Align Probable inositol transporter 2 (characterized)
to candidate 349964 BT0436 arabinose-proton symporter (NCBI ptt file)
Query= SwissProt::Q9C757 (580 letters) >FitnessBrowser__Btheta:349964 Length = 468 Score = 205 bits (521), Expect = 4e-57 Identities = 127/354 (35%), Positives = 208/354 (58%), Gaps = 29/354 (8%) Query: 27 YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86 Y++ L+ A +GG LFGYDT VISG + + F+ +T Q V A+ G+IVG Sbjct: 9 YLIFLSVVAALGGFLFGYDTAVISGTIAQVTQLFQL---DTLQQGWYVGCALIGSIVGVL 65 Query: 87 IGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYI 146 G +DKLGR+ ++++ LF A+ A + + + LVV R+ G+G+G+ S+ +PLYI Sbjct: 66 FAGILSDKLGRKMTMIISATLFSTSALGCAISADFTQLVVYRIIGGVGIGVVSIVSPLYI 125 Query: 147 SEASPAKIRGALVSTNGFLITGGQFLSYLIN---LAFTD--------------VTGTWRW 189 SE + A+ RG LVS +T G +YLIN LA+ + VT WR Sbjct: 126 SEVAVAQYRGRLVSLYQLAVTVGFLGAYLINYQLLAYAESGNQLSMDWLNKIFVTEVWRG 185 Query: 190 MLGIAGIPALLQFVLMFTLPESPRWLYRKGREEEAKAILRRIYSAEDVEQEIRALKDSVE 249 MLG+ +PA+L F+++F +PESPRWL +G+EE+A IL RIY++ V + LK++ + Sbjct: 186 MLGMETLPAVLFFIIIFFIPESPRWLIVRGKEEKAVNILERIYNS--VSEAASQLKET-K 242 Query: 250 TEILEEGSSEKINMIKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFAS 309 + + E SE ++K + + +I GV + + QF+G+N V+YY P+I + AG S Sbjct: 243 SVLTSETKSEWAMLMK----PGIFKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGL-S 297 Query: 310 NRTALLLSLVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVFY 363 +L ++ +N +++++ IDR+GRK+L+ + G+++SL +L GV++ Sbjct: 298 GGDSLFYQVLVGLVNTLTTVLALVIIDRVGRKQLVYYGVSGMVVSL-LLIGVYF 350 Score = 58.5 bits (140), Expect = 6e-13 Identities = 33/104 (31%), Positives = 54/104 (51%) Query: 455 FALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSFLSLT 514 F L+ Y+ + + V +++ SE+YP + RG+ IA A WI ++ Q + Sbjct: 362 FLLVFFLFYVFCCAVSICAVVFVLLSEMYPTKVRGLAMSIAGFALWIGTYLIGQLTPWML 421 Query: 515 EAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKMLER 558 + + + TF +F V+ V +L V VPET G +EEIE+ R Sbjct: 422 QNLTPAGTFFLFAVMCVPYMLIVWKLVPETTGKSLEEIERYWTR 465 Score = 25.0 bits (53), Expect = 0.007 Identities = 11/27 (40%), Positives = 16/27 (59%) Query: 146 ISEASPAKIRGALVSTNGFLITGGQFL 172 +SE P K+RG +S GF + G +L Sbjct: 386 LSEMYPTKVRGLAMSIAGFALWIGTYL 412 Lambda K H 0.324 0.139 0.425 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 684 Number of extensions: 38 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 580 Length of database: 468 Length adjustment: 35 Effective length of query: 545 Effective length of database: 433 Effective search space: 235985 Effective search space used: 235985 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 (21.5 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory