GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Halostagnicola larsenii XH-48

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase HALLA_RS07850
deoC deoxyribose-5-phosphate aldolase HALLA_RS02180
adh acetaldehyde dehydrogenase (not acylating) HALLA_RS14430 HALLA_RS18050
acs acetyl-CoA synthetase, AMP-forming HALLA_RS04270 HALLA_RS04260
Alternative steps:
aacS acetoacetyl-CoA synthetase HALLA_RS14455 HALLA_RS17725
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase HALLA_RS05820 HALLA_RS14160
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase HALLA_RS09780 HALLA_RS01605
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit HALLA_RS14270
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase HALLA_RS16360
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase HALLA_RS09975 HALLA_RS08450

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