Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 197 bits (501), Expect = 3e-55 Identities = 115/305 (37%), Positives = 174/305 (57%), Gaps = 11/305 (3%) Query: 22 LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSV 81 L G + +LLC+ + F T+ N M++L +T+ GI+AVGM +VI++ GIDLSV Sbjct: 38 LHGLGPVIGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSV 97 Query: 82 GSILAFAG-----LCSAMVATQGYGLLAAVSAGMFA---GAMLGVVNGFMVANLSIPPFV 133 GS+ A +AM G + A V + A GA+ G+V+G ++ I PF+ Sbjct: 98 GSMAALIAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFI 157 Query: 134 ATLGMLSIARGMTFILNDGSPIT---DLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMV 190 TLG L I R ++G IT DL D Y + + + +P+ IF +VA++ ++ Sbjct: 158 VTLGTLGIFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGVI 217 Query: 191 LRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQA 250 L T YGRYV A+G NE+ A+ + + V K+ Y++ G+ G+A ++ R SA P Sbjct: 218 LNRTAYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTT 277 Query: 251 GVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLI 310 G+ +EL+AIAAV++GGT L GG GSI GT+ GA+L+ VI+N LNL + S Y A Sbjct: 278 GLLWELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGF 337 Query: 311 IVFAV 315 ++ AV Sbjct: 338 VIIAV 342 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: 268 Number of extensions: 11 Number of successful extensions: 4 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: 350 Length adjustment: 28 Effective length of query: 297 Effective length of database: 322 Effective search space: 95634 Effective search space used: 95634 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