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= 0001.2251.p (243 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312127|ref|YP_003776219.1| biopolymer transport transmembr... 476 e-136 gi|300310025|ref|YP_003774117.1| biopolymer transport transmembr... 218 4e-58 gi|300309940|ref|YP_003774032.1| biopolymer transport transmembr... 179 2e-46 gi|300310552|ref|YP_003774644.1| MotA/TolQ/ExbB proton channel f... 84 1e-17 >gi|300312127|ref|YP_003776219.1| biopolymer transport transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 243 Score = 476 bits (1225), Expect = e-136, Method: Compositional matrix adjust. Identities = 233/243 (95%), Positives = 237/243 (97%) Query: 1 MENYGLANVWLQGDVVTRFLITILLGMSSVSWIVMIVKGMANRRLSRIGLQAHKEFWAAH 60 MENYGLANVWLQGDVVTRFLITILLGMSSVSWIVMIVKGMANRRLSRIGL+AHKEFWAAH Sbjct: 1 MENYGLANVWLQGDVVTRFLITILLGMSSVSWIVMIVKGMANRRLSRIGLKAHKEFWAAH 60 Query: 61 SIEGGIAAIGAGTDNPYSNIATAAVEAHAQKDQPLLEGSTSNTEWVAYCVRNALDEQIAH 120 SIEGGIAAIGAGTDNPYSNIATAAVEA AQKDQPLLEGSTSNTEWVAYCVRN LDEQIAH Sbjct: 61 SIEGGIAAIGAGTDNPYSNIATAAVEAQAQKDQPLLEGSTSNTEWVAYCVRNELDEQIAH 120 Query: 121 LQGGLAVLASIGSTSPFIGLFGTVWGIYHALITIGASGQASLDHVAGPVGESLVMTAVGL 180 LQGGLAVLASIGSTSPFIGLFGTVWGIYHALI IGASGQASLDHVAGPVGESLVMTAVGL Sbjct: 121 LQGGLAVLASIGSTSPFIGLFGTVWGIYHALIAIGASGQASLDHVAGPVGESLVMTAVGL 180 Query: 181 FVAIPAVLGYNYVSRGNRTVAQKLMRFSHQLHVYYVTGNKMKEAQAAKESRHPAHRPATA 240 FVAIPAVLGYNYV+RGNRTVAQKLMRFSHQLHVYYVTGNKM+EAQAAKES +PAH PATA Sbjct: 181 FVAIPAVLGYNYVARGNRTVAQKLMRFSHQLHVYYVTGNKMREAQAAKESGYPAHTPATA 240 Query: 241 TSA 243 T A Sbjct: 241 TRA 243 >gi|300310025|ref|YP_003774117.1| biopolymer transport transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 243 Score = 218 bits (555), Expect = 4e-58, Method: Compositional matrix adjust. Identities = 113/232 (48%), Positives = 151/232 (65%), Gaps = 9/232 (3%) Query: 4 YGLANVWLQGDVVTRFLITILLGMSSVSWIVMIVKGMANRRLSRIGLQAHKEFWAAHSIE 63 YGL ++W QGD VT+ + +LL MS SW V+I K + RL + A +FW ++ Sbjct: 6 YGLESLWAQGDFVTKGVAVLLLAMSIASWYVIITKALQLLRLRKASAAAGHQFWDTTNLP 65 Query: 64 GGIAAIGAGTDNPYSNIATAAVEA--HAQKDQPLLEGSTSNTEWVAYCVRNALDEQIAHL 121 G+A +G DNP++ +A A V A H + L S ++WV +R A+DE L Sbjct: 66 EGVATLG--QDNPFAEVAKAGVTAMSHHTAHKGHLHDQLSVSDWVTLSLRQAIDEASGKL 123 Query: 122 QGGLAVLASIGSTSPFIGLFGTVWGIYHALITIGASGQASLDHVAGPVGESLVMTAVGLF 181 Q G+AVLAS+GST+PF+GLFGTVWGIYHAL++IG +GQAS+D VAGPVGE+L+MTA+GL Sbjct: 124 QAGMAVLASVGSTAPFVGLFGTVWGIYHALVSIGTTGQASIDKVAGPVGEALIMTALGLA 183 Query: 182 VAIPAVLGYNYVSRGNRTVAQKLMRFSHQLHVYYVTGNKMKEAQAAKESRHP 233 VAIPA GYN + RGN+T+ KL +F LH +VTG A+AA E P Sbjct: 184 VAIPATFGYNALVRGNKTILAKLNKFGFDLHALFVTG-----ARAAGEDGQP 230 >gi|300309940|ref|YP_003774032.1| biopolymer transport transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 231 Score = 179 bits (454), Expect = 2e-46, Method: Compositional matrix adjust. Identities = 99/225 (44%), Positives = 137/225 (60%), Gaps = 6/225 (2%) Query: 2 ENYGLANVWLQGDVVTRFLITILLGMSSVSWIVMIVKGMANRRLSRIGLQAHKEFWAAHS 61 +N G A+ W QGD V+ + +LL MS SW ++ K A R+ R G A + FW A + Sbjct: 3 QNIGFAHYWAQGDAVSHSVAYLLLIMSIASWYYILSKAWAAWRIRR-GSNALERFWQAPT 61 Query: 62 IEGGIAAIGA-GTDNPYSNIATAAVEA----HAQKDQPLLEGSTSNTEWVAYCVRNALDE 116 + AA+ ++ Y+ +A A EA Q+ P L +T E + +R ++ Sbjct: 62 LADATAAMQRLDSEQIYTPMAERAAEAADIGTRQQGTPSLNAATDPGELITRTLRREINR 121 Query: 117 QIAHLQGGLAVLASIGSTSPFIGLFGTVWGIYHALITIGASGQASLDHVAGPVGESLVMT 176 A L+ GL +LAS+GST+PF+GLFGTVWGIYHAL+ + ASG +D VAGPVGE+L+MT Sbjct: 122 VSARLERGLTLLASVGSTAPFVGLFGTVWGIYHALVAVSASGTVQIDKVAGPVGEALIMT 181 Query: 177 AVGLFVAIPAVLGYNYVSRGNRTVAQKLMRFSHQLHVYYVTGNKM 221 A+GL VAIPAVL YN +R NR V +L F+H LH Y TG ++ Sbjct: 182 ALGLLVAIPAVLAYNAFTRINRVVLAELDGFAHDLHAYLTTGERV 226 >gi|300310552|ref|YP_003774644.1| MotA/TolQ/ExbB proton channel family protein [Herbaspirillum seropedicae SmR1] Length = 234 Score = 83.6 bits (205), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 52/133 (39%), Positives = 73/133 (54%), Gaps = 9/133 (6%) Query: 81 ATAAVEAHAQKDQP--LLEGSTSNTEWVAYCVRNALDEQIAHLQGGLAVLASIGSTSPFI 138 A A+V A P LL+G+ +R A ++ L+ LA LAS+GS SP++ Sbjct: 100 AKASVAARGGAVDPSLLLDGARR-------AMRAAYQREMDALESHLAFLASVGSVSPYV 152 Query: 139 GLFGTVWGIYHALITIGASGQASLDHVAGPVGESLVMTAVGLFVAIPAVLGYNYVSRGNR 198 GLFGTVWGI +A + QA+L VA + E+L+ TA+GLF AIPAV+ YN S Sbjct: 153 GLFGTVWGIMNAFRGLANVQQATLAAVAPGIAEALIATAIGLFAAIPAVVAYNRYSHDID 212 Query: 199 TVAQKLMRFSHQL 211 +A + F + Sbjct: 213 RLAIRFESFIEEF 225 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 0.319 0.132 0.392 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: 726,595 Number of extensions: 27136 Number of successful extensions: 90 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 88 Number of HSP's successfully gapped: 4 Length of query: 243 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 160 Effective length of database: 1,226,865 Effective search space: 196298400 Effective search space used: 196298400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 129 (54.3 bits)