Align Probable inositol transporter 2 (characterized)
to candidate 353132 BT3606 sugar-proton symporter (NCBI ptt file)
Query= SwissProt::Q9C757 (580 letters) >FitnessBrowser__Btheta:353132 Length = 468 Score = 200 bits (508), Expect = 1e-55 Identities = 161/550 (29%), Positives = 260/550 (47%), Gaps = 111/550 (20%) Query: 27 YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86 Y++ L+ A +GG LFGYDT VISG + + F+ +T Q V A+ G+IVG Sbjct: 9 YIIFLSVVAALGGFLFGYDTAVISGTIAQVTHLFQL---DTLQQGWYVGCALIGSIVGVL 65 Query: 87 IGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYI 146 G +D +GR+ ++++ LF AI A + + LVV R+ G+G+G+ S+ +PLYI Sbjct: 66 FSGILSDSIGRKRTMILSAILFSTSAIGCAFCIDFNQLVVYRIIGGIGIGVVSIVSPLYI 125 Query: 147 SEASPAKIRGALVSTNGFLITGGQFLSYLIN---LAFTD--------------VTGTWRW 189 SE S A+ RG +VS +T G +YL+N LA+++ VT WR Sbjct: 126 SEVSVAQFRGRMVSLYQLAVTVGFLGAYLVNYQLLAYSESGNHLPIAWLEKIVVTEVWRG 185 Query: 190 MLGIAGIPALLQFVLMFTLPESPRWLYRKGREEEAKAILRRIY-SAEDVEQEIRALKDSV 248 MLG+ +PA++ F+++F +PESPRWL KG+E +A IL +IY S ++ + ++ K + Sbjct: 186 MLGMETLPAIIFFIIIFFIPESPRWLIVKGQERKATYILEKIYNSFKEADFQLNETKSVL 245 Query: 249 ETEILEEGSSEKINMIKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFA 308 +E E S + + + +I GV + + QF+G+N V+YY P+I + AG Sbjct: 246 VSETRSEWS--------ILLKPGILKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGL- 296 Query: 309 SNRTALLLSLVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVFYEAATH 368 S +L ++ +N +I+++ ID++GRKKL+ + G+++SL IL G ++ Sbjct: 297 SGGDSLFYQVLVGLVNTLTTILALLIIDKVGRKKLIYYGVSGMVVSL-ILIGSYF----- 350 Query: 369 APAISSLETQRFNNISCPDYKSAMNTNAWDCMTCLKASSPSCGYCSSPIGKEHPGACWIS 428 + NAW+ + + C + C IS Sbjct: 351 -----------------------LFGNAWNISSLFLLAFFLC----------YVFCCAIS 377 Query: 429 DDSVKDLCHNENRLWYTRGCPSNFGWFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFR 488 +V + +E RG + FA L +G Y+I G T PW+ Sbjct: 378 ICAVIFVLLSEMYPTKIRGLAMSIAGFA-LWIGTYLI----GQLT-PWM----------- 420 Query: 489 GICGGIAATANWISNLIVAQSFLSLTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMP 548 + NL A +F +F ++ V +L V VPET G Sbjct: 421 ------------LQNLTPAGTF-------------FLFAIMCVPYMLIVWKLVPETTGKS 455 Query: 549 MEEIEKMLER 558 +EEIE+ R Sbjct: 456 LEEIERYWTR 465 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: 713 Number of extensions: 39 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