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= 0098.0035.p (317 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... 530 e-152 gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ... 186 2e-48 gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ... 117 2e-27 >gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 530 bits (1366), Expect = e-152, Method: Compositional matrix adjust. Identities = 261/317 (82%), Positives = 292/317 (92%), Gaps = 2/317 (0%) Query: 1 LETVDDLEVIDEGEAAEGEEEVVVAVEGVEELKKVLAAELSTDTTQHYLNQIGTRPLLTA 60 ++ +D+ EVID G+A E +E A EGV+ELKKVLAAELSTDTTQHYLN+IG +PLLTA Sbjct: 23 VDEIDEPEVID-GDAGEEVQEAAPA-EGVDELKKVLAAELSTDTTQHYLNKIGAKPLLTA 80 Query: 61 PEELYFATLAKQGDFASRQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDK 120 EEL+FAT AK G+F +RQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDK Sbjct: 81 AEELHFATQAKAGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDK 140 Query: 121 FEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQHHDGR 180 FEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQ DGR Sbjct: 141 FEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGR 200 Query: 181 DATAEDIAHLVDRPVEDVQDVLALSEHAASLDTPLDNDPQASLIDLLPGSLDESPDSKAE 240 DA+AEDIAHLVDRPVE+VQDVLALSEHAASLDTPLDNDPQASL+DLLP +++E PD++AE Sbjct: 201 DASAEDIAHLVDRPVEEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAE 260 Query: 241 YHEVSILIRDWLRNLPDKQRIVITRRFGLDNDDPSTLEQLASEMGITRERVRQVQQEALI 300 E+++LIR+WL++L +KQR+V+ RRFGLDNDDPSTLEQLASEMGITRERVRQVQQEALI Sbjct: 261 SQEMAVLIREWLKSLSEKQRVVVARRFGLDNDDPSTLEQLASEMGITRERVRQVQQEALI 320 Query: 301 KLKRSLLARGVGKDALF 317 KLKR L +RGVG+DALF Sbjct: 321 KLKRLLTSRGVGRDALF 337 >gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 850 Score = 186 bits (472), Expect = 2e-48, Method: Compositional matrix adjust. Identities = 88/227 (38%), Positives = 150/227 (66%), Gaps = 2/227 (0%) Query: 77 SRQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWW 136 ++++M E NLRLV+SIAK Y NRG+ LDLI+EGN+GLM+A+DKFE RG++FSTYATWW Sbjct: 611 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 670 Query: 137 IRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQHHDGRDATAEDIAHLVDRPVE 196 IRQ+I R+I +QART+R+PVHM+ +N++ R + G + +A ++ P + Sbjct: 671 IRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLAIKMEMPED 728 Query: 197 DVQDVLALSEHAASLDTPLDNDPQASLIDLLPGSLDESPDSKAEYHEVSILIRDWLRNLP 256 ++ ++ +++ S++TP+ +D + L D + + +P A + + +++D L +L Sbjct: 729 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLT 788 Query: 257 DKQRIVITRRFGLDNDDPSTLEQLASEMGITRERVRQVQQEALIKLK 303 ++ V+ RFG++ TLE++ + +TRER+RQ++ +AL KL+ Sbjct: 789 PREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835 >gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 117 bits (292), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 94/275 (34%), Positives = 148/275 (53%), Gaps = 23/275 (8%) Query: 48 YLNQIGTRPLLTAPEELYFAT-LAKQGDFASRQKMIEHNLRLVVSIAKHYINRGVALLDL 106 Y++ + P+LT EE+ A L ++ D + QKM+ +LRLVVSIA+ Y+ G+ DL Sbjct: 32 YISAVNRLPMLTHEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADL 91 Query: 107 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMV-RELNQI 165 I+EGN+GLM+A+ +F+P + R +YA WI+ I I+ R V++ R+L Sbjct: 92 IQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFN 151 Query: 166 LRAKYHLEAQHHDGRDATA----EDIAHLVDRPVEDVQDV-LALSEHAASLDTPLDN-DP 219 LR+ H +G DA E +A +D E+V ++ LS +L++P D+ D Sbjct: 152 LRS-------HKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDEDD 204 Query: 220 QASLIDLLPGSLDESPDSKAEYHEVSIL----IRDWLRNLPDKQRIVITRRFGLDNDDPS 275 + + I L S + P E + L + L L ++ R ++ R+ L NDD S Sbjct: 205 KFAPIAYL-SSDNSEPTRVIEAKQYDRLQSEGLEAALSKLDERSRRIVEARW-LANDDGS 262 Query: 276 --TLEQLASEMGITRERVRQVQQEALIKLKRSLLA 308 TL +LA E G++ ER+RQ++ AL K+K SL A Sbjct: 263 GATLHELADEFGVSAERIRQIEAVALKKMKTSLQA 297 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 0.317 0.134 0.375 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: 896,910 Number of extensions: 36615 Number of successful extensions: 110 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 108 Number of HSP's successfully gapped: 3 Length of query: 317 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 232 Effective length of database: 1,217,395 Effective search space: 282435640 Effective search space used: 282435640 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 (21.7 bits) S2: 130 (54.7 bits)