Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate SMc02452 SMc02452 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Smeli:SMc02452 Length = 325 Score = 248 bits (633), Expect = 1e-70 Identities = 142/308 (46%), Positives = 201/308 (65%), Gaps = 7/308 (2%) Query: 5 TITAPVTAAPRN---RLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSIN 61 +IT+ AAP + R+ ++ +G +F++L +V +F S+ F+T RN M+++RQ + Sbjct: 2 SITSASAAAPSSFTPRVLNAIRHYGTFGIFLVLVIVASFWSDAFLTERNLMNVVRQVASG 61 Query: 62 -GILAVGMTYVILTKGIDLSVGSILAFAG-LCSAMVATQGYGLLAAVSAGMFAGAMLGVV 119 GI+A+GM +V+LT+GIDLSVGSI A LC+ +VA QGYG+ A+ + GA GVV Sbjct: 62 AGIMAIGMLFVVLTRGIDLSVGSIAAVGSVLCAHLVAAQGYGVPMAILLVILTGAACGVV 121 Query: 120 NGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPIT-DLPDAYLA-LGIGKIGPIGVPI 177 GF VA + +P FV +L M++IARG++ I++ G PIT P A L G G + I P Sbjct: 122 TGFFVAYMRLPSFVISLAMMAIARGISLIISAGRPITMGSPGASLVDFGSGFLFGIPQPA 181 Query: 178 IIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGV 237 I+ V+ I +VL YT++GR V A+G NE++ R SG+ V + + SVYV+SG LA +AG+ Sbjct: 182 ILMLVIYAIGGVVLLYTSFGRIVTAIGSNEEAVRLSGVPVERYVLSVYVISGALAAVAGI 241 Query: 238 VLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLG 297 V + RT PQ GV ELD IAAVVIGG SL GG G + TL GAL++G+I N +NL G Sbjct: 242 VAAGRTGIGTPQVGVGAELDVIAAVVIGGASLMGGRGGMFNTLLGALILGIITNIMNLAG 301 Query: 298 VSSYYQQV 305 V Y+Q V Sbjct: 302 VPGYHQNV 309 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: 265 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 325 Length of database: 325 Length adjustment: 28 Effective length of query: 297 Effective length of database: 297 Effective search space: 88209 Effective search space used: 88209 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