Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Burk376:H281DRAFT_02714 Length = 331 Score = 277 bits (709), Expect = 2e-79 Identities = 139/315 (44%), Positives = 205/315 (65%), Gaps = 1/315 (0%) Query: 12 AAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYV 71 AA R L + + V +L+ ++++ S YF+T N M + R S+ ++++GM V Sbjct: 15 AADWIRACLRIRELNVLSVLLLVGLLISVFSPYFLTTNNLMGVFRSFSLIALMSIGMMLV 74 Query: 72 ILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPP 131 I+T GIDLSVGS++ + L +A+V GY AA+ AG+ G +G NGFM+ + +PP Sbjct: 75 IITGGIDLSVGSVMGLSSLVTALVFQHGYNAPAAIGAGLAVGIAVGAFNGFMITWIQLPP 134 Query: 132 FVATLGMLSIARGMTFILNDGSPIT-DLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMV 190 F+ATLG LSI RG+ +I+ G P+T D+PD++ +G G IG + P++I + +F +V Sbjct: 135 FIATLGTLSIGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMTAVFSVV 194 Query: 191 LRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQA 250 +R T +GRYVYA GGNE +AR SG+ +V F+VYV+SGL+A +AGV+ +R SA P + Sbjct: 195 MRQTRFGRYVYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFVSAEPAS 254 Query: 251 GVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLI 310 G ELD IAA IGG SLSGG GS+ G + GA L G+I NG+ LL + +Y QQ G + Sbjct: 255 GFGAELDVIAAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYAQQAITGCV 314 Query: 311 IVFAVLIDVWRKKKR 325 I+ AV ID+WR +++ Sbjct: 315 ILIAVSIDIWRVRRK 329 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: 263 Number of extensions: 9 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: 331 Length adjustment: 28 Effective length of query: 297 Effective length of database: 303 Effective search space: 89991 Effective search space used: 89991 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