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/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA... 1285 0.0 gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor Rpo... 194 1e-50 gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas a... 88 1e-18 gi|134094539|ref|YP_001099614.1| sigma F (sigma 28) factor of RN... 61 2e-10 >gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA polymerase [Herminiimonas arsenicoxydans] Length = 858 Score = 1285 bits (3324), Expect = 0.0, Method: Compositional matrix adjust. Identities = 684/855 (80%), Positives = 739/855 (86%), Gaps = 27/855 (3%) Query: 1 MANAMKKPAKTPAASAKSSKTATAVKSTAVVKTTKAVAAKSPVKATVKTVAPVKPTAKTA 60 MANAMKKPAK +A ++TA A K+TK VA K ++ K V+ ++ Sbjct: 26 MANAMKKPAKNQILAASKAETAAA-------KSTKPVAKKVASQSAGKAVS----SSNVK 74 Query: 61 AAATPKKAAVKTAAAKPARAAAPKATATPANKLPQAAEQAVSVKATKTSVTTKKPETKTA 120 A +P KA KTA A A A P++K+ A + VSV+ +K VT KK E K+ Sbjct: 75 AVKSPTKAPTKTATL-----VAKSAAAKPSSKV---AAKPVSVQ-SKAPVTNKKSEVKS- 124 Query: 121 KTTKAAKVEGK-----DVSATAASSVSQTTDAAALAAIDTSGYVLPSVKVPGRRGRKPKE 175 T+K+AKVE K V+ +VSQTTDAA LAAIDTSGY+LPS+KVPGRRGRKPKE Sbjct: 125 -TSKSAKVEPKVESRPGVNVMITPTVSQTTDAATLAAIDTSGYILPSIKVPGRRGRKPKE 183 Query: 176 FQPESDEVAALNTIERTELKAADKAKAKDRKAKEKALLKDAFSSDTEASEEELERRRQKL 235 FQPE+DEVAALN +ER ELKA DKAKAKDRKAKEKALLKDAFS+DTEASEEELE RRQKL Sbjct: 184 FQPENDEVAALNAVERAELKAVDKAKAKDRKAKEKALLKDAFSNDTEASEEELEARRQKL 243 Query: 236 KTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMGISVYEHAPDAETLLLSD 295 KTLIK GKERGFLT++EINDHLPENI+DPEAIEGIIGTF+DMGI+VYE APDAETLLLSD Sbjct: 244 KTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIGTFNDMGIAVYEQAPDAETLLLSD 303 Query: 296 NVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIED 355 NVA VASDD+AEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEI+IAKRIED Sbjct: 304 NVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIDIAKRIED 363 Query: 356 GLKDMIQAISACPTTIAEILAAAERISNDEIKVDEIVDGLVDPNESEQQVEAAASDSDED 415 GL+DMIQAISACPTTIAEI+AAAERIS DE K+DEIVDGLVD N SE + A + D Sbjct: 364 GLRDMIQAISACPTTIAEIMAAAERISKDEAKIDEIVDGLVDMNASEPVIAPPAPAAASD 423 Query: 416 DEEEEEEEEDEEEEENESSGSGAAGFSAEQLEQLKRDALGKFAVIGTQFENMRKAFEKEG 475 +EEEEEEEE+ EEEE + SGAAGFS+EQLEQLKRD+L KF+ I QF+ MRKAFEKEG Sbjct: 424 EEEEEEEEEEAEEEEETPAASGAAGFSSEQLEQLKRDSLAKFSTIAMQFDKMRKAFEKEG 483 Query: 476 YNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLRAQVDEVRTVERQILDVAVNKCNMPR 535 YNSKPYVKAQEIISNELLGIRFTAK+VEKLCDTLR QVDEVR +E+QILD+AVN+C MPR Sbjct: 484 YNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLRGQVDEVRQIEKQILDIAVNRCEMPR 543 Query: 536 AHFIKVFPGNEVNLDWVDGEVAANHDYSAVLSRNVPAIKELQQKLIDLQARVVLPLQDLR 595 HFIKVFPGNE NLDWVDGEV NH YS VL+RNVPA+KELQQKLIDLQARVVLPL DLR Sbjct: 544 NHFIKVFPGNETNLDWVDGEVEGNHPYSIVLARNVPAVKELQQKLIDLQARVVLPLPDLR 603 Query: 596 AINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 655 AIN+KM AGE KAR AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF Sbjct: 604 AINRKMAAGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 663 Query: 656 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPD 715 EYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPD Sbjct: 664 EYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPD 723 Query: 716 PATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHAS 775 PATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHAS Sbjct: 724 PATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHAS 783 Query: 776 MRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835 MR VVKD+LDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR Sbjct: 784 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 843 Query: 836 HPSRSDKLKSFLEGN 850 HPSRSDKLKSFLEGN Sbjct: 844 HPSRSDKLKSFLEGN 858 >gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor RpoS [Herminiimonas arsenicoxydans] Length = 344 Score = 194 bits (493), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 96/227 (42%), Positives = 148/227 (65%), Gaps = 2/227 (0%) Query: 611 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 670 A+++M E NLRLV+SIAK Y NRG+ LDLI+EGN+GLM+A+DKFE RG++FSTYATWW Sbjct: 104 ARQKMIEHNLRLVVSIAKHYINRGVVLLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWW 163 Query: 671 IRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLAIKMEMPED 728 IRQ+I R+I +QART+R+PVH++ +N+ R + G + +A +E + Sbjct: 164 IRQSIERAIMNQARTVRLPVHVVRELNQTLRAKFHLEAQHHDGKDATAEDIAHLVERSVE 223 Query: 729 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLT 788 ++ I+ +++ S++ P+ D S L D ++ ++ P A H M +V+D LD L+ Sbjct: 224 DVQDILALSEHASSLDAPLDGDPQSSLMDLLQGDHANDPDVLAEHQEMIVLVRDWLDKLS 283 Query: 789 PREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835 ++ V+ RFG++ TLEE+ + VTRER+RQI+ +AL KL+ Sbjct: 284 DKQRLVITRRFGLDNDDPATLEELATEMHVTRERVRQIQQEALVKLK 330 >gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas arsenicoxydans] Length = 298 Score = 88.2 bits (217), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 71/238 (29%), Positives = 117/238 (49%), Gaps = 20/238 (8%) Query: 611 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 670 A +++ ++LRLV+SIA+ Y GL DLIQEGNIGLMKAV +F+ +G + +Y+ W Sbjct: 61 AAQKLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHW 120 Query: 671 IRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAE---PDPA-----TLAIK 722 I+ + I R +++ + N S +TG + PD TL +K Sbjct: 121 IKAEMHEYILKNWRLVKVATTKAQRKLFFNLRS----HKTGLDAMTPDQVEALAKTLNVK 176 Query: 723 MEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKD 782 E+ I +++ I++E P D+DD +++ P + + Sbjct: 177 ---REEVIEMETRLSGRDIALEAPTDDEDDKFAPIAYLSSDSQEPTRVLESQRYDRLQTE 233 Query: 783 ILDS----LTPREAKVLRMRF-GIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835 L S L PR +++ R+ + + TL E+ +F V+ ERIRQIE AL+K++ Sbjct: 234 GLSSALGKLDPRSRRIVEARWLANDDGSGATLHELANEFGVSAERIRQIETVALKKMK 291 >gi|134094539|ref|YP_001099614.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late flagellar genes (class 3a and 3b operons) [Herminiimonas arsenicoxydans] Length = 216 Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 49/200 (24%), Positives = 98/200 (49%), Gaps = 11/200 (5%) Query: 639 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI-RIPVHMIETIN 697 DLIQ G IGL+ AV ++E G +F TYA IR A+ D+ R+ +P M + + Sbjct: 13 DLIQAGMIGLLDAVGRYEETHGAQFETYAVQRIRGAML----DELRSSDWMPRSMRQNMR 68 Query: 698 KMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMK--IAKEPISMETPIGDDDDSHL 755 K+ + Q+ G P+ + +A ++++ + ++ + + E +D+ H Sbjct: 69 KIEVAMNSLQQKLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHF 128 Query: 756 GDFIEDNNTLAPADAALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQ 815 D + + P ++ R+ V +++L RE ++ + + EM+ L+E+G Sbjct: 129 LDRYCTDESPDPLQNLMNTGFRSAVIAAIEALPEREKILMSLYYEQEMN----LKEIGAV 184 Query: 816 FDVTRERIRQIEAKALRKLR 835 VT R+ Q+ ++A+ ++R Sbjct: 185 MGVTESRVSQLHSQAIARMR 204 Database: BlastDatabases/690/690 Posted date: Apr 9, 2011 4:48 AM Number of letters in database: 1,000,347 Number of sequences in database: 3295 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: 3295 Number of Hits to DB: 1,087,343 Number of extensions: 38856 Number of successful extensions: 103 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 101 Number of HSP's successfully gapped: 5 Length of query: 850 Length of database: 1,000,347 Length adjustment: 90 Effective length of query: 760 Effective length of database: 703,797 Effective search space: 534885720 Effective search space used: 534885720 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: 133 (55.8 bits)