Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 251 bits (641), Expect = 2e-71 Identities = 132/299 (44%), Positives = 201/299 (67%), Gaps = 5/299 (1%) Query: 32 ILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAGLC 91 +++C+ ++ +S F+T +I+ Q S+ GI AVG T+VI+T GIDLSVGS++A G+ Sbjct: 34 VIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVALTGMV 93 Query: 92 SAMV----ATQGYGL-LAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMT 146 +A V + GL +A + A + GA G +NG VA L + PF+ TL M+++ARG+T Sbjct: 94 AATVMAGSSPGAIGLGIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLAMMAMARGLT 153 Query: 147 FILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGN 206 ++DG D P+A+ A G + + +P+I+ V+ +I ++LR TT+G V+AVGGN Sbjct: 154 LAISDGRTKFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFGHQVFAVGGN 213 Query: 207 EKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGG 266 +++AR +GI V +V+F Y+++G+ A +AG+VL+ R SALP A EL IAAVVIGG Sbjct: 214 QEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQVIAAVVIGG 273 Query: 267 TSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKKR 325 TSL+GG GSIVGT G +LIGVIN GL+LLGV+ ++ Q +G +I AVL+D ++++ Sbjct: 274 TSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLLDALSQRRK 332 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: 286 Number of extensions: 16 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: 333 Length adjustment: 28 Effective length of query: 297 Effective length of database: 305 Effective search space: 90585 Effective search space used: 90585 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