Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Pedo557:CA265_RS08575 Length = 422 Score = 306 bits (785), Expect = 6e-88 Identities = 169/410 (41%), Positives = 252/410 (61%), Gaps = 5/410 (1%) Query: 25 YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84 Y + ++ S+FF+WG L+ ILIPHLK LN ++ L+ + F AYFLM++PAG+ Sbjct: 13 YLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFLMAIPAGM 72 Query: 85 LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144 ++ + GYK +++GL GA F PAA Y FL ALF++ G+T+L+ +AN Y A Sbjct: 73 ILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLETSANPYAA 132 Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQE 204 +LG A+SRL LA + N L +AP GGL ILS + E++A ++ A + +Y ++E Sbjct: 133 VLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFILSGKSHTKEELAAMTDAGRNSYFLEE 192 Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAI 264 A +V+ PY+ L IVL ++A Y LP + K+ K S LRH H+ + V+A Sbjct: 193 AASVKTPYITLGIVLLVIAAIFYFIHLPEIKTKSIDGEAK-GSFFGALRHKHLKWAVVAQ 251 Query: 265 FFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRK 324 FFYVG +V + SF + G E+ AA+++A Y L +GRF G+A+L +S K Sbjct: 252 FFYVGAQVCVTSFFIRMAQQG--GGFDEKTAASYLAIYGLLFTVGRFAGTAILQFVSSHK 309 Query: 325 LLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSL 384 LLAI+A I++ L L ++ KG+ +Y++ +IG F SIMFPTIF+LGI+ +G T SS Sbjct: 310 LLAIYAVISILLCLVAILGKGSYVVYALGAIGFFMSIMFPTIFALGIDGIGDDTKPGSSW 369 Query: 385 LIMAIVGGAIVPFVQGLFADHIG--VQHAFFLPLLCYAYIVFYGLYGSRI 432 LIM+IVGGAI+PF G D G +Q + +PL+C+ I+++GL G +I Sbjct: 370 LIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPLVCFLVILYFGLRGYKI 419 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: 489 Number of extensions: 24 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: 422 Length adjustment: 32 Effective length of query: 410 Effective length of database: 390 Effective search space: 159900 Effective search space used: 159900 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