Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate WP_110806514.1 C8J30_RS14100 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >NCBI__GCF_003217355.1:WP_110806514.1 Length = 339 Score = 231 bits (590), Expect = 1e-65 Identities = 135/336 (40%), Positives = 203/336 (60%), Gaps = 21/336 (6%) Query: 5 TITAPVTAAPRN---RLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSIN 61 T A + AAPR + + G+ LVF +L + S + M+ ++ Q S+ Sbjct: 6 TTGAEIKAAPRRLPPEVNILFVLVGIALVFEILGWIFQGQS-FLMSIDRLKIMILQVSVI 64 Query: 62 GILAVGMTYVILTKGIDLSVGSIL---AFAGLCSAMVATQGYGL---------LAAVSAG 109 GI++VG+T VI+ GIDLS GS++ A + A V+T + + ++ G Sbjct: 65 GIISVGVTQVIIAGGIDLSSGSVVGAVAMFAMSFAQVSTYARAVYPDLTDLPAIVPIALG 124 Query: 110 MFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGK 169 + AGA++G++NG ++A IPPF+ATLG + ARG G PI+ D + +G G Sbjct: 125 LMAGALVGLINGALIAYAKIPPFIATLGTMVTARGFAKWYTKGQPISFPTDDFAFIGKGM 184 Query: 170 IGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSG 229 + P+ IF VA IF + ++YT YG++ YA+G N+++AR SGI V + VYVV+ Sbjct: 185 M-----PVAIFLAVAAIFHVAMKYTRYGKFTYAIGANQQAARVSGINVEHHLIKVYVVAA 239 Query: 230 LLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVI 289 LA LAG+V++AR +A G++YELDAIA VIGG SL+GG GSI+GT+ G ++ GVI Sbjct: 240 TLAALAGMVVAARGQTAQAGMGLAYELDAIAMAVIGGVSLTGGRGSILGTMIGMVIFGVI 299 Query: 290 NNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKKR 325 +G L + +YYQ++ KG+IIV AV+ DV+R+KKR Sbjct: 300 ISGFTFLRLDAYYQEMIKGVIIVAAVVADVYRQKKR 335 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: 280 Number of extensions: 13 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: 339 Length adjustment: 28 Effective length of query: 297 Effective length of database: 311 Effective search space: 92367 Effective search space used: 92367 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 24 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