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= 0001.1028.p (234 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310552|ref|YP_003774644.1| MotA/TolQ/ExbB proton channel f... 435 e-123 gi|300309940|ref|YP_003774032.1| biopolymer transport transmembr... 99 4e-22 gi|300310025|ref|YP_003774117.1| biopolymer transport transmembr... 90 2e-19 gi|300312127|ref|YP_003776219.1| biopolymer transport transmembr... 82 4e-17 >gi|300310552|ref|YP_003774644.1| MotA/TolQ/ExbB proton channel family protein [Herbaspirillum seropedicae SmR1] Length = 234 Score = 435 bits (1118), Expect = e-123, Method: Compositional matrix adjust. Identities = 229/234 (97%), Positives = 231/234 (98%) Query: 1 MNVTQDLSFISLIANASVLVQLVMLLLLSASVTSWTYIFRKMFTIRSARVQTEEFERVFW 60 MNVTQDLSFISLIANASVLVQLVMLLLLSAS+ SWTYIFRKMFTIR+ARVQTEEFERVFW Sbjct: 1 MNVTQDLSFISLIANASVLVQLVMLLLLSASIISWTYIFRKMFTIRAARVQTEEFERVFW 60 Query: 61 SGGNLSALYQDALSNRRKAGGEGGALERIFQAGMGEFTKAKASVAARGGAVDPGLLLDGA 120 SGGNLSALYQDALSNRRKAGG GGALERIFQAGMGEFTKAKASVAARGGAVDP LLLDGA Sbjct: 61 SGGNLSALYQDALSNRRKAGGAGGALERIFQAGMGEFTKAKASVAARGGAVDPSLLLDGA 120 Query: 121 RRAMRAAYQREMDALESHLAFLASVGSVSPYVGLFGTVWGIMNAFRGLANVQQATLAAVA 180 RRAMRAAYQREMDALESHLAFLASVGSVSPYVGLFGTVWGIMNAFRGLANVQQATLAAVA Sbjct: 121 RRAMRAAYQREMDALESHLAFLASVGSVSPYVGLFGTVWGIMNAFRGLANVQQATLAAVA 180 Query: 181 PGIAEALIATAIGLFAAIPAVVAYNRYSHDIDRLAIRFESFIEEFSNILQRQAR 234 PGIAEALIATAIGLFAAIPAVVAYNRYSHDIDRLAIRFESFIEEFSNILQRQAR Sbjct: 181 PGIAEALIATAIGLFAAIPAVVAYNRYSHDIDRLAIRFESFIEEFSNILQRQAR 234 >gi|300309940|ref|YP_003774032.1| biopolymer transport transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 231 Score = 98.6 bits (244), Expect = 4e-22, Method: Compositional matrix adjust. Identities = 79/238 (33%), Positives = 110/238 (46%), Gaps = 23/238 (9%) Query: 5 QDLSFISLIANASVLVQLVMLLLLSASVTSWTYIFRKMFTIRSARVQTEEFERVFWSGGN 64 Q++ F A + V LLL S+ SW YI K + R + ER FW Sbjct: 3 QNIGFAHYWAQGDAVSHSVAYLLLIMSIASWYYILSKAWAAWRIRRGSNALER-FWQAPT 61 Query: 65 LSALYQDALSNRRKAGGEGGALERIFQAGMGEFTKAKASVAAR-------GGAVDPGLLL 117 L+ DA + ++ E +I+ M E A + R A DPG L+ Sbjct: 62 LA----DATAAMQRLDSE-----QIYTP-MAERAAEAADIGTRQQGTPSLNAATDPGELI 111 Query: 118 DGARRAMRAAYQREMDALESHLAFLASVGSVSPYVGLFGTVWGIMNAFRGLANVQQATLA 177 R +R R LE L LASVGS +P+VGLFGTVWGI +A ++ + Sbjct: 112 T---RTLRREINRVSARLERGLTLLASVGSTAPFVGLFGTVWGIYHALVAVSASGTVQID 168 Query: 178 AVAPGIAEALIATAIGLFAAIPAVVAYNRYSHDIDRLAI-RFESFIEEFSNILQRQAR 234 VA + EALI TA+GL AIPAV+AYN ++ I+R+ + + F + L R Sbjct: 169 KVAGPVGEALIMTALGLLVAIPAVLAYNAFTR-INRVVLAELDGFAHDLHAYLTTGER 225 >gi|300310025|ref|YP_003774117.1| biopolymer transport transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 243 Score = 89.7 bits (221), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 65/195 (33%), Positives = 94/195 (48%), Gaps = 11/195 (5%) Query: 11 SLIANASVLVQLVMLLLLSASVTSWTYIFRKMFTIRSARVQTEEFERVFWSGGNLSALYQ 70 SL A + + V +LLL+ S+ SW I K + R + FW NL Sbjct: 10 SLWAQGDFVTKGVAVLLLAMSIASWYVIITKALQLLRLRKASAAAGHQFWDTTNLP---- 65 Query: 71 DALSNRRKAGGEGGALERIFQAGMGEFTKAKASVAARGGAVDPGLLLDGARRAMRAAYQR 130 + ++ G+ + +AG+ T A +G D + D ++R A Sbjct: 66 EGVATL----GQDNPFAEVAKAGV---TAMSHHTAHKGHLHDQLSVSDWVTLSLRQAIDE 118 Query: 131 EMDALESHLAFLASVGSVSPYVGLFGTVWGIMNAFRGLANVQQATLAAVAPGIAEALIAT 190 L++ +A LASVGS +P+VGLFGTVWGI +A + QA++ VA + EALI T Sbjct: 119 ASGKLQAGMAVLASVGSTAPFVGLFGTVWGIYHALVSIGTTGQASIDKVAGPVGEALIMT 178 Query: 191 AIGLFAAIPAVVAYN 205 A+GL AIPA YN Sbjct: 179 ALGLAVAIPATFGYN 193 >gi|300312127|ref|YP_003776219.1| biopolymer transport transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 243 Score = 82.0 bits (201), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 66/200 (33%), Positives = 98/200 (49%), Gaps = 35/200 (17%) Query: 18 VLVQLVMLLLLSASVTSW-TYIFRKMFTIRSARVQTEEFERVFWSGGNLSALYQDALSNR 76 V+ + ++ +LL S SW I + M R +R+ + + FW+ ++ Sbjct: 15 VVTRFLITILLGMSSVSWIVMIVKGMANRRLSRIGLKAHKE-FWAAHSI----------- 62 Query: 77 RKAGGEGGALERIFQAGMGEFTK----AKASVAARGGAVDPGLLLDGARR-------AMR 125 EGG I G G A A+V A+ P LL+G+ +R Sbjct: 63 -----EGG----IAAIGAGTDNPYSNIATAAVEAQAQKDQP--LLEGSTSNTEWVAYCVR 111 Query: 126 AAYQREMDALESHLAFLASVGSVSPYVGLFGTVWGIMNAFRGLANVQQATLAAVAPGIAE 185 ++ L+ LA LAS+GS SP++GLFGTVWGI +A + QA+L VA + E Sbjct: 112 NELDEQIAHLQGGLAVLASIGSTSPFIGLFGTVWGIYHALIAIGASGQASLDHVAGPVGE 171 Query: 186 ALIATAIGLFAAIPAVVAYN 205 +L+ TA+GLF AIPAV+ YN Sbjct: 172 SLVMTAVGLFVAIPAVLGYN 191 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 0.324 0.134 0.379 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: 643,410 Number of extensions: 26932 Number of successful extensions: 146 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 145 Number of HSP's successfully gapped: 5 Length of query: 234 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 152 Effective length of database: 1,231,600 Effective search space: 187203200 Effective search space used: 187203200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 129 (54.3 bits)