Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Echvi_3909 Echvi_3909 Fucose permease
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Cola:Echvi_3909 Length = 469 Score = 343 bits (881), Expect = 5e-99 Identities = 197/460 (42%), Positives = 273/460 (59%), Gaps = 78/460 (16%) Query: 31 VLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLL----- 85 ++T +FFMWGF+TC+NDILIPHL+ VF L +AML+Q FFGAYF +SL L+ Sbjct: 29 LVTMLFFMWGFITCMNDILIPHLQQVFTLQNWQAMLIQTAFFGAYFFISLGYYLISITKG 88 Query: 86 --VARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYV 143 + R+GYK GI+ GL ++ VG F+PAA++ + FL ALFVLA+GIT+LQ+AAN YV Sbjct: 89 DPIGRIGYKNGIILGLVISAVGCLFFYPAASLVSFGFFLFALFVLASGITILQIAANPYV 148 Query: 144 ALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQ 203 +LG ASSRL + QA NSLGT +AP GG LI A + I+ Sbjct: 149 TILGKPSGASSRLNMTQAFNSLGTTIAPLIGGYLIFGA--IGDVDIS------------- 193 Query: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLA 263 A +V+ PY+ LA+ L L+A+ LF+LP E Q + S L+H H++ G+ A Sbjct: 194 -ADSVKMPYVALALTLLLIALIFKLFKLP---EIGSQGVIISDS--GALKHRHLMLGIGA 247 Query: 264 IFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLA----- 318 IF YVGGEV +GS L+N+ +P+I + E A++++A +W GAM+GRF G+ LA Sbjct: 248 IFAYVGGEVTVGSNLINFARLPEIAGLDEAEASHYLALFWGGAMVGRFFGAVALADFKHN 307 Query: 319 --------------------------------------------KLSPRKLLAIFAAINM 334 + P + L +F + Sbjct: 308 LNRFLIIGAITAISYVTIYYVYGGEMALYALAFIGLNIVVIIIGQFIPNRTLWLFGITGI 367 Query: 335 ALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAI 394 L++ ++T G +A++S+V++GLFNSIMFPTIFSL I+ +G T +ASSLL+MAIVGGAI Sbjct: 368 GLLVIGLLTSGQLALWSIVALGLFNSIMFPTIFSLAIKGLGKYTAQASSLLVMAIVGGAI 427 Query: 395 VPFVQGLFADHIG-VQHAFFLPLLCYAYIVFYGLYGSRIK 433 VP +QGL AD G VQ +F +PL CY YIVFYG+ G R++ Sbjct: 428 VPLLQGLLADISGSVQLSFLVPLACYLYIVFYGMKGYRVE 467 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: 629 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 442 Length of database: 469 Length adjustment: 33 Effective length of query: 409 Effective length of database: 436 Effective search space: 178324 Effective search space used: 178324 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