Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_091372396.1 BLU33_RS11040 L-fucose:H+ symporter permease
Query= uniprot:A0A1I2JXG1 (442 letters) >NCBI__GCF_900105165.1:WP_091372396.1 Length = 444 Score = 249 bits (636), Expect = 1e-70 Identities = 141/412 (34%), Positives = 227/412 (55%), Gaps = 6/412 (1%) Query: 27 MAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLV 86 ++ ++T +F +WG +NDILI F+L+ +A L+Q F+ YF +++P+GL++ Sbjct: 21 VSFSLVTMLFLIWGIPNNMNDILIKQFMKSFELSRTQAGLIQSAFYMGYFFLAVPSGLIM 80 Query: 87 ARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALL 146 + YK G++AGL + +G FWPAA Y FL ALFV+A+G+T L+ AN ++ L Sbjct: 81 KKYSYKTGLIAGLLLFALGCCLFWPAAIAGKYGLFLFALFVIASGLTFLETGANIFIVKL 140 Query: 147 GPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIA--KLSPAEQVAYRVQE 204 G +SA RL +QA N +G L G + ILS + +IA KLS E Y QE Sbjct: 141 GSSQSAERRLNFSQAFNPIGAVLGVLIGTIFILSGIEHNPVKIAVMKLS-GEYQHYLKQE 199 Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAI 264 V PYL LA L ++ + + P T++ ++ + + L++PH GVL+ Sbjct: 200 TMRVVTPYLVLAAFAVLWSILLMFTKFPKGTDELKEETQAPANAKELLKYPHFYKGVLSQ 259 Query: 265 FFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRK 324 FFY G + SF + Y+ D E+ A ++ + +GRF + ++ +SP K Sbjct: 260 FFYCGAQTCTWSFFIQYVQ--DYTGEPEKIAGYFLTGTLVAFGLGRFSATYIMRYVSPGK 317 Query: 325 LLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSL 384 L+ I+ IN+ALV+ ++ G V ++++ F S+M+PT F+L I +G S+ Sbjct: 318 LMGIYGVINIALVVIAILFPGVVGVWAIFFTSFFMSLMYPTNFALSIRSLGNNAKIGGSI 377 Query: 385 LIMAIVGGAIVPFVQGLFADHI-GVQHAFFLPLLCYAYIVFYGLYGSRIKSD 435 ++MAIVGGA P + GL A+ + A +PL+CY YI +Y GS+I ++ Sbjct: 378 MVMAIVGGAFFPPIMGLIAESAKSMAVAMVIPLICYLYIAYYAFRGSKIPNE 429 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: 504 Number of extensions: 28 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 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