GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Mesorhizobium ciceri WSM1271

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, 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 Mesci_1336 Mesci_3778
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit Mesci_1337
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component Mesci_4081 Mesci_5476
deoxyribonate-transport 2-deoxy-D-ribonate transporter
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase Mesci_5300 Mesci_0106
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme Mesci_6265 Mesci_5298
garK glycerate 2-kinase Mesci_0361
aacS acetoacetyl-CoA synthetase Mesci_2424 Mesci_2534
atoB acetyl-CoA C-acetyltransferase Mesci_1329 Mesci_1095
Alternative steps:
ackA acetate kinase Mesci_3747
acs acetyl-CoA synthetase, AMP-forming Mesci_1162 Mesci_0223
adh acetaldehyde dehydrogenase (not acylating) Mesci_0701 Mesci_5289
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
deoC deoxyribose-5-phosphate aldolase Mesci_0700
deoK deoxyribokinase Mesci_4408 Mesci_1753
deoP deoxyribose transporter
pta phosphate acetyltransferase Mesci_0182 Mesci_4113

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