
           3697 sequences; 1,221,021 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor ...   525   e-150
gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor Rpo...   122   2e-29
gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma fa...    89   3e-19

>gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor
           [Janthinobacterium sp. Marseille]
          Length = 298

 Score =  525 bits (1353), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 257/299 (85%), Positives = 277/299 (92%), Gaps = 1/299 (0%)

Query: 1   MKTASAHTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTQEEEVKLARDLREKNDL 60
           MK  SA TAL+P  SN LALGFSG+LGNIDAYISAVNRLPMLT EEE+ LAR LR++NDL
Sbjct: 1   MKAVSASTALVP-NSNMLALGFSGALGNIDAYISAVNRLPMLTHEEEMSLARRLRDENDL 59

Query: 61  GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH 120
           GAAQK+VLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDP Q VRLVSY+MH
Sbjct: 60  GAAQKLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMH 119

Query: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180
           WIKAE+HEYILKNWRLVKVATTKAQRKLFFNLRSHK GLD+MTP QV+ LAKTL+VKREE
Sbjct: 120 WIKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKTGLDSMTPDQVDELAKTLNVKREE 179

Query: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNAEPTRVIEAKQYDRLQSEGLEAAL 240
           VIEMETRLSGRDIALE+PTDDEDDKFAPIAYLSSD  EPT+V+E++Q+DRLQ+EGL  AL
Sbjct: 180 VIEMETRLSGRDIALEAPTDDEDDKFAPIAYLSSDMQEPTKVLESQQFDRLQTEGLSNAL 239

Query: 241 SKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTALQAYS 299
            KLD RSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMK +L AY+
Sbjct: 240 GKLDARSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKGSLAAYA 298


>gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor RpoS
           [Janthinobacterium sp. Marseille]
          Length = 345

 Score =  122 bits (307), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 97/273 (35%), Positives = 149/273 (54%), Gaps = 23/273 (8%)

Query: 32  YISAVNRLPMLTQEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 91
           Y++ +   P+LT  EEV  A  L ++ +  A QKM+  +LRLVVSIA+ Y+  G+   DL
Sbjct: 76  YLNQIGTRPLLTVPEEVHFAT-LAKQGNFAARQKMIEHNLRLVVSIAKHYINRGVILLDL 134

Query: 92  IQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFN 151
           I+EGN+GLM+A+ +F+P +  R  +YA  WI+  I   I+   R V++      R+L   
Sbjct: 135 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLP-VHVVRELNQT 193

Query: 152 LRS-------HKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDEDD 204
           LR+       H +G DA      E +A  +D   E+V ++   LS    +L++P D  D 
Sbjct: 194 LRAKFHLEAQHHDGKDAT----AEDIAHLVDRSVEDVQDI-LALSEHATSLDAPLDG-DP 247

Query: 205 KFAPIAYLSSDNA-EPTRVIEAKQYDRLQSEGLEAALSKLDDRSRRIVEARW-LANDDGS 262
           + + +  L  D+A +P  + E  +   L  + LE    KL D+ R ++  R+ L NDD  
Sbjct: 248 QSSLMDLLQGDHANDPDALAEHNEMTVLVHDWLE----KLPDKQRLVITRRFGLDNDD-- 301

Query: 263 GATLHELADEFGVSAERIRQIEAVALKKMKTAL 295
            ATL  LA E  V+ ER+RQI+  AL K+K +L
Sbjct: 302 PATLEALAAEMHVTRERVRQIQQEALVKLKRSL 334


>gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma
           factor [Janthinobacterium sp. Marseille]
          Length = 826

 Score = 89.0 bits (219), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 117/234 (50%), Gaps = 12/234 (5%)

Query: 62  AAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHW 121
           A ++M  ++LRLV+SIA+ Y   GL   DLIQEGNIGLMKAV +F+  +  +  +YA  W
Sbjct: 587 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 646

Query: 122 IKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKR--- 178
           I+  I   I    R +++     +     N  S +     +     E    TL +K    
Sbjct: 647 IRQAITRSIADQARTIRIPVHMIETINKMNRISRQ----ILQETGAEPDPATLAIKMEMP 702

Query: 179 EEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNAEPTRVIEAKQYDRLQSEGLEA 238
           E+ I    +++   I++E+P  D+DD         ++   P    +A  +  ++   ++ 
Sbjct: 703 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPA---DAALHASMRG-VVKD 758

Query: 239 ALSKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMK 292
            L  L  R  +++  R+   +  +  TL E+  +F V+ ERIRQIEA AL+K++
Sbjct: 759 VLDSLTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 811


  Database: BlastDatabases/707/707
    Posted date:  Apr 13, 2011 12:58 PM
  Number of letters in database: 1,221,021
  Number of sequences in database:  3697
  
Lambda     K      H
   0.316    0.130    0.358 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3697
Number of Hits to DB: 648,105
Number of extensions: 24948
Number of successful extensions: 109
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 104
Number of HSP's successfully gapped: 3
Length of query: 299
Length of database: 1,221,021
Length adjustment: 83
Effective length of query: 216
Effective length of database: 914,170
Effective search space: 197460720
Effective search space used: 197460720
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)