GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB

Also see fitness data for the top candidates

Rules

Overview: Deoxyribose utilization in GapMind is based on MetaCyc pathways 2-deoxy-D-ribose degradation I via deoxyribose 5-phosphate aldolase (link) and pathway II via oxidation to 2-deoxy-3-dehydro-D-ribonate (link).

19 steps (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit H281DRAFT_01474 H281DRAFT_05399
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit H281DRAFT_05400 H281DRAFT_01475
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component H281DRAFT_05401 H281DRAFT_01762
deoxyribonate-transport 2-deoxy-D-ribonate transporter H281DRAFT_00642 H281DRAFT_01229
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase H281DRAFT_00644 H281DRAFT_03703
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme H281DRAFT_00641 H281DRAFT_03174
garK glycerate 2-kinase H281DRAFT_00894
atoA acetoacetyl-CoA transferase, A subunit H281DRAFT_04495 H281DRAFT_01597
atoD acetoacetyl-CoA transferase, B subunit H281DRAFT_04496 H281DRAFT_01596
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
Alternative steps:
aacS acetoacetyl-CoA synthetase H281DRAFT_02398 H281DRAFT_06226
ackA acetate kinase H281DRAFT_00303 H281DRAFT_01409
acs acetyl-CoA synthetase, AMP-forming H281DRAFT_04953 H281DRAFT_05523
adh acetaldehyde dehydrogenase (not acylating) H281DRAFT_01117 H281DRAFT_02299
ald-dh-CoA acetaldehyde dehydrogenase, acylating H281DRAFT_01665
deoC deoxyribose-5-phosphate aldolase H281DRAFT_01118
deoK deoxyribokinase H281DRAFT_01116 H281DRAFT_05229
deoP deoxyribose transporter
pta phosphate acetyltransferase H281DRAFT_01410 H281DRAFT_06308

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

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