Align Glucose/galactose porter (characterized)
to candidate N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease
Query= TCDB::P0C105 (412 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease Length = 442 Score = 413 bits (1062), Expect = e-120 Identities = 216/408 (52%), Positives = 282/408 (69%), Gaps = 16/408 (3%) Query: 20 NYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAG 79 +Y A+ LT +FFMWGF+TCLNDILIPHLK VF+LNY ++ML+QF FFGAYF++SLPAG Sbjct: 24 DYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAG 83 Query: 80 QLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYV 139 LV R+ YK+GIV GL VA +G A F PAA+ Y FLGALFVLA+G+T+LQVAAN YV Sbjct: 84 LLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYV 143 Query: 140 TILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVN--------------A 185 +LG ++A+SRLTL QA NSLGT +AP FG +LILSAA + Sbjct: 144 ALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQ 203 Query: 186 EADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKEG--SAWQYRHLVLGAIG 243 EA V+ PYL LA+ +LA+ + + P + E S K+ S ++ H++ G + Sbjct: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLA 263 Query: 244 IFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDG 303 IF YVG EV++GSFLVN+LS P + +SE AA+ VAY+W GAM+GRFIGSA + + Sbjct: 264 IFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPR 323 Query: 304 KALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSG 363 K LA A + + L+ T+ T G +AM+SV++IGLFNSIMFPTIFSL + +G T + S Sbjct: 324 KLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASS 383 Query: 364 ILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGLIGSK 411 +L +AIVGGAIVP +QG AD IG+ AF +P++CYAYI FYGL GS+ Sbjct: 384 LLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSR 431 Lambda K H 0.328 0.141 0.420 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: 596 Number of extensions: 29 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: 412 Length of database: 442 Length adjustment: 32 Effective length of query: 380 Effective length of database: 410 Effective search space: 155800 Effective search space used: 155800 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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