GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Collimonas arenae Ter10

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 CAter10_RS19685 CAter10_RS14955
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) CAter10_RS02910 CAter10_RS18190
acs acetyl-CoA synthetase, AMP-forming CAter10_RS15840 CAter10_RS16665
Alternative steps:
aacS acetoacetyl-CoA synthetase CAter10_RS19070
ackA acetate kinase CAter10_RS14415 CAter10_RS10715
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit CAter10_RS13190
atoB acetyl-CoA C-acetyltransferase CAter10_RS02100 CAter10_RS21010
atoD acetoacetyl-CoA transferase, B subunit CAter10_RS13185 CAter10_RS02130
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CAter10_RS05885 CAter10_RS01150
deoxyribonate-transport 2-deoxy-D-ribonate transporter CAter10_RS13675 CAter10_RS16495
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit CAter10_RS09950 CAter10_RS00520
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit CAter10_RS11315 CAter10_RS00515
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component CAter10_RS01155 CAter10_RS16060
garK glycerate 2-kinase CAter10_RS16330 CAter10_RS01900
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase CAter10_RS10720 CAter10_RS03950

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 24 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 (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