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 Pf6N2E2_668 2,3-butanediol dehydrogenase, R-alcohol forming, (R)- and (S)-acetoin-specific (EC 1.1.1.4)
Query= curated2:Q9Z9U1 (343 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_668 Length = 364 Score = 196 bits (497), Expect = 1e-54 Identities = 124/326 (38%), Positives = 169/326 (51%), Gaps = 17/326 (5%) Query: 9 HGTGHFAVQEKPEP-TPGKHQVKIKVKYTGVCGSDIHTYEG---HYPVAAP--------- 55 HG V++ P P +P V+I+V++ G+CGSD+H Y PV AP Sbjct: 17 HGRNDIRVEDVPLPVSPPAGWVQIRVQWCGICGSDLHEYVAGPVFIPVDAPHPLTGIKGQ 76 Query: 56 VTLGHEFSGEIVELGEGVTGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLGNQQ 115 LGHEF GEIVELG GV GF+VG+ V ++ CG C YCT G YN+C + G Sbjct: 77 CILGHEFCGEIVELGAGVEGFSVGEPVAADACQH-CGTCYYCTHGLYNICENLAFTGLMN 135 Query: 116 DGSFAKYVIARQESLHHLPAGVDDRSAAMTEPLACTHHAIAKTSINKGDLVVVTGPGPIG 175 +G+FA+ V L+ LPA + A+ EPLA HA+ K G VVV G G IG Sbjct: 136 NGAFAELVNVPANLLYKLPADFPAEAGALIEPLAVGMHAVKKAGSLLGQNVVVVGAGTIG 195 Query: 176 LLAAQVAKSHGGTVIITGLSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSELTDGYGADV 235 L AK+ G +I L R KA EVG + ID E D V LT G GADV Sbjct: 196 LCTIMCAKAAGAAQVI-ALEMSGARKAKALEVGASHVIDPNECDALAEVRRLTGGLGADV 254 Query: 236 VLECSGAVPAAKQGIDLLRKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVGSRSQKPADW 295 EC G AK IDL+RK G+ VG+F +P QFNF +++ E V+G+ + ++ Sbjct: 255 SFECIGNKHTAKLAIDLIRKAGKCVLVGIFEEPS-QFNFFELVSTEKQVLGALAYN-GEF 312 Query: 296 EPALSLLNEKKVNAKTLVTHEYTISE 321 ++ + + +++ LVT + E Sbjct: 313 ADVIAFIADGRLDISPLVTGRIQLEE 338 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: 373 Number of extensions: 20 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: 364 Length adjustment: 29 Effective length of query: 314 Effective length of database: 335 Effective search space: 105190 Effective search space used: 105190 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