Align Sorbitol dehydrogenase; SDH; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.56; EC 1.1.1.9 (characterized)
to candidate GFF759 PGA1_c07730 putative zinc-binding alcohol dehydrogenase
Query= SwissProt::Q9FJ95 (364 letters) >FitnessBrowser__Phaeo:GFF759 Length = 326 Score = 122 bits (306), Expect = 1e-32 Identities = 88/293 (30%), Positives = 133/293 (45%), Gaps = 34/293 (11%) Query: 25 GINTLKIQPFLLPSVGPHDVRVRMKAVGICGSDVH-YLKTMRCADFVVKEPMVIGHECAG 83 G+ TL + + + P + +R+ A GICGSD+H YL D P+++GHE AG Sbjct: 8 GVETLVFRDVPMVAARPGEHLIRIHASGICGSDMHAYLGH----DNRRPAPLILGHEAAG 63 Query: 84 IIEEVGEEVKHLVVGDRVALEPGISCWRCNLCREGRYNLCPEMKFFATPPVHGSLANQVV 143 IE+ + G RV + P ++C C C GR NLC + + PP G+ A V Sbjct: 64 TIEDGPQ------AGRRVTINPLVTCGSCAACAAGRENLCASRQIISMPPREGAFAQFVA 117 Query: 144 HPADLCFKLPENVSLEEGAMCEPLSVGVHACRRA----EVGPETNVLVMGAGPIGLVTML 199 P +PE+V L + A+ EPL+V HA R A E LV+G G IGL L Sbjct: 118 MPERNLVTVPEDVPLSKAALAEPLAVSWHAARLALKALHPDMERRALVIGGGAIGLAAAL 177 Query: 200 AARAFSVPRIVIVDVDENRLA-VAKQLGADEIVQVTTNLEDVGSEVEQIQKAMGSNIDVT 258 A RA V + + + + R A +A G + +E + I + + Sbjct: 178 ALRAMGVEDVAVQEPNAARRAFLADHCGQQAV-----------AEFQGI-------VPLV 219 Query: 259 FDCAGFNKTMSTALAATRCGGKVCLVGMGHGIMTVPLTPAAAREVDVVGVFRY 311 D G+ T + A AA GG + VG+G + + +E+ +G + Y Sbjct: 220 LDAVGYAATRAAASAAAAPGGVIAHVGLGEDAGGLDIRRMTLQEITFIGTYTY 272 Lambda K H 0.321 0.137 0.417 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: 312 Number of extensions: 24 Number of successful extensions: 4 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: 364 Length of database: 326 Length adjustment: 29 Effective length of query: 335 Effective length of database: 297 Effective search space: 99495 Effective search space used: 99495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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