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= 0001.2932.p (319 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38... 625 e-180 gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ... 190 2e-49 gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ... 114 1e-26 >gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 625 bits (1611), Expect = e-180, Method: Compositional matrix adjust. Identities = 310/319 (97%), Positives = 313/319 (98%) Query: 1 MDDPVDEIDEPEVIDGEAAGEPQEAAPAEGVDELKKVLAAELSTDTTQHYLNKIGAKPLL 60 +DD VDEIDEPEVIDG+A E QEAAPAEGVDELKKVLAAELSTDTTQHYLNKIGAKPLL Sbjct: 19 LDDSVDEIDEPEVIDGDAGEEVQEAAPAEGVDELKKVLAAELSTDTTQHYLNKIGAKPLL 78 Query: 61 TAAEELHFATQAKAGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAI 120 TAAEELHFATQAKAGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAI Sbjct: 79 TAAEELHFATQAKAGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAI 138 Query: 121 DKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRD 180 DKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRD Sbjct: 139 DKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRD 198 Query: 181 GRDASAEDIAHLVDRPVEEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTR 240 GRDASAEDIAHLVDRPVEEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTR Sbjct: 199 GRDASAEDIAHLVDRPVEEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTR 258 Query: 241 AESQEMAVLIREWLKSLSEKQRVVVARRFGLDNDDPSTLEQLAGEMGITRERVRQVQQEA 300 AESQEMAVLIREWLKSLSEKQRVVVARRFGLDNDDPSTLEQLA EMGITRERVRQVQQEA Sbjct: 259 AESQEMAVLIREWLKSLSEKQRVVVARRFGLDNDDPSTLEQLASEMGITRERVRQVQQEA 318 Query: 301 LVKLKRLLASRGVGRDALF 319 L+KLKRLL SRGVGRDALF Sbjct: 319 LIKLKRLLTSRGVGRDALF 337 >gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 850 Score = 190 bits (482), Expect = 2e-49, Method: Compositional matrix adjust. Identities = 91/228 (39%), Positives = 151/228 (66%), Gaps = 2/228 (0%) Query: 78 VARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATW 137 +A+++M E NLRLV+SIAK Y NRG+ LDLI+EGN+GLM+A+DKFE RG++FSTYATW Sbjct: 610 MAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 669 Query: 138 WIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHLVDRPV 197 WIRQ+I R+I +QART+R+PVHM+ +N++ R + Q G + +A ++ P Sbjct: 670 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLAIKMEMPE 727 Query: 198 EEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSL 257 ++++ ++ +++ S++TP+ +D + L D + P A M ++++ L SL Sbjct: 728 DKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSL 787 Query: 258 SEKQRVVVARRFGLDNDDPSTLEQLAGEMGITRERVRQVQQEALVKLK 305 + ++ V+ RFG++ TLE++ + +TRER+RQ++ +AL KL+ Sbjct: 788 TPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835 >gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 114 bits (284), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 94/273 (34%), Positives = 148/273 (54%), Gaps = 23/273 (8%) Query: 50 YLNKIGAKPLLTAAEELHFATQAK-AGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDL 108 Y++ + P+LT EE+ A + + A QKM+ +LRLVVSIA+ Y+ G+ DL Sbjct: 32 YISAVNRLPMLTHEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 91 Query: 109 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMV-RELNQI 167 I+EGN+GLM+A+ +F+P + R +YA WI+ I I+ R V++ R+L Sbjct: 92 IQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFN 151 Query: 168 LRAKYHLEAQQRDGRD----ASAEDIAHLVDRPVEEVQDV-LALSEHAASLDTPLDN-DP 221 LR+ ++G D A E +A +D EEV ++ LS +L++P D+ D Sbjct: 152 LRS-------HKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDEDD 204 Query: 222 QASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKS----LSEKQRVVVARRFGLDNDDPS 277 + + + L S E P E+++ L E L++ L E+ R +V R+ L NDD S Sbjct: 205 KFAPIAYLSSDNSE-PTRVIEAKQYDRLQSEGLEAALSKLDERSRRIVEARW-LANDDGS 262 Query: 278 --TLEQLAGEMGITRERVRQVQQEALVKLKRLL 308 TL +LA E G++ ER+RQ++ AL K+K L Sbjct: 263 GATLHELADEFGVSAERIRQIEAVALKKMKTSL 295 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 0.132 0.367 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: 850,536 Number of extensions: 34467 Number of successful extensions: 133 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 132 Number of HSP's successfully gapped: 3 Length of query: 319 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 234 Effective length of database: 1,217,395 Effective search space: 284870430 Effective search space used: 284870430 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)