Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Pf6N2E2_1003 Fucose permease
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1003 Length = 460 Score = 255 bits (651), Expect = 2e-72 Identities = 150/423 (35%), Positives = 231/423 (54%), Gaps = 23/423 (5%) Query: 20 ERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMS 79 E+ + +A +TS+FFMWG L D+L H + ++ ++ LVQ +FGAYF+++ Sbjct: 56 EKLSSTRLAFIFVTSLFFMWGLSHGLLDVLNKHFQDTLHISRGQSGLVQTAYFGAYFIIA 115 Query: 80 LPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAA 139 LP GL + R GYK GI+AGLA+ +GA F PA+ + + FL ALFVLA G+ L+ AA Sbjct: 116 LPVGLFMERFGYKAGILAGLALFAIGALLFIPASMVGTFMPFLVALFVLACGLGCLETAA 175 Query: 140 NAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVA 199 N Y A LG + RLT AQ+ N LG F+ P GG + A + Sbjct: 176 NLYAAALGDPAKSEQRLTFAQSFNGLGAFIGPVIGGAVFF---------------APPIE 220 Query: 200 YRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPAL-TEKTEQASVKQHSLVSPLRHPHVL 258 + V Y LAI++ L+ V +LP + EK+ + VS + + Sbjct: 221 FNGNRVDLVSVTYAALAIIVMLMFVAFARIQLPEIRNEKSSDVLLPSAGEVSLWKKSNFT 280 Query: 259 FGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLA 318 ++A F VG V IG+F +NY ++ +S Q A+ ++ L M+GRF G+ ++ Sbjct: 281 GALVAQFCNVGAYVGIGAFFINY-AIDHWQGISAQKASYLLSLGMLAYMVGRFAGTWVMR 339 Query: 319 KLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMT 378 + R LL + + ++M L + + +++++V +I LF S+M+PTIF++GI +G T Sbjct: 340 YVPARSLLILNSLVSMVLCIVAIAGFERISIFAVAAIYLFMSVMYPTIFAMGIRGLGTQT 399 Query: 379 GEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSRIKSDTPV 438 +A S L+M +VGGA VP + G ADH G+ AF++PL C+A I +YGL S PV Sbjct: 400 KKAGSCLVMTLVGGAFVPLLMGALADHFGIAAAFYVPLACFAAIAWYGL------SQPPV 453 Query: 439 AAT 441 A+ Sbjct: 454 TAS 456 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: 553 Number of extensions: 33 Number of successful extensions: 5 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: 460 Length adjustment: 33 Effective length of query: 409 Effective length of database: 427 Effective search space: 174643 Effective search space used: 174643 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