GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudovibrio axinellae Ad2

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase PsAD2_RS19340
deoC deoxyribose-5-phosphate aldolase PsAD2_RS00220
adh acetaldehyde dehydrogenase (not acylating) PsAD2_RS08775 PsAD2_RS20005
acs acetyl-CoA synthetase, AMP-forming PsAD2_RS07830 PsAD2_RS06350
Alternative steps:
aacS acetoacetyl-CoA synthetase PsAD2_RS03405 PsAD2_RS19145
ackA acetate kinase PsAD2_RS00020 PsAD2_RS14055
ald-dh-CoA acetaldehyde dehydrogenase, acylating PsAD2_RS20005
atoA acetoacetyl-CoA transferase, A subunit PsAD2_RS20290 PsAD2_RS17690
atoB acetyl-CoA C-acetyltransferase PsAD2_RS01745 PsAD2_RS08175
atoD acetoacetyl-CoA transferase, B subunit PsAD2_RS20285 PsAD2_RS17685
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase PsAD2_RS00800 PsAD2_RS18230
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit PsAD2_RS05790 PsAD2_RS19405
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit PsAD2_RS19410
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase PsAD2_RS10045
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme PsAD2_RS00840
pta phosphate acetyltransferase PsAD2_RS00025 PsAD2_RS14060

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