GapMind for catabolism of small carbon sources

 

Finding step dopDH for D-glucuronate catabolism in Paraburkholderia bryophila 376MFSha3.1

5 candidates for dopDH: 2,5-dioxopentanonate dehydrogenase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi H281DRAFT_01155 2,5-dioxopentanoate dehydrogenase (NAD+) Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 87% 100% 838.6 6-oxohexanoate dehydrogenase (EC 1.2.1.63) 49% 470.7
hi H281DRAFT_05316 NADP-dependent aldehyde dehydrogenase Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized) 64% 99% 655.6
hi H281DRAFT_02333 aldehyde dehydrogenase (NAD+) 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 61% 100% 578.2
hi H281DRAFT_03360 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 43% 98% 389 6-oxohexanoate dehydrogenase (EC 1.2.1.63) 41% 371.7
med H281DRAFT_03540 succinate semialdehyde dehydrogenase (EC 1.2.1.16) Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 44% 96% 373.2 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 63% 622.5

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step dopDH

Or cluster all characterized dopDH proteins

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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