Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 6937507 Sama_1663 glucose/galactose transporter (RefSeq)
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__SB2B:6937507 Length = 415 Score = 431 bits (1109), Expect = e-125 Identities = 228/417 (54%), Positives = 294/417 (70%), Gaps = 24/417 (5%) Query: 25 YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84 Y A+ LT++FFMWGF+TCLNDILIPHLKAVF LNYA+AML+QF FFGAYFL+S+PAG+ Sbjct: 20 YGFALTSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLVSVPAGV 79 Query: 85 LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144 LV RLGY+KGIV GL A +G F+PAA Y FLGALFVLA+GITVLQVAAN YV Sbjct: 80 LVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVAANPYVT 139 Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAV-LSAEQIAKLSPAEQVAYRVQ 203 LGP ++ASSRLTL QA NSLGT +AP FG +LILS AV SAE Sbjct: 140 ALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVGASAE---------------A 184 Query: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLA 263 EA V+ PYL L +L +LAV L +LP + ++ ++ + S L H H++ G + Sbjct: 185 EADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ---SALAHRHLVLGAIG 241 Query: 264 IFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPR 323 IF YVGGEVAIGSFLVN+L + M+E AA+++A+YW GAM+GRFIG+A++ K+ Sbjct: 242 IFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGAAVMQKVDAG 301 Query: 324 KLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASS 383 K+L A + LVL M + G +AM++++++GLFNSIMFPTIFSL ++ +GP T + S Sbjct: 302 KVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNLGPATAQGSG 361 Query: 384 LLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSRIKSDTPVAA 440 +L +AIVGGA+VP +QGL AD +G+ +F LP+LCY YI+FYGL G + PVAA Sbjct: 362 ILCLAIVGGALVPLLQGLLADSVGLSASFILPVLCYGYILFYGLKGCK-----PVAA 413 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: 589 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