GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase HTA01S_RS10655
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) HTA01S_RS03325 HTA01S_RS11515
acs acetyl-CoA synthetase, AMP-forming HTA01S_RS22665 HTA01S_RS06610
Alternative steps:
aacS acetoacetyl-CoA synthetase HTA01S_RS11125 HTA01S_RS10250
ackA acetate kinase HTA01S_RS04935
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit HTA01S_RS02180
atoB acetyl-CoA C-acetyltransferase HTA01S_RS02090 HTA01S_RS06660
atoD acetoacetyl-CoA transferase, B subunit HTA01S_RS02175
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase HTA01S_RS05325 HTA01S_RS01910
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit HTA01S_RS14805 HTA01S_RS13690
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit HTA01S_RS14800
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component HTA01S_RS05515
garK glycerate 2-kinase HTA01S_RS13215
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase HTA01S_RS23970

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