Align Sorbitol dehydrogenase; SDH; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 (characterized)
to candidate SM_b20445 SM_b20445 alcohol dehydrogenase
Query= SwissProt::Q58D31 (356 letters) >FitnessBrowser__Smeli:SM_b20445 Length = 352 Score = 200 bits (508), Expect = 5e-56 Identities = 119/327 (36%), Positives = 186/327 (56%), Gaps = 8/327 (2%) Query: 13 VHGPGDLRLENYPIPEPGPNEVLLKMHSVGICGSDVHYWQHGRIGDFVVKKPMVLGHEAS 72 ++GP DLRLE +P PG EVLLKM + GICGSD+HY+Q G G V++P++ GHEAS Sbjct: 13 LYGPRDLRLEVADVPAPGDGEVLLKMAAGGICGSDLHYYQDGGFGPVRVREPIIPGHEAS 72 Query: 73 GTVVKVGSLVRHLQPGDRVAIEPGAPRETDEFCKIGRYNLSPTIFFCAT----PPDDGNL 128 G V +G+ V L D VA+ P P T FC G + F + P G Sbjct: 73 GRVAVLGAGVSGLAIDDLVAVNPSQPCGTCRFCGEGLPVHCLDMRFLGSAMRLPHTQGMF 132 Query: 129 CRFYKHNANFCYKLPDNVTFEEGALIEPLSVGIHACRRAGVTLGNKVLVCGAGPIGLVSL 188 + A C+ V+ E A EPL+V +HA +AG G KVLV GAGPIG + + Sbjct: 133 RDWLVVPAVQCHPAGSQVSPGEAACAEPLAVCLHAAAQAGEIRGKKVLVTGAGPIGALVV 192 Query: 189 LAAKAMGAAQVVVTDLSASRLSKAKEVGADFILQISNESPQEIAKKVEGLLGSKPEVTIE 248 AA+ GA ++VVTDL+ + L +AK +GA I+ + + A + + K V E Sbjct: 193 AAARHAGADEIVVTDLADAALDRAKAMGATRIVNVHRDPAGLAAYEAD---KGKFHVAFE 249 Query: 249 CTGVETSIQAGIYATHSGGTLVLVGLGSEMTSVPLVHAATREVDIKGVFRYCNTWPMAIS 308 C+ E +++ + A GT+V VG+ E+T +PL +E+ + G R+ + +A++ Sbjct: 250 CSAAEPALRGAVAAVRPRGTIVQVGVTGEIT-LPLHALVGKELRLVGSQRFDGEFALAVA 308 Query: 309 MLASKSVNVKPLVTHRFPLEKALEAFE 335 +++ + ++V+P+++H+FP+++A+ AFE Sbjct: 309 LISDRRIDVRPIISHQFPVDEAVRAFE 335 Lambda K H 0.318 0.136 0.410 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: 341 Number of extensions: 18 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: 356 Length of database: 352 Length adjustment: 29 Effective length of query: 327 Effective length of database: 323 Effective search space: 105621 Effective search space used: 105621 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: 41 (21.7 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