GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Rhizobium etli CFN 42

Best path

deoP, deoK, deoC, adh, acs

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase RHE_RS02070 RHE_RS23340
deoC deoxyribose-5-phosphate aldolase RHE_RS00980
adh acetaldehyde dehydrogenase (not acylating) RHE_RS19035 RHE_RS20725
acs acetyl-CoA synthetase, AMP-forming RHE_RS21025 RHE_RS21035
Alternative steps:
aacS acetoacetyl-CoA synthetase RHE_RS03640 RHE_RS04635
ackA acetate kinase RHE_RS17585
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit RHE_RS25065
atoB acetyl-CoA C-acetyltransferase RHE_RS20545 RHE_RS23190
atoD acetoacetyl-CoA transferase, B subunit RHE_RS25070
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase RHE_RS23955 RHE_RS29990
deoxyribonate-transport 2-deoxy-D-ribonate transporter RHE_RS24105
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component RHE_RS04980 RHE_RS06225
garK glycerate 2-kinase RHE_RS09170
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme RHE_RS23475
pta phosphate acetyltransferase RHE_RS01970 RHE_RS12030

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 Apr 09 2024. 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 (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:

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. 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