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 BWI76_RS11535 BWI76_RS11535 putative oxidoreductase, Zn-dependent and NAD(P)-binding protein
Query= curated2:Q9Z9U1 (343 letters) >FitnessBrowser__Koxy:BWI76_RS11535 Length = 358 Score = 181 bits (459), Expect = 3e-50 Identities = 113/358 (31%), Positives = 180/358 (50%), Gaps = 23/358 (6%) Query: 1 MKALVKTQHGTGHFAVQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYPVAAPVTL-- 58 MKAL + G + + + PEP G V I++K +CG+D+ HY V + Sbjct: 1 MKALARFGKAFGGYKMIDVPEPVCGPDDVVIEIKAAAICGADMK----HYNVDSGSDQFN 56 Query: 59 ---GHEFSGEIVELGEGVTGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLG--- 112 GHEF+G IV +G+ V + VG RV S+ + +CG C C GD+ C+ + LG Sbjct: 57 SIRGHEFAGAIVRVGDKVKDWKVGQRVVSDNSGHVCGVCPACEQGDFLCCAEKVNLGLDN 116 Query: 113 NQQDGSFAKYVIA-------RQESLHHLPAGVDDRSAAMTEPLACTHHAIAKTS-INKGD 164 N G F+KY + + +L +P GVD AA+ +P+ + ++A+ S G Sbjct: 117 NTWGGGFSKYCLVPGEILKIHRHALWEIPPGVDYEDAAVLDPICNAYKSLAQQSKFLPGQ 176 Query: 165 LVVVTGPGPIGLLAAQVAKSHGG-TVIITGLSND-QVRLKKAKEVGIDYAIDTQEVDIKE 222 VVV G GP+GL + Q+A+ G +++ GL D VR AK +G ++ D+ Sbjct: 177 DVVVFGTGPLGLFSVQMARIMGAVNIVMVGLEEDVAVRFPIAKALGATAVVNASTEDVVA 236 Query: 223 LVSELTDGYGADVVLECSGAVPAAKQGIDLLRKKGQYAQVGLFAQPEIQFNFEKIIQKEI 282 + +V+ECSGA A KQ I++LR G+ +VG+ QP + F+ I Sbjct: 237 RCQAICGKDNLGLVIECSGANIALKQSIEMLRPNGEVVRVGMGFQP-LDFSINDITTWNK 295 Query: 283 SVVGSRSQKPADWEPALSLLNEKKVNAKTLVTHEYTISEWDKAYHAIKSGEAIKVLLT 340 S++G + W A+ LL + K ++TH +S+W + + A+ AIKV++T Sbjct: 296 SIIGHMAYDSTSWRNAIRLLASGAIKVKPMITHRIGLSQWREGFDAMVDKTAIKVIMT 353 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: 343 Number of extensions: 23 Number of successful extensions: 6 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: 358 Length adjustment: 29 Effective length of query: 314 Effective length of database: 329 Effective search space: 103306 Effective search space used: 103306 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