Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 191 bits (486), Expect = 2e-53 Identities = 115/313 (36%), Positives = 178/313 (56%), Gaps = 21/313 (6%) Query: 27 LPLVFILLCVV---MAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGS 83 +PL+ ++ + + S++F + + IL+Q I GI+A + VILT GIDLSVG+ Sbjct: 47 VPLIVLVAAIAVFGLLLGSKFFSPFALTL-ILQQVQIVGIVAAAQSLVILTAGIDLSVGA 105 Query: 84 ILAFAGLCSAMVATQGYGLLA--AVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSI 141 I+ + + T YGL AV+ G+ G +LG +NG++VA + +PPF+ TLGM I Sbjct: 106 IMVMSSVVMGQF-TFRYGLPVEVAVACGLLCGTLLGFINGWLVAKVKLPPFIVTLGMWQI 164 Query: 142 ARGMTFI-----------LNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMV 190 F+ + D +P+ L +G ++ GV ++ V+ L + Sbjct: 165 VLAANFLYSRNETIRSQDIRDQAPLLQFFGTTLEIGGARL-TYGVIFMVLLVIVLAY--A 221 Query: 191 LRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQA 250 LR+T +GR+VYAVG + ++A SG+ V + + SVY++SGL+ AG L R S P + Sbjct: 222 LRHTAWGRHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRIGSVSPTS 281 Query: 251 GVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLI 310 G +++I AVVIGG SL GG GSI+G FGAL++GV GL LLG + + + GL+ Sbjct: 282 GQLANIESITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGADAQWTFLLIGLL 341 Query: 311 IVFAVLIDVWRKK 323 I+ AV +D W +K Sbjct: 342 IIAAVAVDQWIRK 354 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: 245 Number of extensions: 7 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: 357 Length adjustment: 28 Effective length of query: 297 Effective length of database: 329 Effective search space: 97713 Effective search space used: 97713 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