Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_057508914.1 ABB28_RS12315 glucose/galactose MFS transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >NCBI__GCF_001431535.1:WP_057508914.1 Length = 438 Score = 579 bits (1492), Expect = e-170 Identities = 296/412 (71%), Positives = 343/412 (83%), Gaps = 1/412 (0%) Query: 27 MAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLV 86 MA+GV T+IFFMWGFLTCLNDILIPHLKAVF+LNYA AMLVQFTFFGAYFLMSLPAG LV Sbjct: 24 MALGVATTIFFMWGFLTCLNDILIPHLKAVFELNYARAMLVQFTFFGAYFLMSLPAGRLV 83 Query: 87 ARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALL 146 A LGYKKGIVAGL +AGVGA GFWPAA + Y AFLGALFVLATGITVLQVAAN YVALL Sbjct: 84 AHLGYKKGIVAGLLIAGVGALGFWPAAELREYSAFLGALFVLATGITVLQVAANPYVALL 143 Query: 147 GPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQ 206 GP +++SSRLTLAQALNSLGT +AP FGGLLIL V SA++I LS AEQ AYR EAQ Sbjct: 144 GPVETSSSRLTLAQALNSLGTAIAPIFGGLLILGNTVKSADEINALSVAEQAAYRAAEAQ 203 Query: 207 TVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQA-SVKQHSLVSPLRHPHVLFGVLAIF 265 +VQGPY+GLAI L LLA+FVYLFRLP L+E E+ Q S + LRH H+LF VL IF Sbjct: 204 SVQGPYIGLAIALVLLALFVYLFRLPTLSESAEKVDDGPQQSYGAALRHRHLLFAVLGIF 263 Query: 266 FYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRKL 325 FYVG EV+IGSFLVNYLSMP IG +EQ A ++V+ YW AMIGRF GSALL + SPR + Sbjct: 264 FYVGAEVSIGSFLVNYLSMPTIGGFTEQQATHYVSAYWTMAMIGRFAGSALLTRYSPRHM 323 Query: 326 LAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLL 385 LA+FA IN+ L+ TTM + G VA+YSVV+IGLFNSIMFPTIF+LGIER+GP+T +ASSLL Sbjct: 324 LALFAGINVLLLGTTMASSGQVALYSVVAIGLFNSIMFPTIFALGIERLGPLTNKASSLL 383 Query: 386 IMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSRIKSDTP 437 IMAIVGGA+VP++QG+ ADHIG+Q +F LPLLCY Y++F+GL G+R+ + P Sbjct: 384 IMAIVGGALVPYLQGVLADHIGLQPSFILPLLCYGYVIFFGLVGARLPAIAP 435 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: 631 Number of extensions: 18 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: 438 Length adjustment: 32 Effective length of query: 410 Effective length of database: 406 Effective search space: 166460 Effective search space used: 166460 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 24 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