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= 0031.0154.p (299 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 ... 607 e-175 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 = 607 bits (1566), Expect = e-175, Method: Compositional matrix adjust. Identities = 298/299 (99%), Positives = 299/299 (100%) Query: 1 MKTASAQTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDL 60 MKTASAQTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDL Sbjct: 1 MKTASAQTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDL 60 Query: 61 GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH 120 GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH Sbjct: 61 GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH 120 Query: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE Sbjct: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180 Query: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEPSRVIEAKQYDRLQSEGLEAAL 240 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEP+RVIEAKQYDRLQSEGLEAAL Sbjct: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAAL 240 Query: 241 SKLDERSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQAYS 299 SKLDERSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQAYS 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 = 93/270 (34%), Positives = 147/270 (54%), Gaps = 23/270 (8%) Query: 32 YISAVNRLPMLTHEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 91 Y++ + P+LT EE+ A + + A QKM+ +LRLVVSIA+ Y+ G+ DL Sbjct: 68 YLNKIGAKPLLTAAEELHFATQAK-AGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDL 126 Query: 92 IQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFN 151 I+EGN+GLM+A+ +F+P + R +YA WI+ I I+ R V++ R+L Sbjct: 127 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMV-RELNQI 185 Query: 152 LRS-------HKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDEDD 204 LR+ ++G D A E +A +D EEV ++ LS +L++P D+ D Sbjct: 186 LRAKYHLEAQQRDGRD----ASAEDIAHLVDRPVEEVQDV-LALSEHAASLDTPLDN-DP 239 Query: 205 KFAPIAYLSSDNSE-PSRVIEAKQYDRLQSEGLEAALSKLDERSRRIVEARW-LANDDGS 262 + + + L S E P E+++ L E L++ L E+ R +V R+ L NDD S Sbjct: 240 QASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKS----LSEKQRVVVARRFGLDNDDPS 295 Query: 263 GATLHELADEFGVSAERIRQIEAVALKKMK 292 TL +LA E G++ ER+RQ++ AL K+K Sbjct: 296 --TLEQLASEMGITRERVRQVQQEALIKLK 323 >gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 850 Score = 90.1 bits (222), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 78/255 (30%), Positives = 128/255 (50%), Gaps = 25/255 (9%) Query: 52 RDLREKND-LGAAQK--------MVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKA 102 +DLR N +GA +K M ++LRLV+SIA+ Y GL DLIQEGNIGLMKA Sbjct: 592 QDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 651 Query: 103 VKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAM 162 V +F+ + + +YA WI+ I I R +++ + N S + + Sbjct: 652 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ----IL 707 Query: 163 TPAQVEALAKTLDVKR---EEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSE- 218 E TL +K E+ I +++ I++E+P D+DD + DN+ Sbjct: 708 QETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSH--LGDFIEDNNTL 765 Query: 219 -PSRVIEAKQYDRLQSEGLEAALSKLDERSRRIVEARWLANDDGSGATLHELADEFGVSA 277 P+ +A + +++ ++ L L R +++ R+ + + TL E+ +F V+ Sbjct: 766 APA---DAALHASMRN-VVKDILDSLTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVTR 820 Query: 278 ERIRQIEAVALKKMK 292 ERIRQIEA AL+K++ Sbjct: 821 ERIRQIEAKALRKLR 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 0.315 0.130 0.356 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: 857,724 Number of extensions: 33776 Number of successful extensions: 127 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 124 Number of HSP's successfully gapped: 3 Length of query: 299 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 214 Effective length of database: 1,217,395 Effective search space: 260522530 Effective search space used: 260522530 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: 130 (54.7 bits)