Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease
Query= uniprot:A0A1I2JXG1 (442 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease Length = 442 Score = 859 bits (2220), Expect = 0.0 Identities = 442/442 (100%), Positives = 442/442 (100%) Query: 1 MAFAAPPAPSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLN 60 MAFAAPPAPSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLN Sbjct: 1 MAFAAPPAPSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLN 60 Query: 61 YAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPA 120 YAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPA Sbjct: 61 YAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPA 120 Query: 121 FLGALFVLATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILS 180 FLGALFVLATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILS Sbjct: 121 FLGALFVLATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILS 180 Query: 181 AAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQ 240 AAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQ Sbjct: 181 AAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQ 240 Query: 241 ASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVA 300 ASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVA Sbjct: 241 ASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVA 300 Query: 301 YYWLGAMIGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNS 360 YYWLGAMIGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNS Sbjct: 301 YYWLGAMIGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNS 360 Query: 361 IMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYA 420 IMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYA Sbjct: 361 IMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYA 420 Query: 421 YIVFYGLYGSRIKSDTPVAATH 442 YIVFYGLYGSRIKSDTPVAATH Sbjct: 421 YIVFYGLYGSRIKSDTPVAATH 442 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: 812 Number of extensions: 20 Number of successful extensions: 1 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: 442 Length adjustment: 32 Effective length of query: 410 Effective length of database: 410 Effective search space: 168100 Effective search space used: 168100 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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