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_b21375 SM_b21375 sugar uptake ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Smeli:SM_b21375 Length = 320 Score = 254 bits (648), Expect = 3e-72 Identities = 139/317 (43%), Positives = 208/317 (65%), Gaps = 4/317 (1%) Query: 11 TAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTY 70 TAA +R G+ L ++LC+V +F + FMT N+M+IL+Q ++ I A GMT+ Sbjct: 5 TAAKAALVRALKQYGGIFLSLVMLCIVFSFFNPRFMTVVNFMNILQQVAVVAIAAFGMTW 64 Query: 71 VILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIP 130 VIL IDLSVGSI+A AG+ A G G A++ + AGA++G++NG + A L +P Sbjct: 65 VILLGEIDLSVGSIIAVAGMVGAQCFAFGMGFAPAIALTLAAGALMGMLNGVLTAKLLLP 124 Query: 131 PFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVAL--IFW 188 F+ T+ + I RGM + +G+P + + A+G +G+PIII+ V L I Sbjct: 125 SFIVTVATMGIYRGMVSLPTNGAPAMIENETWTAIGTESF--LGLPIIIWVVAVLFVINQ 182 Query: 189 MVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALP 248 +VL T++GR Y GGN ++A SGI V ++ ++++SG++A ++GV+LS+R SA Sbjct: 183 IVLSKTSFGRRAYLTGGNREAAVYSGIKVDRLKILIFMISGVMAAISGVLLSSRLFSAQT 242 Query: 249 QAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKG 308 AG+SYELDAIAA V+GGTSL+GG G++VGTL GAL+IGV+NNG+N+L V +YQ + KG Sbjct: 243 NAGMSYELDAIAAAVLGGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSVPYFYQLIVKG 302 Query: 309 LIIVFAVLIDVWRKKKR 325 L+I+ AV +DV K+ + Sbjct: 303 LVILVAVWLDVRAKQAK 319 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: 290 Number of extensions: 20 Number of successful extensions: 1 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: 320 Length adjustment: 28 Effective length of query: 297 Effective length of database: 292 Effective search space: 86724 Effective search space used: 86724 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: 48 (23.1 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