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= 0032.0037.p (856 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor ... 1285 0.0 gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38... 190 4e-49 gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ... 88 3e-18 gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase... 70 5e-13 >gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 850 Score = 1285 bits (3325), Expect = 0.0, Method: Compositional matrix adjust. Identities = 717/860 (83%), Positives = 757/860 (88%), Gaps = 18/860 (2%) Query: 1 MKKTAKTPTPSAKNTKPAVKPASKSTPVSRSVPKKTAAAKPTGKATA-TAVRATSSPAKA 59 MKK AKTP S K++K + + K TAAA+PT A + V+ T+ A Sbjct: 5 MKKPAKTPAASTKSSK------------TVTAAKPTAAARPTKAVAAKSPVKGTAKAADT 52 Query: 60 ASTASAKKSSAKPASTAVRAAVPVVAKATTKAAATPTKKNLSQASIKPASVQ-SKASVTT 118 T + ++A P TAV+ A+A A L QA+ + SV+ +K SVTT Sbjct: 53 VKTTAKTAAAATPKKTAVKTTAAKPARAAAPKATATPANKLPQAAEQAVSVKATKTSVTT 112 Query: 119 KKPEPKTAKPAAKAAVKSEVKDVSVMIAPGVSQTTDAAALAAIDTSGYILPSVKVPGRRG 178 KKPE KTAK A V E KDVS A VSQTTDAAALAAIDTSGY+LPSVKVPGRRG Sbjct: 113 KKPETKTAKTTKAAKV--EGKDVSATAASSVSQTTDAAALAAIDTSGYVLPSVKVPGRRG 170 Query: 179 RKPKEFQPENDEIAALNAVERAELKAVDKAKAKDRKAKEKALLKDAFSSDTEATEEELER 238 RKPKEFQPE+DE+AALN +ER ELKA DKAKAKDRKAKEKALLKDAFSSDTEA+EEELER Sbjct: 171 RKPKEFQPESDEVAALNTIERTELKAADKAKAKDRKAKEKALLKDAFSSDTEASEEELER 230 Query: 239 RRQKLKTLIKQGKERGYLTFSEINDHLPENIVDPEAIEGIIGTFNDMGISVYEHAPDAET 298 RRQKLKTLIK GKERG+LTFSEINDHLPENIVDPEAIEGIIGTF+DMGISVYEHAPDAET Sbjct: 231 RRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMGISVYEHAPDAET 290 Query: 299 LLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIA 358 LLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIA Sbjct: 291 LLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIA 350 Query: 359 KRIEDGLKDMIQAISACPTTIAEILVAADKISKDEIKVDEIVDGLVDMSEGEVVV-AAAS 417 KRIEDGLKDMIQAISACPTTIAEIL AA++ISKDEIKVDEIVDGLVD +E E V AA+S Sbjct: 351 KRIEDGLKDMIQAISACPTTIAEILAAAERISKDEIKVDEIVDGLVDPNESEQQVEAASS 410 Query: 418 DEEDEEDDEEDGEEEEEEGESSNTG-GAAGFSAEQLEQLKRDALGKFATISTQFDNMRKA 476 D +++++DEE+ EE+EEE ES +TG GAAGFSAEQLEQLKRDALGKFA I TQF+NMRKA Sbjct: 411 DSDEDDEDEEEEEEDEEEEESESTGSGAAGFSAEQLEQLKRDALGKFAVIGTQFENMRKA 470 Query: 477 FEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLRAQVDEVRQIERQILDVAVNK 536 FEKEGYNSKPYVKAQEIISNELLGIRFTAK+VEKLCDTLRAQVDEVR +ERQILDVAVNK Sbjct: 471 FEKEGYNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLRAQVDEVRTVERQILDVAVNK 530 Query: 537 CNMPRAHFIKVFPGNESNLDWVDGEVNGNHAYSVVLARNVPAIKELQQKLIDLQARVVLP 596 CNMPRAHFIKVFPGNE NLDWVDGEV NH YS VL+RNVPAIKELQQKLIDLQARVVLP Sbjct: 531 CNMPRAHFIKVFPGNEVNLDWVDGEVAANHDYSAVLSRNVPAIKELQQKLIDLQARVVLP 590 Query: 597 LPDLRGINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 656 L DLR INKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK Sbjct: 591 LQDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 650 Query: 657 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 716 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET Sbjct: 651 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 710 Query: 717 GAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADA 776 GAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADA Sbjct: 711 GAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADA 770 Query: 777 ALHASMRGVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 836 ALHASMR VVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA Sbjct: 771 ALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 830 Query: 837 LRKLRHPSRSDKLKSFLEGN 856 LRKLRHPSRSDKLKSFLEGN Sbjct: 831 LRKLRHPSRSDKLKSFLEGN 850 >gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 190 bits (483), Expect = 4e-49, Method: Compositional matrix adjust. Identities = 91/228 (39%), Positives = 151/228 (66%), Gaps = 2/228 (0%) Query: 616 MAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 675 +A+++M E NLRLV+SIAK Y NRG+ LDLI+EGN+GLM+A+DKFE RG++FSTYATW Sbjct: 96 VARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATW 155 Query: 676 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLAIKMEMPE 733 WIRQ+I R+I +QART+R+PVHM+ +N++ R + Q G + +A ++ P Sbjct: 156 WIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHLVDRPV 215 Query: 734 DKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRGVVKDILDSL 793 ++++ ++ +++ S++TP+ +D + L D + P A M ++++ L SL Sbjct: 216 EEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSL 275 Query: 794 TPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 841 + ++ V+ RFG++ TLE++ + +TRER+RQ++ +AL KL+ Sbjct: 276 SEKQRVVVARRFGLDNDDPSTLEQLASEMGITRERVRQVQQEALIKLK 323 >gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 87.8 bits (216), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 75/244 (30%), Positives = 119/244 (48%), Gaps = 20/244 (8%) Query: 611 EKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 670 EK A ++M ++LRLV+SIA+ Y GL DLIQEGNIGLMKAV +F+ + + Sbjct: 56 EKNDLGAAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLV 115 Query: 671 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ----ILQETGAEPDPATLA 726 +YA WI+ I I R +++ + N S + + E TL Sbjct: 116 SYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLD 175 Query: 727 IKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSH--LGDFIEDNN---TLAPADAALHAS 781 +K E+ I +++ I++E+P D+DD + DN+ + A Sbjct: 176 VK---REEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQ 232 Query: 782 MRGVVKDILDSLTPREAKVLRMRFGIEMSTDH----TLEEVGKQFDVTRERIRQIEAKAL 837 G ++ L L R +++ R+ ++ D TL E+ +F V+ ERIRQIEA AL Sbjct: 233 SEG-LEAALSKLDERSRRIVEARW---LANDDGSGATLHELADEFGVSAERIRQIEAVAL 288 Query: 838 RKLR 841 +K++ Sbjct: 289 KKMK 292 >gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase sigma factor [Herbaspirillum seropedicae SmR1] Length = 244 Score = 70.5 bits (171), Expect = 5e-13, Method: Composition-based stats. Identities = 60/236 (25%), Positives = 114/236 (48%), Gaps = 15/236 (6%) Query: 613 KARMAKREMTEANLRLVISIAKKYTNR---GLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 669 K + K ++ E + LV +A + + ++ DLIQ G +GL+ AV+++E G +F Sbjct: 5 KGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETHGAQF 64 Query: 670 STYATWWIRQAITRSIADQARTIR-IPVHMIETINKMNRISRQILQETGAEPDPATLAIK 728 TYA IR A+ D+ R+ +P + + K+ + +LQ+ G +P A LA Sbjct: 65 ETYAVQRIRGAML----DELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH 120 Query: 729 MEMP-EDKIRKIMKIAKEPISMETPIGDDD--DSHLGDFIEDNNTLAPADAALHASMRGV 785 M++ ED + + + DDD H D + +++ P ++ R Sbjct: 121 MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA 180 Query: 786 VKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 841 V D + +L RE ++ + + EM+ L+E+G V+ R+ Q+ ++A+ ++R Sbjct: 181 VVDSIKALPEREQILMALYYEQEMN----LKEIGAVMGVSESRVCQLHSQAISRMR 232 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 0.311 0.127 0.340 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: 1,844,128 Number of extensions: 65080 Number of successful extensions: 196 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 196 Number of HSP's successfully gapped: 4 Length of query: 856 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 763 Effective length of database: 1,179,515 Effective search space: 899969945 Effective search space used: 899969945 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 135 (56.6 bits)