Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate BWI76_RS14605 BWI76_RS14605 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Koxy:BWI76_RS14605 Length = 336 Score = 223 bits (567), Expect = 7e-63 Identities = 127/309 (41%), Positives = 184/309 (59%), Gaps = 6/309 (1%) Query: 14 PRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVIL 73 PR L + L F+ CVV + + F+T NW++I+RQ++ I+A MT VI Sbjct: 17 PRRLLHNHSGVVSIALFFVFCCVVFSLITSNFLTGTNWLNIIRQSAPLLIVATAMTLVIT 76 Query: 74 TKGIDLSVGSILAFAGLCSAMVATQGYGLL--AAVSAGMFAGAMLGVVNGFMVANLSIPP 131 T GIDLSVGS LA G SA +A +GL + G+ G ++G +NGF +A IP Sbjct: 77 TGGIDLSVGSTLALVGALSA-IALNNWGLPWPVVLLGGLLLGGIVGAINGFFIAYEGIPA 135 Query: 132 FVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPI--IIFAVVALIFWM 189 F+ TL L++ RG+ ++ G I +P L IG+ +G+P+ +I ++ LI + Sbjct: 136 FIVTLATLAVVRGIALLVTQGYSIP-VPADSLFTFIGRAWVVGIPMPALIGIMILLIGHI 194 Query: 190 VLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQ 249 VL + +GRYV A+G N + AR SGI + V VY++SG+ A LAG++++AR S Sbjct: 195 VLNHMRFGRYVTAIGANAEGARRSGINTKAVTMKVYIISGMAAALAGMIITARLGSGSSN 254 Query: 250 AGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGL 309 G +EL IAAVV+G TSL GG G+I+GTL GAL I VI NGL L +S +Y Q+A G Sbjct: 255 QGEGFELQVIAAVVLGSTSLFGGFGTIIGTLLGALSIAVIQNGLILSHISPFYTQIATGT 314 Query: 310 IIVFAVLID 318 II+ A+ ++ Sbjct: 315 IILLAIWLN 323 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: 234 Number of extensions: 18 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: 336 Length adjustment: 28 Effective length of query: 297 Effective length of database: 308 Effective search space: 91476 Effective search space used: 91476 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