Align Sorbitol dehydrogenase; SDH; EC 1.1.1.-; Glucitol dehydrogenase; L-iditol 2-dehydrogenase; EC 1.1.1.14; Polyol dehydrogenase; Xylitol dehydrogenase; EC 1.1.1.9 (uncharacterized)
to candidate RR42_RS09405 RR42_RS09405 butanediol dehydrogenase
Query= curated2:Q9Z9U1 (343 letters) >FitnessBrowser__Cup4G11:RR42_RS09405 Length = 357 Score = 209 bits (531), Expect = 1e-58 Identities = 133/335 (39%), Positives = 177/335 (52%), Gaps = 21/335 (6%) Query: 1 MKALVKTQHGTGHFAVQEKPEPT-PGKHQVKIKVKYTGVCGSDIHTYEGHYPVAAPVT-- 57 MKA V G V+E P P + VKI+V + G+CGSD+H Y PV PV Sbjct: 1 MKAAV--WRGRHDVRVEEVRVPDKPAEGWVKIRVHWCGICGSDLHEYVAG-PVFIPVDHP 57 Query: 58 -----------LGHEFSGEIVELGEGVTGFNVGDRVTSETTYSICGKCSYCTSGDYNLCS 106 LGHEFSGEI ELG GVTGF VG+RVT++ CGKC YCT G YN+C Sbjct: 58 HPLTGLKGQCILGHEFSGEIAELGAGVTGFKVGERVTADACQH-CGKCYYCTHGLYNICE 116 Query: 107 HRKGLGNQQDGSFAKYVIARQESLHHLPAGVDDRSAAMTEPLACTHHAIAKTSINKGDLV 166 G +G+FA+YV E L+ LP + A+ EPLA HA+ K G V Sbjct: 117 SLAFTGLMNNGAFAEYVNVPAELLYKLPENFPTEAGALIEPLAVGLHAVKKAGNIVGQTV 176 Query: 167 VVTGPGPIGLLAAQVAKSHGGTVIITGLSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSE 226 VV G G IGL AK+ G II L R KKA EVG + ID +E D V Sbjct: 177 VVVGAGTIGLCTIMCAKAAGAGRII-ALEMSSARKKKALEVGANVVIDPKECDAIAQVKA 235 Query: 227 LTDGYGADVVLECSGAVPAAKQGIDLLRKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVG 286 LT GYGADV EC G AK ID++RK G+ VG+F +P FNF +I+ E ++G Sbjct: 236 LTGGYGADVSFECIGNKATAKLAIDVIRKAGKCVMVGIFEEPS-AFNFFEIVSTEKEIIG 294 Query: 287 SRSQKPADWEPALSLLNEKKVNAKTLVTHEYTISE 321 S + ++ + + + +++ + L+T ++++ Sbjct: 295 SLAYN-GEFADVIRFIADGRIDVQPLITGRISLAD 328 Lambda K H 0.315 0.133 0.388 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: 379 Number of extensions: 19 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: 343 Length of database: 357 Length adjustment: 29 Effective length of query: 314 Effective length of database: 328 Effective search space: 102992 Effective search space used: 102992 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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