Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate BWI76_RS23685 BWI76_RS23685 MFS transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Koxy:BWI76_RS23685 Length = 444 Score = 234 bits (597), Expect = 4e-66 Identities = 137/401 (34%), Positives = 216/401 (53%), Gaps = 8/401 (1%) Query: 35 IFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKG 94 +F +WG LNDILI K F L + LVQ FF YF ++LPA L+ R YK Sbjct: 39 LFALWGMAGNLNDILIAQFKKGFDLTDTQTALVQSIFFLGYFFVALPAAALIKRYSYKAA 98 Query: 95 IVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGPEKSASS 154 I+ GL + +G F PAA + Y AFL L V+A G++ L+ +AN Y +LLGP +S++ Sbjct: 99 IIIGLCLYALGCFLFVPAAQIMTYGAFLACLGVIACGLSFLETSANTYSSLLGPIQSSTQ 158 Query: 155 RLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYLG 214 R+ +Q NSLG G +++ S EQ+ + A A R Q V GPYL Sbjct: 159 RINFSQIFNSLGVISGVLIGQVMVFGENDPSHEQLLAMPAAAADAARHQMVGQVVGPYLI 218 Query: 215 LAIVLFLLAVFVYLFRLPALT-EKTEQASVKQHSLVSPLRH----PHVLFGVLAIFFYVG 269 + VL +LA+ + P+ ++Q + S+ S L+ P G+L+ F YVG Sbjct: 219 IGSVLVVLALVFVFIKFPSCKGTPSQQQQIPTESMGSTLKRLFAIPRFRLGILSQFLYVG 278 Query: 270 GEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRKLLAIF 329 +V + SF + ++ + G SE +A W+ + +G+ + + L+ +L+P LL F Sbjct: 279 AQVGVWSFTIRFVQLVQQGT-SEHSATYWLLASLVIYAVGKTVATWLMNRLNPALLLGTF 337 Query: 330 AAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAI 389 A L+L + + +A+Y+++ + + +PT F L I+ MG T A S+++M+I Sbjct: 338 ALAATVLLLIAVFSSSMLAVYALILVSFCMAPCWPTNFGLVIKGMGKDTQTAGSIVVMSI 397 Query: 390 VGGAIVPFVQGLFADHIG--VQHAFFLPLLCYAYIVFYGLY 428 +GGA++P V G+ +D G +Q AF PLLC+ Y+ FYG + Sbjct: 398 IGGAVIPLVMGIISDMNGGNMQIAFIAPLLCFVYVAFYGFW 438 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: 457 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: 444 Length adjustment: 32 Effective length of query: 410 Effective length of database: 412 Effective search space: 168920 Effective search space used: 168920 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 Apr 09 2024. 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