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/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 ... 600 e-173 gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38... 112 3e-26 gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ... 90 3e-19 >gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 600 bits (1546), Expect = e-173, Method: Compositional matrix adjust. Identities = 294/299 (98%), Positives = 297/299 (99%) Query: 1 MKTASAHTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTQEEEVKLARDLREKNDL 60 MKTASA TALMPAESNALALGFSGSLGNIDAYISAVNRLPMLT EEEVKLARDLREKNDL Sbjct: 1 MKTASAQTALMPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDL 60 Query: 61 GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH 120 GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH Sbjct: 61 GAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMH 120 Query: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE Sbjct: 121 WIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREE 180 Query: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNAEPTRVIEAKQYDRLQSEGLEAAL 240 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDN+EPTRVIEAKQYDRLQSEGLEAAL Sbjct: 181 VIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAAL 240 Query: 241 SKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTALQAYS 299 SKLD+RSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKT+LQAYS Sbjct: 241 SKLDERSRRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQAYS 299 >gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 112 bits (281), Expect = 3e-26, Method: Compositional matrix adjust. Identities = 90/272 (33%), Positives = 145/272 (53%), Gaps = 21/272 (7%) Query: 32 YISAVNRLPMLTQEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 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 KFAPIAYLSSDNAE-PTRVIEAKQYDRLQSEGLEAALSKLDDRSRRIVEARWLANDDGSG 263 + + + L S E P E+++ L E L++ K +R+V AR D+ Sbjct: 240 QASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEK-----QRVVVARRFGLDNDDP 294 Query: 264 ATLHELADEFGVSAERIRQIEAVALKKMKTAL 295 +TL +LA E G++ ER+RQ++ AL K+K L Sbjct: 295 STLEQLASEMGITRERVRQVQQEALIKLKRLL 326 >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 = 3e-19, Method: Compositional matrix adjust. Identities = 78/256 (30%), Positives = 123/256 (48%), Gaps = 27/256 (10%) 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---EEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDN--- 216 E TL +K E+ I +++ I++E+P D+DD + DN Sbjct: 708 QETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSH--LGDFIEDNNTL 765 Query: 217 AEPTRVIEAKQYDRLQSEGLEAALSKLDDRSRRIVEARWLANDDGSGATLHELADEFGVS 276 A + A + ++ L L R +++ R+ + + TL E+ +F V+ Sbjct: 766 APADAALHASMRNVVKD-----ILDSLTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVT 819 Query: 277 AERIRQIEAVALKKMK 292 ERIRQIEA AL+K++ Sbjct: 820 RERIRQIEAKALRKLR 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 0.316 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: 4735 Number of Hits to DB: 871,703 Number of extensions: 34356 Number of successful extensions: 133 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 130 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)