Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 264 bits (674), Expect = 3e-75 Identities = 158/324 (48%), Positives = 205/324 (63%), Gaps = 6/324 (1%) Query: 1 MNAKTITAPV-TAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTS 59 M A + AP+ T PR L + L +LL V ++E F+T RN ++IL + S Sbjct: 1 MTAPSSPAPLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVS 60 Query: 60 INGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYG-----LLAAVSAGMFAGA 114 I GI+AVGMT+VIL GID++VGS+LAFA + +A V T G L A+ G Sbjct: 61 IYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGL 120 Query: 115 MLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIG 174 G V G V L +P F+ TLG +++ RG T +LNDG PI+ DAY G G+I + Sbjct: 121 AGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLP 180 Query: 175 VPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGL 234 VP++IFA+VA + LRYT YGR VYAVGGN ++AR SG+ V + SVY + G LAGL Sbjct: 181 VPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGL 240 Query: 235 AGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLN 294 +G +LSAR SA AG YEL IA+VVIGG SL+GG+G + GT+ GALLIGV++NGL Sbjct: 241 SGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLV 300 Query: 295 LLGVSSYYQQVAKGLIIVFAVLID 318 +L V+SY QQV GLIIV AV D Sbjct: 301 MLHVTSYVQQVVIGLIIVAAVAFD 324 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: 241 Number of extensions: 9 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: 332 Length adjustment: 28 Effective length of query: 297 Effective length of database: 304 Effective search space: 90288 Effective search space used: 90288 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