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_061940318.1 CPter91_RS11535 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >NCBI__GCF_001584185.1:WP_061940318.1 Length = 334 Score = 182 bits (461), Expect = 1e-50 Identities = 117/306 (38%), Positives = 168/306 (54%), Gaps = 12/306 (3%) Query: 22 LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSV 81 L G L I LC+ + F T N M++L +T+ GI+AVGMT+VI++ GIDLSV Sbjct: 21 LKGLGPVLGLIGLCIAGTLLNGDFATVDNLMNVLTRTAFIGIIAVGMTFVIISGGIDLSV 80 Query: 82 GSILAFAG---------LCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPF 132 GS+ A L SA LL ++ + G G ++G ++ I F Sbjct: 81 GSMAALIAGSMIYFMNMLMSAGTLGPLTILLIGIAMALLLGLAFGCLHGLLITKGKIEAF 140 Query: 133 VATLGMLSIARGMTFILNDGSPIT---DLPDAYLALGIGKIGPIGVPIIIFAVVALIFWM 189 + TLG L I R + L DG +T L D Y + + I +PI +F VAL + Sbjct: 141 IVTLGTLGIFRSVLTYLADGGALTLDNQLSDLYSPVYYTSLLGIPIPIWVFLAVALGGAL 200 Query: 190 VLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQ 249 +L T +GR+V A+G NE+ AR + I V V Y++ G+ G+A V+ R SA P Sbjct: 201 ILNRTAFGRHVQAIGSNEQVARYAAIRVDFVKTCTYMLLGVCVGIATVLYVPRLGSASPT 260 Query: 250 AGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGL 309 G+ +EL+AIAAVV+GGT+L GG+G IVGT+ GA+L+ VI+N LNL + S Y A Sbjct: 261 TGLLWELEAIAAVVVGGTALKGGSGRIVGTVVGAILLSVISNILNLTSIISVYLNAAVQG 320 Query: 310 IIVFAV 315 +++ AV Sbjct: 321 VVIIAV 326 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: 236 Number of extensions: 10 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: 334 Length adjustment: 28 Effective length of query: 297 Effective length of database: 306 Effective search space: 90882 Effective search space used: 90882 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