Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate Dsui_2312 Dsui_2312 3-hydroxybutyrate dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__PS:Dsui_2312 Length = 260 Score = 110 bits (276), Expect = 2e-29 Identities = 79/259 (30%), Positives = 131/259 (50%), Gaps = 16/259 (6%) Query: 12 ITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-----EDVKDVAAQINPSRTLALQ 66 ++ K+A+VTG+ SGIG A+A + GA V+L + E ++ A + Sbjct: 2 LSGKIALVTGSTSGIGLAVARALARNGAAVMLNGSRPAAEAEGLRAAMAAEFGVKVAYTS 61 Query: 67 VDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLM 126 D+ ++ + A +K +DIL N+AG+ + ++ PEE WD+ + +NL F Sbjct: 62 ADLADAASVRALAAAAEKQLGVVDILVNNAGIQHVAAVDEFPEEKWDQLIAINLSSVFHA 121 Query: 127 AQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVN 186 + + M A G+IVN+AS ++A Y ASK A+V ++ +A+E A I N Sbjct: 122 TKAVLPGMKARNWGRIVNIASAHGLVASPFKAPYTASKHAVVGFSKAVALEVAETGITCN 181 Query: 187 AISPTVILTELGKKAWAGQ-----VGED--MKKLI----PAGRFGYPEEVAACALFLVSD 235 A+ P + T L +K A Q + ED ++ +I P RF +++A LFL S Sbjct: 182 AVCPGYVRTPLVEKQVAAQAKVHNLPEDQVIRDVILAAQPNKRFLEADDLAEFVLFLCSP 241 Query: 236 AASLITGENLIIDGGYTIK 254 A + +TG L +DG +T + Sbjct: 242 AGAGMTGAALPMDGAWTAR 260 Lambda K H 0.316 0.133 0.369 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: 146 Number of extensions: 13 Number of successful extensions: 3 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: 254 Length of database: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 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 (21.6 bits) S2: 47 (22.7 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