GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Cupriavidus basilensis 4G11

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit RR42_RS04000 RR42_RS23005
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit RR42_RS09125 RR42_RS25790
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component RR42_RS10775 RR42_RS21615
deoxyribonate-transport 2-deoxy-D-ribonate transporter RR42_RS25070 RR42_RS04270
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase RR42_RS10315 RR42_RS13550
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme RR42_RS33585 RR42_RS25175
garK glycerate 2-kinase RR42_RS19865 RR42_RS33740
atoA acetoacetyl-CoA transferase, A subunit RR42_RS06555 RR42_RS35925
atoD acetoacetyl-CoA transferase, B subunit RR42_RS06560 RR42_RS35920
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
Alternative steps:
aacS acetoacetyl-CoA synthetase RR42_RS26915 RR42_RS10085
ackA acetate kinase RR42_RS03800 RR42_RS22745
acs acetyl-CoA synthetase, AMP-forming RR42_RS13880 RR42_RS10650
adh acetaldehyde dehydrogenase (not acylating) RR42_RS34255 RR42_RS25005
ald-dh-CoA acetaldehyde dehydrogenase, acylating RR42_RS27895 RR42_RS32630
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase RR42_RS28860
deoP deoxyribose transporter
pta phosphate acetyltransferase RR42_RS33690 RR42_RS03805

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, the preprint on GapMind for carbon sources, 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