Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_082679223.1 V473_RS17505 L-fucose:H+ symporter permease
Query= uniprot:A0A1I2JXG1 (442 letters) >NCBI__GCF_001046645.1:WP_082679223.1 Length = 392 Score = 257 bits (656), Expect = 5e-73 Identities = 158/400 (39%), Positives = 226/400 (56%), Gaps = 21/400 (5%) Query: 29 MGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVAR 88 M + T +FF+WG LND+LI H + VF L+ ++ LVQ F+ YF ++PA L R Sbjct: 1 MVLTTGLFFLWGVANNLNDVLIAHFRHVFSLSDFQSGLVQSAFYLGYFCFAIPAALAAER 60 Query: 89 LGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGP 148 LGYK ++ GL + G GA F PA+ Y FL ALFV+A+G+ L+ AAN VA +GP Sbjct: 61 LGYKATVILGLLLFGGGALLFLPASIQLSYGFFLVALFVIASGLAFLETAANPMVAAMGP 120 Query: 149 EKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTV 208 + A+ RL LAQA N LG+ G LILS A P + VA A V Sbjct: 121 AEGAAQRLNLAQAFNPLGSIAGVALGATLILSDA-----------PQQGVA----GAAAV 165 Query: 209 QGPYLGLAIVLFLLAVFVYLFRLP-ALTEKTEQASVKQHSLVSPLRHPHVLFGVLAIFFY 267 Q PYLG+A+V+ + A + R P A T+ + LR P + GV A FFY Sbjct: 166 QLPYLGIALVVLVWAAVLTFTRFPRAATQADGSGGSALAGYGALLRRPRYMAGVAAQFFY 225 Query: 268 VGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGA-MIGRFIGSALLAKLSPRKLL 326 VG +V I S+L+ Y G +++AA W+ L M+GRFIG+ALL++ +L+ Sbjct: 226 VGAQVGIWSYLIRYAESVVPGIGAQKAA--WLLTLSLALFMVGRFIGAALLSRSDGARLM 283 Query: 327 AIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLI 386 A+FA IN+ L L + G V + +VV+ F SIM+PTIF L + +GP+T +S+++ Sbjct: 284 ALFAGINIILSLVA-VAGGIVGLAAVVATSFFMSIMYPTIFVLSLRGLGPLTKAGASMIV 342 Query: 387 MAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAYIVFY 425 MAI+GGA++ GL +D G ++ A +P LC+A + Y Sbjct: 343 MAIIGGAVLTMAMGLLSDLTGTIRAAMLVPALCFAVVTLY 382 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: 455 Number of extensions: 24 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: 442 Length of database: 392 Length adjustment: 31 Effective length of query: 411 Effective length of database: 361 Effective search space: 148371 Effective search space used: 148371 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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