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_085121058.1 B9O00_RS01465 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 215 bits (547), Expect = 1e-60 Identities = 125/299 (41%), Positives = 180/299 (60%), Gaps = 4/299 (1%) Query: 20 LSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDL 79 L L GL LV + V++ S YF+T N +IL Q+ + GIL++GMT+VILT GIDL Sbjct: 32 LELRMLGLALV---IGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDL 88 Query: 80 SVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGML 139 SVGS+ +G+ + A + Y + A+ G+ GA +G+V+G ++ + FV TLGM+ Sbjct: 89 SVGSVAGLSGIVLGL-ALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGMM 147 Query: 140 SIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRY 199 +I R + +I + + I+ P ++ + I ++ L+ W L YT GR Sbjct: 148 AIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTKGGRT 207 Query: 200 VYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAI 259 +YA+G N+++AR +G+GV YVVSG LA +A A+ S P G ELDAI Sbjct: 208 IYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGNGMELDAI 267 Query: 260 AAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLID 318 AAVVIGG SL GG GSIVGTL G L++ +I NGLNLLGVS ++Q A G II+ A+L++ Sbjct: 268 AAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMALLVE 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: 257 Number of extensions: 18 Number of successful extensions: 2 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: 335 Length adjustment: 28 Effective length of query: 297 Effective length of database: 307 Effective search space: 91179 Effective search space used: 91179 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 Apr 09 2024. 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