Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate N515DRAFT_0592 N515DRAFT_0592 glucose/galactose transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Dyella79:N515DRAFT_0592 Length = 430 Score = 221 bits (563), Expect = 3e-62 Identities = 144/416 (34%), Positives = 217/416 (52%), Gaps = 13/416 (3%) Query: 29 MGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVAR 88 M ++ +FF++GF+T LN LI +K F L+ A LV F+ +YF ++LP+ ++ R Sbjct: 21 MLIIGLLFFIFGFVTWLNGPLITFVKLAFSLDDVNAFLVPMVFYCSYFFLALPSSAVLKR 80 Query: 89 LGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGP 148 G KKG+ GL V +GA F +M Y L LFV+ G+ +LQ A+N Y+++LGP Sbjct: 81 TGMKKGMALGLFVMAIGAVLFGQFVSMRVYGGALAGLFVIGAGLALLQTASNPYISILGP 140 Query: 149 EKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQI-AKLSPAEQVAYRVQEAQT 207 SA+ R+ N + LAP G L+LS +Q+ A +P + A A Sbjct: 141 IDSAAQRIAFMGICNKVAGALAPFVFGWLVLSGIDTFDQQVKAAPTPEAREALLNTFAAK 200 Query: 208 VQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVK-QHSLVSPLRHPHVLFGVLAIFF 266 V PYL +A +L LLAV+V LP + + + H+ + L PH+ GVL +F Sbjct: 201 VHMPYLAMAGLLVLLAVWVLRSPLPEIKPSGANSEAEIGHAKGNLLSFPHLWLGVLCLFL 260 Query: 267 YVGGEVAIGSFLVNY---LSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAK-LSP 322 YVG EV G + Y L +P A ++ ++ ++G G L+ K +S Sbjct: 261 YVGVEVMAGDAIGTYGQGLGLP------LDATKHFTSFTLFAMLLGYLAGLVLIPKIISQ 314 Query: 323 RKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEAS 382 + LA+ A + +A + T G ++ V ++G N++M+P IF L I+ +G T S Sbjct: 315 QSYLAVSAVLGVAFTVGAWATTGYTSVGFVAALGFANAMMWPAIFPLAIKGLGRWTEAGS 374 Query: 383 SLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLL-CYAYIVFYGLYGSRIKSDTP 437 +LLIMAIVGGA+VP H Q F L ++ CY YI+FYGL G R+ P Sbjct: 375 ALLIMAIVGGALVPQAFVHLKQHYDFQLVFMLLMVPCYLYILFYGLRGHRVGQHAP 430 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: 514 Number of extensions: 29 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: 430 Length adjustment: 32 Effective length of query: 410 Effective length of database: 398 Effective search space: 163180 Effective search space used: 163180 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