Align Sorbitol dehydrogenase; SDH; Galactitol 2-dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; EC 1.1.1.-; EC 1.1.1.16; EC 1.1.1.14 (characterized)
to candidate WP_078210695.1 BXU11_RS01105 SDR family NAD(P)-dependent oxidoreductase
Query= SwissProt::Q59787 (256 letters) >NCBI__GCF_002017945.1:WP_078210695.1 Length = 250 Score = 97.8 bits (242), Expect = 2e-25 Identities = 66/186 (35%), Positives = 97/186 (52%), Gaps = 4/186 (2%) Query: 6 KTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGP--AACAIALDVTDQ 63 KTALITG+ GIG+A A + ++ + + A E+ A + DV D+ Sbjct: 3 KTALITGATSGIGKATATLLAQNNFKIVLCGRRKDRLEALEKELSAFTAVHTLCFDVRDK 62 Query: 64 ASIDRCVAELLDRWGSIDILVNNAA-LFDLAPIVEITRESYDRLFAINVSGTLFMMQAVA 122 ++ +A L + + IDILVNNA L I + +D + INV G L++ +A+ Sbjct: 63 KAVFESIASLPEAFSDIDILVNNAGNAHGLDSIQNGDMDDWDAMIDINVKGLLYISKAII 122 Query: 123 RAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAP 182 MIA G IIN+ S AG+ VYCA+K AV +L QS ++L +GI V I P Sbjct: 123 PKMIAK-ESGHIINIGSIAGKEVYPNGNVYCASKYAVDALNQSMRMDLNPYGIRVGGIHP 181 Query: 183 GVVDGE 188 G+V+ E Sbjct: 182 GMVETE 187 Lambda K H 0.321 0.135 0.392 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: 130 Number of extensions: 7 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: 256 Length of database: 250 Length adjustment: 24 Effective length of query: 232 Effective length of database: 226 Effective search space: 52432 Effective search space used: 52432 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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