Align Glucose/galactose porter (characterized)
to candidate N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Dyella79:N515DRAFT_1918 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:
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