Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate SM_b20714 SM_b20714 sugar uptake ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Smeli:SM_b20714 Length = 341 Score = 244 bits (623), Expect = 2e-69 Identities = 135/320 (42%), Positives = 197/320 (61%), Gaps = 18/320 (5%) Query: 18 LRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGI 77 L + L G+ LV+ +L + S + M + ++ Q S+ GI+AVG+T VI+T GI Sbjct: 25 LNIFLVLIGIALVYEVLGWLFVGQS-FLMNSQRLTIMILQVSVIGIIAVGVTQVIITGGI 83 Query: 78 DLSVGSILAFAGLCSAMVATQG------------YGLLAAVSAGMFAGAMLGVVNGFMVA 125 DLS GS++ + SA VA + + G+ G + G +NG ++A Sbjct: 84 DLSSGSVVGMTAMISASVAQASTWPRALYPSLTDLPAIVPIGLGVGIGLLAGFINGQLIA 143 Query: 126 NLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVAL 185 IPPF+ATLGM+ ARG++ G P++ L + + +G G P+I+F VVAL Sbjct: 144 RTKIPPFIATLGMMVSARGVSKWYTKGQPVSGLTEQFNFIGTGIW-----PVIVFLVVAL 198 Query: 186 IFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTS 245 IF + LRYT YG++ YA+G N ++AR SGI V + VY ++G+LAGLAGVV +AR + Sbjct: 199 IFHIALRYTRYGKFTYAIGANVQAARVSGINVEAHLVKVYAIAGMLAGLAGVVTAARAQT 258 Query: 246 ALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQV 305 A GV YELDAIAA VIGGTSL+GG G + GT+ G +++GV+ +G L V +YYQ++ Sbjct: 259 AQAGMGVMYELDAIAATVIGGTSLTGGVGRVTGTVIGTVILGVMTSGFTFLRVDAYYQEI 318 Query: 306 AKGLIIVFAVLIDVWRKKKR 325 KG+IIV AV++DV+R+K R Sbjct: 319 VKGIIIVAAVVVDVYRQKGR 338 Lambda K H 0.326 0.141 0.412 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: 275 Number of extensions: 14 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: 325 Length of database: 341 Length adjustment: 28 Effective length of query: 297 Effective length of database: 313 Effective search space: 92961 Effective search space used: 92961 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 (21.6 bits) S2: 49 (23.5 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