GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Herbaspirillum aquaticum IEH 4430

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit CEJ45_RS18930
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit CEJ45_RS18925
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component CEJ45_RS18920 CEJ45_RS09485
deoxyribonate-transport 2-deoxy-D-ribonate transporter CEJ45_RS11375 CEJ45_RS04045
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CEJ45_RS09020 CEJ45_RS04050
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme CEJ45_RS09015
garK glycerate 2-kinase CEJ45_RS02860
atoA acetoacetyl-CoA transferase, A subunit CEJ45_RS12845 CEJ45_RS16020
atoD acetoacetyl-CoA transferase, B subunit CEJ45_RS12850 CEJ45_RS16025
atoB acetyl-CoA C-acetyltransferase CEJ45_RS14415 CEJ45_RS09425
Alternative steps:
aacS acetoacetyl-CoA synthetase CEJ45_RS14175
ackA acetate kinase CEJ45_RS14515 CEJ45_RS03830
acs acetyl-CoA synthetase, AMP-forming CEJ45_RS19345 CEJ45_RS12485
adh acetaldehyde dehydrogenase (not acylating) CEJ45_RS12165 CEJ45_RS06185
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase CEJ45_RS12160
deoK deoxyribokinase CEJ45_RS04290 CEJ45_RS12175
deoP deoxyribose transporter
pta phosphate acetyltransferase CEJ45_RS14510 CEJ45_RS09385

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