Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 234 bits (596), Expect = 3e-66 Identities = 131/325 (40%), Positives = 201/325 (61%), Gaps = 9/325 (2%) Query: 1 MNAKTITAPVTAAPRNRLRLSLDRFGLPLVFI-LLCVVMAFSSEYFMTWRNWMDILRQTS 59 MN T+ P++A R+ F L + LLC+++A +S+ F+T N +++LRQ S Sbjct: 1 MNTATLFPPLSADARS--------FAYRLFALGLLCLLLAVASDAFLTLGNILNVLRQAS 52 Query: 60 INGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVV 119 + +LA G+T VILT G+DLSVG+ +A + +A V + V AG+ GA++G+ Sbjct: 53 LLFLLASGVTLVILTGGLDLSVGANVAMSACVAATVMKATGSTMLGVGAGLGTGALIGLA 112 Query: 120 NGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIII 179 NG +VA L IPPF+AT GML + G+T+ G I P A+ A+G G + + +P+ + Sbjct: 113 NGLLVAMLRIPPFIATYGMLWVLHGVTYWFMAGETIHGFPPAFRAIGSGYLWGVPIPVYL 172 Query: 180 FAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVL 239 V + + + TTYG+ +YA+G N +AR SG+ VR+ + VY+VSG +AG+A +V Sbjct: 173 MLVFLVAGTAMSQKTTYGQEIYAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVF 232 Query: 240 SARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVS 299 AR SA G + L AIAAV+IGGTSL GG G + GTL GA+++ ++ NG+NLL VS Sbjct: 233 LARLNSAEGDIGEALTLPAIAAVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVS 292 Query: 300 SYYQQVAKGLIIVFAVLIDVWRKKK 324 + +Q + G+I+V AV +D +K+ Sbjct: 293 ANWQPLVTGVIVVLAVFLDTLSRKR 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: 253 Number of extensions: 7 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: 322 Length adjustment: 28 Effective length of query: 297 Effective length of database: 294 Effective search space: 87318 Effective search space used: 87318 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