Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate N515DRAFT_1222 N515DRAFT_1222 MFS transporter, FHS family, L-fucose permease
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Dyella79:N515DRAFT_1222 Length = 422 Score = 286 bits (733), Expect = 7e-82 Identities = 158/402 (39%), Positives = 234/402 (58%), Gaps = 3/402 (0%) Query: 26 PMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLL 85 P+ + ++ S+FF+WG LND+LIP K F LN +A LVQ F+ YFL+++PAG+ Sbjct: 13 PLPLALIVSLFFLWGVANNLNDVLIPQFKKAFVLNDFQAGLVQSAFYLGYFLVAMPAGIY 72 Query: 86 VARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVAL 145 + R GYK +V GLA+ G+GA FWPAA Y FL ALFV+A+G+ L+ +AN +V L Sbjct: 73 MRRFGYKSAVVFGLALYGLGALLFWPAAQQGTYGFFLFALFVIASGLAFLETSANPFVTL 132 Query: 146 LGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEA 205 LGP +SA+ RL LAQA N LG+ G I S + EQ+A LS AE+ A+ E Sbjct: 133 LGPRESAARRLNLAQAFNPLGSITGILIGQHFIFSGVEHTPEQLAALSAAERAAFVAHET 192 Query: 206 QTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAI- 264 VQ PYL + +V+ + + L R PA+ E A + H ++ L LA Sbjct: 193 AAVQLPYLAIGLVVLAWGLLILLTRFPAVHAVEEGAVPRDHGALARLLGDRRFLATLAAQ 252 Query: 265 FFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRK 324 FFYVG +V + S+L+ Y+ G + + AAN++ M GRF GSAL+ ++PR+ Sbjct: 253 FFYVGAQVGVWSYLIRYVQATMPGTPA-KLAANYMLVSLACFMAGRFAGSALMRYVAPRR 311 Query: 325 LLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGE-ASS 383 LLA+FAA+N+AL + + G ++V+ F S+M+PTIF+LG+E G + S+ Sbjct: 312 LLALFAAVNVALTVFAVAVPGVAGACALVACSFFMSVMYPTIFALGVEGRGDDERKLGSA 371 Query: 384 LLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFY 425 LL+M I+GGA++ G +D G+ A +P + I+ + Sbjct: 372 LLVMTIIGGAVLTAAMGAVSDAAGISRAMLVPAASFVVILLF 413 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: 497 Number of extensions: 26 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