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/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas a...   522   e-150
gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor Rpo...   121   4e-29
gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA...    89   3e-19

>gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas
           arsenicoxydans]
          Length = 298

 Score =  522 bits (1345), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 253/299 (84%), Positives = 278/299 (92%), Gaps = 1/299 (0%)

Query: 1   MKTASAHTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTQEEEVKLARDLREKNDL 60
           MK  SA TA++ + SN ++LGFSG+LGNIDAYISAVNRLPMLT EEE+ LA+ LR+ NDL
Sbjct: 1   MKATSASTAMI-SPSNMMSLGFSGALGNIDAYISAVNRLPMLTHEEEISLAKRLRDDNDL 59

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

Query: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180
           WIKAE+HEYILKNWRLVKVATTKAQRKLFFNLRSHK GLDAMTP QVEALAKTL+VKREE
Sbjct: 120 WIKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKTGLDAMTPDQVEALAKTLNVKREE 179

Query: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNAEPTRVIEAKQYDRLQSEGLEAAL 240
           VIEMETRLSGRDIALE+PTDDEDDKFAPIAYLSSD+ EPTRV+E+++YDRLQ+EGL +AL
Sbjct: 180 VIEMETRLSGRDIALEAPTDDEDDKFAPIAYLSSDSQEPTRVLESQRYDRLQTEGLSSAL 239

Query: 241 SKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTALQAYS 299
            KLD RSRRIVEARWLANDDGSGATLHELA+EFGVSAERIRQIE VALKKMK +L A++
Sbjct: 240 GKLDPRSRRIVEARWLANDDGSGATLHELANEFGVSAERIRQIETVALKKMKGSLAAFA 298


>gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor RpoS
           [Herminiimonas arsenicoxydans]
          Length = 344

 Score =  121 bits (304), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 96/273 (35%), Positives = 151/273 (55%), Gaps = 23/273 (8%)

Query: 32  YISAVNRLPMLTQEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 91
           Y++ +   P+LT  EEV  A  L ++ +  A QKM+  +LRLVVSIA+ Y+  G+   DL
Sbjct: 75  YLNQIGARPLLTVPEEVHFAT-LAKQGNFAARQKMIEHNLRLVVSIAKHYINRGVVLLDL 133

Query: 92  IQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFN 151
           I+EGN+GLM+A+ +F+P +  R  +YA  WI+  I   I+   R V++      R+L   
Sbjct: 134 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLP-VHVVRELNQT 192

Query: 152 LRS-------HKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDEDD 204
           LR+       H +G DA      E +A  ++   E+V ++   LS    +L++P D  D 
Sbjct: 193 LRAKFHLEAQHHDGKDATA----EDIAHLVERSVEDVQDI-LALSEHASSLDAPLDG-DP 246

Query: 205 KFAPIAYLSSDNA-EPTRVIEAKQYDRLQSEGLEAALSKLDDRSRRIVEARW-LANDDGS 262
           + + +  L  D+A +P  + E ++   L  + L+    KL D+ R ++  R+ L NDD  
Sbjct: 247 QSSLMDLLQGDHANDPDVLAEHQEMIVLVRDWLD----KLSDKQRLVITRRFGLDNDD-- 300

Query: 263 GATLHELADEFGVSAERIRQIEAVALKKMKTAL 295
            ATL ELA E  V+ ER+RQI+  AL K+K +L
Sbjct: 301 PATLEELATEMHVTRERVRQIQQEALVKLKRSL 333


>gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA
           polymerase [Herminiimonas arsenicoxydans]
          Length = 858

 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: 619 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 678

Query: 122 IKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVK---R 178
           I+  I   I    R +++     +     N  S +     +     E    TL +K    
Sbjct: 679 IRQAITRSIADQARTIRIPVHMIETINKMNRISRQ----ILQETGAEPDPATLAIKMEMP 734

Query: 179 EEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNAEPTRVIEAKQYDRLQSEGLEA 238
           E+ I    +++   I++E+P  D+DD         ++   P    +A  +  ++   ++ 
Sbjct: 735 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPA---DAALHASMRG-VVKD 790

Query: 239 ALSKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMK 292
            L  L  R  +++  R+   +  +  TL E+  +F V+ ERIRQIEA AL+K++
Sbjct: 791 VLDSLTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 843


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
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: 3295
Number of Hits to DB: 531,879
Number of extensions: 20648
Number of successful extensions: 78
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 74
Number of HSP's successfully gapped: 3
Length of query: 299
Length of database: 1,000,347
Length adjustment: 81
Effective length of query: 218
Effective length of database: 733,452
Effective search space: 159892536
Effective search space used: 159892536
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: 128 (53.9 bits)