Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 239 bits (611), Expect = 5e-68 Identities = 137/326 (42%), Positives = 192/326 (58%), Gaps = 16/326 (4%) Query: 15 RNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILT 74 + R R + +F ++L V + +S F + N M + Q + L V T VI+T Sbjct: 17 QQRRRDLIQKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQVTSIAYLGVAATCVIIT 76 Query: 75 KGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVA 134 GIDLSVGS+LA AG+ +A++ G + A+ GM GA G VNG V + +PPF+A Sbjct: 77 GGIDLSVGSVLALAGVAAALLVKAGVPIPVAMLGGMLVGAACGWVNGICVTRMGLPPFIA 136 Query: 135 TLGMLSIARGMTFILNDGSPITDLPDAYLALGIG---KIGPIGV-------------PII 178 TLGM+ +ARG+ + P++ L DA+ LG G +I IG P++ Sbjct: 137 TLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFRISHIGADGFPDTVFPGIPYPVV 196 Query: 179 IFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVV 238 I V+ ++L T+ GR++YAVG N ++AR SG+ V+ V YV+SGLLAG G V Sbjct: 197 IMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCV 256 Query: 239 LSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGV 298 L +R +A P GV YELDAIA+ VIGGTSL GG G+I GT GA +IGV+ NGLN+ GV Sbjct: 257 LMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGV 316 Query: 299 SSYYQQVAKGLIIVFAVLIDVWRKKK 324 SS+ QQ+ G++I+ V ID R +K Sbjct: 317 SSFIQQIIIGVVILGTVWIDQLRNRK 342 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: 248 Number of extensions: 7 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: 343 Length adjustment: 28 Effective length of query: 297 Effective length of database: 315 Effective search space: 93555 Effective search space used: 93555 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