Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Ga0059261_0767 Ga0059261_0767 glucose/galactose transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Korea:Ga0059261_0767 Length = 434 Score = 337 bits (863), Expect = 6e-97 Identities = 197/430 (45%), Positives = 267/430 (62%), Gaps = 7/430 (1%) Query: 4 AAPPAPSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAE 63 AAP ++ P + + + P + ++FF++G +T LND++IP LK +F LNY + Sbjct: 2 AAPVTQLSSTDPASGDAQGINAPDLQVFVFALFFIFGGITSLNDVIIPKLKELFTLNYTQ 61 Query: 64 AMLVQFTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLG 123 AMLVQF FF AY ++ +P LV +LGY +G VAGL VG F PA+ Y FL Sbjct: 62 AMLVQFCFFTAYLVIGIPGAKLVKKLGYMRGAVAGLLTMMVGCLLFIPASQYATYGVFLF 121 Query: 124 ALFVLATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLIL-SAA 182 ALFVLA+G+ ++QV AN ++LLG ++A SRLT AQA NSLGT + P G +LIL S A Sbjct: 122 ALFVLASGVVIVQVVANPLISLLGKPETAHSRLTFAQAFNSLGTTVFPIVGSILILGSLA 181 Query: 183 VLSAEQIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQAS 242 ++A+Q++ PA + AYRV E++ + YLG+A L ++A V+LFR L + QAS Sbjct: 182 TVTADQLS--GPALE-AYRVAESKAIMHGYLGIAAALAVVAGVVWLFR-NRLKGERHQAS 237 Query: 243 VKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYY 302 L L P FG L IF YVG EV+IGS +VNYL P + + EQAA + +Y Sbjct: 238 AGLAGL-DLLGRPRFGFGALCIFLYVGAEVSIGSLIVNYLMQPGVMGLQEQAAGKLIGFY 296 Query: 303 WLGAMIGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIM 362 W GAM+GRFIGS L+ +SP KLLA A +AL+L + T G VA YS+++IGL NSIM Sbjct: 297 WGGAMVGRFIGSGLMRVISPGKLLAFVAVGAVALILISTNTTGHVAGYSLLAIGLMNSIM 356 Query: 363 FPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAY 421 FPTIFSL E++G + S ++ +AI GGA+VP G AD G + A LP +CYA Sbjct: 357 FPTIFSLASEKLGGRAADGSGIINIAIFGGAVVPLATGALADATGSLGLALILPAICYAI 416 Query: 422 IVFYGLYGSR 431 I +G Y R Sbjct: 417 IAGFGYYARR 426 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: 515 Number of extensions: 21 Number of successful extensions: 3 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: 434 Length adjustment: 32 Effective length of query: 410 Effective length of database: 402 Effective search space: 164820 Effective search space used: 164820 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