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= 0027.0166.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|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ... 587 e-169 gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38... 113 2e-26 gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ... 89 4e-19 >gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 587 bits (1514), Expect = e-169, Method: Compositional matrix adjust. Identities = 287/289 (99%), Positives = 289/289 (100%) Query: 1 MPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEEIKLARDLREKNDLGAAQKMVLSH 60 MPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEE+KLARDLREKNDLGAAQKMVLSH Sbjct: 11 MPAESNALALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDLGAAQKMVLSH 70 Query: 61 LRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYI 120 LRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYI Sbjct: 71 LRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYI 130 Query: 121 LKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSG 180 LKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSG Sbjct: 131 LKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSG 190 Query: 181 RDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAALSKLDDRSRRI 240 RDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAALSKLD+RSRRI Sbjct: 191 RDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAALSKLDERSRRI 250 Query: 241 VEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQAYS 289 VEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQAYS Sbjct: 251 VEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQAYS 299 >gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 113 bits (283), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 89/269 (33%), Positives = 144/269 (53%), Gaps = 21/269 (7%) Query: 22 YISAVNRLPMLTHEEEIKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 81 Y++ + P+LT EE+ A + + A QKM+ +LRLVVSIA+ Y+ G+ DL Sbjct: 68 YLNKIGAKPLLTAAEELHFATQAK-AGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDL 126 Query: 82 IQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFN 141 I+EGN+GLM+A+ +F+P + R +YA WI+ I I+ R V++ R+L Sbjct: 127 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMV-RELNQI 185 Query: 142 LRS-------HKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDEDD 194 LR+ ++G D A E +A +D EEV ++ LS +L++P D+ D Sbjct: 186 LRAKYHLEAQQRDGRD----ASAEDIAHLVDRPVEEVQDV-LALSEHAASLDTPLDN-DP 239 Query: 195 KFAPIAYLSSDNSE-PTRVIEAKQYDRLQSEGLEAALSKLDDRSRRIVEARWLANDDGSG 253 + + + L S E P E+++ L E L++ K +R+V AR D+ Sbjct: 240 QASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEK-----QRVVVARRFGLDNDDP 294 Query: 254 ATLHELADEFGVSAERIRQIEAVALKKMK 282 +TL +LA E G++ ER+RQ++ AL K+K Sbjct: 295 STLEQLASEMGITRERVRQVQQEALIKLK 323 >gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 850 Score = 89.0 bits (219), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 77/253 (30%), Positives = 126/253 (49%), Gaps = 21/253 (8%) Query: 42 RDLREKND-LGAAQK--------MVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKA 92 +DLR N +GA +K M ++LRLV+SIA+ Y GL DLIQEGNIGLMKA Sbjct: 592 QDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 651 Query: 93 VKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAM 152 V +F+ + + +YA WI+ I I R +++ + N S + + Sbjct: 652 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ----IL 707 Query: 153 TPAQVEALAKTLDVKR---EEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEP 209 E TL +K E+ I +++ I++E+P D+DD + DN+ Sbjct: 708 QETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSH--LGDFIEDNNTL 765 Query: 210 TRVIEAKQYDRLQSEGLEAALSKLDDRSRRIVEARWLANDDGSGATLHELADEFGVSAER 269 +A + +++ ++ L L R +++ R+ + + TL E+ +F V+ ER Sbjct: 766 APA-DAALHASMRN-VVKDILDSLTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVTRER 822 Query: 270 IRQIEAVALKKMK 282 IRQIEA AL+K++ Sbjct: 823 IRQIEAKALRKLR 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 0.131 0.363 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: 848,260 Number of extensions: 33329 Number of successful extensions: 117 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 114 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 130 (54.7 bits)