Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate SM_b20854 SM_b20854 sugar uptake ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Smeli:SM_b20854 Length = 331 Score = 242 bits (618), Expect = 8e-69 Identities = 131/300 (43%), Positives = 196/300 (65%), Gaps = 4/300 (1%) Query: 22 LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQT-SINGILAVGMTYVILTKGIDLS 80 + RFG +F++L V + S+ F+T N +++LRQ S GI+AVGM +VILT+GIDLS Sbjct: 23 VQRFGTLAIFLVLVAVATWWSDSFLTRGNLLNVLRQVASTAGIMAVGMLFVILTRGIDLS 82 Query: 81 VGSILAFAGLCSA-MVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGML 139 VGS++A + + A GYG A + + GA G+V G +A L +P FV +L M+ Sbjct: 83 VGSVMALGSVLTGYFCAMLGYGTGATIFLVLLCGAACGLVTGGFIAYLRLPSFVMSLAMM 142 Query: 140 SIARGMTFILNDGSPI--TDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYG 197 ++ARG++ I+++G PI +D A+ + G G + I P+I+ + + +VL +T +G Sbjct: 143 AVARGLSLIISEGRPIPLSDAGAAFSSFGSGFVLGIPQPVILMFAIYIAGGVVLNFTRFG 202 Query: 198 RYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELD 257 R + A+G NE++ R SGI V + + +VYV+SGLLAGLAG++ ++RT Q G+ EL+ Sbjct: 203 RVITAIGSNEEAVRLSGIAVPRYIVAVYVISGLLAGLAGIIAASRTGVGSAQVGIGAELN 262 Query: 258 AIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLI 317 IAAVVIGG SL GG G ++ TL GAL++G+I N +NL GV Y+QQV G IIV A+L+ Sbjct: 263 VIAAVVIGGASLMGGKGGVINTLLGALVMGIITNIMNLAGVPGYHQQVYMGAIIVVAMLL 322 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: 267 Number of extensions: 10 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: 331 Length adjustment: 28 Effective length of query: 297 Effective length of database: 303 Effective search space: 89991 Effective search space used: 89991 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