Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 178 bits (452), Expect = 1e-49 Identities = 105/300 (35%), Positives = 169/300 (56%), Gaps = 8/300 (2%) Query: 32 ILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAGLC 91 +LL ++A F+ N + TS +LA+G VILT+ IDLSV + LA G+ Sbjct: 18 LLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANLALTGMV 77 Query: 92 SAMV--ATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFIL 149 +MV A G ++ ++ + G +LG+ NG +V L IPP V TLG ++I RG+ F++ Sbjct: 78 VSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFRGIIFLI 137 Query: 150 NDGSPIT--DLPDAYLALGIGKIGPIGVPII--IFAVVALIFWMVLRYTTYGRYVYAVGG 205 +DG + ++ A+ A ++ +G+P++ I + ++F +V+ TT GR YA GG Sbjct: 138 SDGKWVNSHEMSPAFKAFPRAEL--LGLPVLSWIAILAVILFTIVMTRTTLGRAFYAAGG 195 Query: 206 NEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIG 265 N +A +GI V K F + +SG LAGL G + +R + +ELD +AA VIG Sbjct: 196 NPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFELDVVAACVIG 255 Query: 266 GTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKKR 325 G S+ GG G++ G L GAL +G+I N L ++ +S ++Q G I+ AV ++ +K+ Sbjct: 256 GVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAVALNAQANRKK 315 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: 252 Number of extensions: 12 Number of successful extensions: 3 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: 327 Length adjustment: 28 Effective length of query: 297 Effective length of database: 299 Effective search space: 88803 Effective search space used: 88803 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