Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 6937233 Sama_1403 glucose/galactose transporter (RefSeq)
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__SB2B:6937233 Length = 415 Score = 435 bits (1118), Expect = e-126 Identities = 226/408 (55%), Positives = 292/408 (71%), Gaps = 19/408 (4%) Query: 24 DYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAG 83 +Y A+G LT++FFMWGF+TCLNDILIPHLKAVF LNYA+AML+QF FFGAYFL+S+PAG Sbjct: 19 NYRFALGSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLVSVPAG 78 Query: 84 LLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYV 143 +LV RLGY+KGIV GL A +G F+PAA Y FLGALFVLA+GITVLQVAAN YV Sbjct: 79 VLVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVAANPYV 138 Query: 144 ALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAV-LSAEQIAKLSPAEQVAYRV 202 LGP ++ASSRLTL QA NSLGT +AP FG +LILS AV SAE Sbjct: 139 TALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVGASAE--------------- 183 Query: 203 QEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVL 262 EA V+ PYL L +L +LAV L +LP + ++ ++ + S L H H++ G + Sbjct: 184 AEADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ---SALAHRHLVLGAI 240 Query: 263 AIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSP 322 IF YVGGEVAIGSFLVN+L + M+E AA+++A+YW GAM+GRFIG+A++ K+ Sbjct: 241 GIFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGAAVMQKVDA 300 Query: 323 RKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEAS 382 K+L A + LVL M + G +AM++++++GLFNSIMFPTIFSL ++ +GP T + S Sbjct: 301 GKVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNLGPATAQGS 360 Query: 383 SLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGS 430 +L +AIVGGA+VP +QGL AD +G+ +F LP+LCY YI+FYGL GS Sbjct: 361 GILCLAIVGGALVPLLQGLLADSVGLSASFILPVLCYGYILFYGLKGS 408 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: 594 Number of extensions: 24 Number of successful extensions: 2 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: 415 Length adjustment: 32 Effective length of query: 410 Effective length of database: 383 Effective search space: 157030 Effective search space used: 157030 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