GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Acidovorax sp. GW101-3H11

Best path

deoP, deoK, deoC, adh, acs

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase Ac3H11_1839 Ac3H11_700
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
acs acetyl-CoA synthetase, AMP-forming Ac3H11_951 Ac3H11_191
Alternative steps:
aacS acetoacetyl-CoA synthetase Ac3H11_3009 Ac3H11_4867
ackA acetate kinase Ac3H11_4666
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit Ac3H11_132 Ac3H11_3922
atoB acetyl-CoA C-acetyltransferase Ac3H11_178 Ac3H11_2303
atoD acetoacetyl-CoA transferase, B subunit Ac3H11_131 Ac3H11_3921
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase Ac3H11_493 Ac3H11_2762
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit Ac3H11_2238 Ac3H11_3699
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit Ac3H11_3700 Ac3H11_2239
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component Ac3H11_2872 Ac3H11_3427
garK glycerate 2-kinase Ac3H11_1084
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme Ac3H11_1929
pta phosphate acetyltransferase Ac3H11_1079 Ac3H11_4331

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 (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