Align D-fructose transporter, sugar porter family (characterized)
to candidate BWI76_RS10225 BWI76_RS10225 MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >FitnessBrowser__Koxy:BWI76_RS10225 Length = 483 Score = 269 bits (688), Expect = 1e-76 Identities = 153/449 (34%), Positives = 242/449 (53%), Gaps = 22/449 (4%) Query: 22 IILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGA 81 +I A A++ G++ G+D +VISG L LT A G+ V++ ++G ++G+ G Sbjct: 11 LIFICAIASVSGIILGYDASVISGVIDPLTEHLSLTPAQSGWAVSNVILGCIVGAWGVGR 70 Query: 82 PADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVS 141 DRFGRK ++ AI + +S++G+ LA DL F+V+R +GGLA+G AS VTP+YIAEVS Sbjct: 71 FTDRFGRKATLIITAILFAISAIGSALANDLTWFVVYRMIGGLAVGMASAVTPLYIAEVS 130 Query: 142 PARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYD----VAWRWMFGIVAVPSTIFLL 197 P RGR++ M Q+ +V G L+ ++ NY+IA + ++ + WRWM +P +FL+ Sbjct: 131 PKDLRGRMLGMQQMLMVGGQLVVYIVNYLIARGMAHEWVVSIGWRWMLASALIPCVLFLV 190 Query: 198 VTLLLPESPRWLAIHGQADRARDVMQRLG--------FADPRAELARIELAEAREEAAGK 249 + +PESPRW A+ Q +++ V+ L +A+ R +A + G Sbjct: 191 MVFFMPESPRWYAMRNQKEKSLKVLTSLSNPGHAERLYAEIRTSIATDSALLSIPTPRGI 250 Query: 250 PRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNL 309 R + S+ + CAIA+ Q+SGIN L+Y+AP + + ++ QSI +G L Sbjct: 251 LRDKKSSYILWIGCAIAV--LQQVSGINILMYFAPSLLQNVTGNTQDSMFQSIFLGLALL 308 Query: 310 VFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAM 369 AL DR GR PLL GS+ CAA LL W + + G L + GL+GFI F M Sbjct: 309 AGVSIALVAFDRIGRLPLLRWGSLGCAAFLLFTSWAFMN-EVKGYLPIVGLVGFIFVFGM 367 Query: 370 SQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASV-------GGWVF 422 S W+ ISE+FP+ +R + WV +T +FP+ + G + Sbjct: 368 SWSLGAWLLISEIFPNRMRAVAMGYAFCSMWVSNFIVTQSFPMMNRNPVLMEHFHGAFPL 427 Query: 423 AFFGAMMLLQLLWTWKFMPETNGIALEDM 451 ++ + +F+PET G++LE++ Sbjct: 428 LLCSGFSIIAFWFVGRFLPETKGVSLENI 456 Lambda K H 0.327 0.139 0.420 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: 646 Number of extensions: 33 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 458 Length of database: 483 Length adjustment: 33 Effective length of query: 425 Effective length of database: 450 Effective search space: 191250 Effective search space used: 191250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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