GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Rhodopseudomonas pseudopalustris DSM 123

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BMY71_RS14905 BMY71_RS13400
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component BMY71_RS10630 BMY71_RS15450
deoxyribonate-transport 2-deoxy-D-ribonate transporter
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BMY71_RS22535 BMY71_RS01625
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme BMY71_RS10960
garK glycerate 2-kinase BMY71_RS09745
atoA acetoacetyl-CoA transferase, A subunit BMY71_RS05605
atoD acetoacetyl-CoA transferase, B subunit BMY71_RS05610
atoB acetyl-CoA C-acetyltransferase BMY71_RS08240 BMY71_RS16330
Alternative steps:
aacS acetoacetyl-CoA synthetase BMY71_RS03035 BMY71_RS04345
ackA acetate kinase BMY71_RS04040 BMY71_RS22280
acs acetyl-CoA synthetase, AMP-forming BMY71_RS23035 BMY71_RS06665
adh acetaldehyde dehydrogenase (not acylating) BMY71_RS03050 BMY71_RS01975
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase BMY71_RS24195
deoP deoxyribose transporter
pta phosphate acetyltransferase BMY71_RS22275 BMY71_RS04035

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