Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Ga0059261_3850 Ga0059261_3850 Fucose permease
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Korea:Ga0059261_3850 Length = 423 Score = 240 bits (613), Expect = 5e-68 Identities = 157/400 (39%), Positives = 214/400 (53%), Gaps = 18/400 (4%) Query: 28 AMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVA 87 A + ++FF WGF+ ND LI ++ VF+L++ EA+L FF A+ +SLPA L+A Sbjct: 11 AFAAVAALFFAWGFVCANNDPLIAAVRHVFRLSWTEALLTHIVFFFAFATVSLPAAALLA 70 Query: 88 RLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAF---LGALFVLATGITVLQVAANAYVA 144 R G + I+ L G AG A+ + PAF LG LF+LA G+ LQVAAN A Sbjct: 71 RAGATRTILIAL---GSMLAGCLVIQAVRWVPAFGVVLGGLFLLAAGVATLQVAANPLAA 127 Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQE 204 LGP RLTLA +LNSLG FG +L+ L+PA A RV Sbjct: 128 ALGPPGQRHFRLTLAHSLNSLGMVCGAHFGAQFLLAEV--------NLTPA-MPASRVAG 178 Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAI 264 A T+ +L + + F LA+ R E+ A L LR + G AI Sbjct: 179 APTIAHAFLVIGGLTFGLALLTLAVR--RTIERAAPAPAPGGGLGDALRSRWAIAGAAAI 236 Query: 265 FFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVA-YYWLGAMIGRFIGSALLAKLSPR 323 YVG EV+IGS L+ +LS PD + A +VA YW GA+ GRF+GS L + Sbjct: 237 GLYVGAEVSIGSVLIPFLSSPDTLGLPAAVAGAYVANLYWGGALAGRFLGSWALRFIPAA 296 Query: 324 KLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASS 383 +LLA+FA AL L ++ G A + V++IGLFNSI+FPT+F L +ER G S Sbjct: 297 RLLALFAGSAAALCLAALVLPGPAAAWCVLAIGLFNSILFPTVFGLTLERSGVSEAATSG 356 Query: 384 LLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIV 423 LL +AI GA++PF+ G AD G+ F +P++ Y YI+ Sbjct: 357 LLCVAIGAGAVLPFLVGRIADLAGLGWTFVIPMIGYVYIL 396 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: 23 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: 423 Length adjustment: 32 Effective length of query: 410 Effective length of database: 391 Effective search space: 160310 Effective search space used: 160310 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