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= 0001.0732.p (850 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 ... 1453 0.0 gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38... 191 3e-49 gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor ... 88 2e-18 gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase... 71 5e-13 >gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 850 Score = 1453 bits (3761), Expect = 0.0, Method: Compositional matrix adjust. Identities = 828/850 (97%), Positives = 833/850 (98%) Query: 1 MANAMKKPAKTPAASAKSSKTATAVKSTAVVKTTKAVAAKSPVKATVKTVAPVKPTAKTA 60 MANAMKKPAKTPAAS KSSKT TA K TA + TKAVAAKSPVK T K VK TAKTA Sbjct: 1 MANAMKKPAKTPAASTKSSKTVTAAKPTAAARPTKAVAAKSPVKGTAKAADTVKTTAKTA 60 Query: 61 AAATPKKAAVKTAAAKPARAAAPKATATPANKLPQAAEQAVSVKATKTSVTTKKPETKTA 120 AAATPKK AVKT AAKPARAAAPKATATPANKLPQAAEQAVSVKATKTSVTTKKPETKTA Sbjct: 61 AAATPKKTAVKTTAAKPARAAAPKATATPANKLPQAAEQAVSVKATKTSVTTKKPETKTA 120 Query: 121 KTTKAAKVEGKDVSATAASSVSQTTDAAALAAIDTSGYVLPSVKVPGRRGRKPKEFQPES 180 KTTKAAKVEGKDVSATAASSVSQTTDAAALAAIDTSGYVLPSVKVPGRRGRKPKEFQPES Sbjct: 121 KTTKAAKVEGKDVSATAASSVSQTTDAAALAAIDTSGYVLPSVKVPGRRGRKPKEFQPES 180 Query: 181 DEVAALNTIERTELKAADKAKAKDRKAKEKALLKDAFSSDTEASEEELERRRQKLKTLIK 240 DEVAALNTIERTELKAADKAKAKDRKAKEKALLKDAFSSDTEASEEELERRRQKLKTLIK Sbjct: 181 DEVAALNTIERTELKAADKAKAKDRKAKEKALLKDAFSSDTEASEEELERRRQKLKTLIK 240 Query: 241 LGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMGISVYEHAPDAETLLLSDNVANV 300 LGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMGISVYEHAPDAETLLLSDNVANV Sbjct: 241 LGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMGISVYEHAPDAETLLLSDNVANV 300 Query: 301 ASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKDM 360 ASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKDM Sbjct: 301 ASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKDM 360 Query: 361 IQAISACPTTIAEILAAAERISNDEIKVDEIVDGLVDPNESEQQVEAAASDSDEDDEEEE 420 IQAISACPTTIAEILAAAERIS DEIKVDEIVDGLVDPNESEQQVEAA+SDSDEDDE+EE Sbjct: 361 IQAISACPTTIAEILAAAERISKDEIKVDEIVDGLVDPNESEQQVEAASSDSDEDDEDEE 420 Query: 421 EEEEDEEEEENESSGSGAAGFSAEQLEQLKRDALGKFAVIGTQFENMRKAFEKEGYNSKP 480 EEEEDEEEEE+ES+GSGAAGFSAEQLEQLKRDALGKFAVIGTQFENMRKAFEKEGYNSKP Sbjct: 421 EEEEDEEEEESESTGSGAAGFSAEQLEQLKRDALGKFAVIGTQFENMRKAFEKEGYNSKP 480 Query: 481 YVKAQEIISNELLGIRFTAKIVEKLCDTLRAQVDEVRTVERQILDVAVNKCNMPRAHFIK 540 YVKAQEIISNELLGIRFTAKIVEKLCDTLRAQVDEVRTVERQILDVAVNKCNMPRAHFIK Sbjct: 481 YVKAQEIISNELLGIRFTAKIVEKLCDTLRAQVDEVRTVERQILDVAVNKCNMPRAHFIK 540 Query: 541 VFPGNEVNLDWVDGEVAANHDYSAVLSRNVPAIKELQQKLIDLQARVVLPLQDLRAINKK 600 VFPGNEVNLDWVDGEVAANHDYSAVLSRNVPAIKELQQKLIDLQARVVLPLQDLRAINKK Sbjct: 541 VFPGNEVNLDWVDGEVAANHDYSAVLSRNVPAIKELQQKLIDLQARVVLPLQDLRAINKK 600 Query: 601 MGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 660 MGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG Sbjct: 601 MGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 660 Query: 661 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLA 720 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLA Sbjct: 661 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLA 720 Query: 721 IKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVV 780 IKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVV Sbjct: 721 IKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVV 780 Query: 781 KDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 840 KDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS Sbjct: 781 KDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 840 Query: 841 DKLKSFLEGN 850 DKLKSFLEGN Sbjct: 841 DKLKSFLEGN 850 >gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 191 bits (484), Expect = 3e-49, Method: Compositional matrix adjust. Identities = 91/228 (39%), Positives = 151/228 (66%), Gaps = 2/228 (0%) Query: 610 MAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 669 +A+++M E NLRLV+SIAK Y NRG+ LDLI+EGN+GLM+A+DKFE RG++FSTYATW Sbjct: 96 VARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATW 155 Query: 670 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLAIKMEMPE 727 WIRQ+I R+I +QART+R+PVHM+ +N++ R + Q G + +A ++ P Sbjct: 156 WIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHLVDRPV 215 Query: 728 DKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSL 787 ++++ ++ +++ S++TP+ +D + L D + P A M ++++ L SL Sbjct: 216 EEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSL 275 Query: 788 TPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835 + ++ 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 = 88.2 bits (217), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 78/255 (30%), Positives = 127/255 (49%), Gaps = 25/255 (9%) Query: 592 QDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 651 +DLR N +GA +K M ++LRLV+SIA+ Y GL DLIQEGNIGLMKA Sbjct: 52 RDLREKND-LGAAQK--------MVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKA 102 Query: 652 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ----IL 707 V +F+ + + +YA WI+ I I R +++ + N S + + Sbjct: 103 VKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAM 162 Query: 708 QETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSH--LGDFIEDNNTL 765 E TL +K E+ I +++ I++E+P D+DD + DN+ Sbjct: 163 TPAQVEALAKTLDVK---REEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSE- 218 Query: 766 APA---DAALHASMRN-VVKDILDSLTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVTR 820 P +A + +++ ++ L L R +++ R+ + + TL E+ +F V+ Sbjct: 219 -PTRVIEAKQYDRLQSEGLEAALSKLDERSRRIVEARWLANDDGSGATLHELADEFGVSA 277 Query: 821 ERIRQIEAKALRKLR 835 ERIRQIEA AL+K++ Sbjct: 278 ERIRQIEAVALKKMK 292 >gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase sigma factor [Herbaspirillum seropedicae SmR1] Length = 244 Score = 70.9 bits (172), Expect = 5e-13, Method: Composition-based stats. Identities = 60/236 (25%), Positives = 114/236 (48%), Gaps = 15/236 (6%) Query: 607 KARMAKREMTEANLRLVISIAKKYTNR---GLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 663 K + K ++ E + LV +A + + ++ DLIQ G +GL+ AV+++E G +F Sbjct: 5 KGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETHGAQF 64 Query: 664 STYATWWIRQAITRSIADQARTIR-IPVHMIETINKMNRISRQILQETGAEPDPATLAIK 722 TYA IR A+ D+ R+ +P + + K+ + +LQ+ G +P A LA Sbjct: 65 ETYAVQRIRGAML----DELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH 120 Query: 723 MEMP-EDKIRKIMKIAKEPISMETPIGDDD--DSHLGDFIEDNNTLAPADAALHASMRNV 779 M++ ED + + + DDD H D + +++ P ++ R Sbjct: 121 MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA 180 Query: 780 VKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835 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 0.126 0.334 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: 1,743,826 Number of extensions: 61389 Number of successful extensions: 188 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 184 Number of HSP's successfully gapped: 5 Length of query: 850 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 757 Effective length of database: 1,179,515 Effective search space: 892892855 Effective search space used: 892892855 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)