Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS22920 BWI76_RS22920 MFS transporter Length = 436 Score = 266 bits (681), Expect = 7e-76 Identities = 154/412 (37%), Positives = 234/412 (56%), Gaps = 6/412 (1%) Query: 25 YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84 Y + +L S+FF+W LNDIL+P + F L +A L+Q F+ YF++ +PAG+ Sbjct: 22 YIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFVIPIPAGI 81 Query: 85 LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144 L+ +L YK GI+ GL + GAA FWPAA + Y FL LF++A G+ L+ AAN +V Sbjct: 82 LMKKLSYKAGIITGLFLYAFGAALFWPAAEVMNYTLFLIGLFIIAAGLGCLETAANPFVT 141 Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIA-KLSPAEQVAYRVQ 203 +LGPE RL LAQ NS G +A FG LILS ++ + K++P + AY+ Sbjct: 142 VLGPESGGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMAPEQLSAYKHS 201 Query: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQH---SLVSPLRHPHVLFG 260 +VQ PY+ + V+ L+A+ + L + PAL + + SL +R H + Sbjct: 202 LVLSVQTPYMIIVAVVLLVALLIMLTKFPALQSDDHSDATQSSFSASLARLVRVRHWRWA 261 Query: 261 VLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKL 320 VLA F YVG + A S+L+ Y ++ +I M+ AAN++ + IGRF G+ L+++ Sbjct: 262 VLAQFCYVGAQTACWSYLIRY-AIEEIPGMTPGFAANYLTGTMVCFFIGRFSGTWLISRF 320 Query: 321 SPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGE 380 +P K+LA +A ++M L L + T G V + ++ F SI +PTIFSLGI+ +G T Sbjct: 321 APHKVLAAYALLSMILCLISAFTGGHVGLLALTLCSAFMSIQYPTIFSLGIKNLGQDTKY 380 Query: 381 ASSLLIMAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAYIVFYGLYGSR 431 SS ++M I+GG IV V G +D G + A +P LC+A I + + S+ Sbjct: 381 GSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELVPALCFAVIFIFARFRSQ 432 Lambda K H 0.327 0.140 0.414 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: 487 Number of extensions: 31 Number of successful extensions: 4 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: 442 Length of database: 436 Length adjustment: 32 Effective length of query: 410 Effective length of database: 404 Effective search space: 165640 Effective search space used: 165640 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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