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_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 279 bits (714), Expect = 6e-80 Identities = 150/301 (49%), Positives = 201/301 (66%), Gaps = 5/301 (1%) Query: 22 LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSV 81 +++ L + +L+ +V S +F T N +IL+QTS+N I+AVGMT VILT GIDLSV Sbjct: 18 MEQKSLIALLVLIAIVSTMSPNFF-TVNNLFNILQQTSVNAIMAVGMTLVILTSGIDLSV 76 Query: 82 GSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSI 141 GS+LA G +A + L AV+A + GA +G V G +VA + F+ATL M+ + Sbjct: 77 GSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLL 136 Query: 142 ARGMTFILNDGSPI----TDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYG 197 RG+T + +GSP+ TD D + GIG+ I P+ I A+V L W +L +T G Sbjct: 137 LRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFLAAWYMLHHTRLG 196 Query: 198 RYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELD 257 RY+YA+GGNE + R SGI V KV VY + G+LA LAG++ AR +SA P AG YELD Sbjct: 197 RYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTAGTGYELD 256 Query: 258 AIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLI 317 AIAAVV+GGTSL+GG G IVGTL GAL++G +NNGLNLLGVSSYYQ + K ++I+ AVL+ Sbjct: 257 AIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLV 316 Query: 318 D 318 D Sbjct: 317 D 317 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: 232 Number of extensions: 7 Number of successful extensions: 2 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: 321 Length adjustment: 28 Effective length of query: 297 Effective length of database: 293 Effective search space: 87021 Effective search space used: 87021 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 Apr 09 2024. 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