Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 166 bits (421), Expect = 6e-46 Identities = 104/323 (32%), Positives = 173/323 (53%), Gaps = 13/323 (4%) Query: 21 LALPASRGKRARSELARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALV 80 + P + R R L+ L L LL V+ AF S F+T N + +L ++ ++ Sbjct: 6 ITAPVTAAPRNRLRLS-LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGIL 64 Query: 81 VLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVI 140 + + ++LT DLS+ S + A AM+ A+ G+G+ +AG+ A GA++ Sbjct: 65 AVGMTYVILTKGIDLSVGSILAFAGLCSAMV----ATQGYGLLAAVSAGMFA----GAML 116 Query: 141 GFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIV--LGLP 198 G +NGF+V L + F+ TL ML + RGM G + D+P ++ AL + +G+P Sbjct: 117 GVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVP 176 Query: 199 LSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASV 258 + ++ A I +LRY GR +YA+GGN ++AR +GI V ++ + V+V+ +LA + Sbjct: 177 IIIFAVVAL--IFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGL 234 Query: 259 GGLIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLT 318 G++++ + G AA VIGG SL GG G++ G L G LL+GV+ N L Sbjct: 235 AGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLN 294 Query: 319 LAQVPSFWIQAIYGAIILGSLMV 341 L V S++ Q G II+ ++++ Sbjct: 295 LLGVSSYYQQVAKGLIIVFAVLI 317 Lambda K H 0.326 0.140 0.397 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: 246 Number of extensions: 12 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: 351 Length of database: 325 Length adjustment: 28 Effective length of query: 323 Effective length of database: 297 Effective search space: 95931 Effective search space used: 95931 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