GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Sphingomonas histidinilytica UM2

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit B5X82_RS05920 B5X82_RS07160
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit B5X82_RS05915 B5X82_RS20220
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribonate-transport 2-deoxy-D-ribonate transporter B5X82_RS15820
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase B5X82_RS11260 B5X82_RS14100
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme B5X82_RS18255 B5X82_RS00980
garK glycerate 2-kinase
atoA acetoacetyl-CoA transferase, A subunit B5X82_RS06855 B5X82_RS24535
atoD acetoacetyl-CoA transferase, B subunit B5X82_RS06850 B5X82_RS24530
atoB acetyl-CoA C-acetyltransferase B5X82_RS18105 B5X82_RS24295
Alternative steps:
aacS acetoacetyl-CoA synthetase B5X82_RS11030 B5X82_RS02835
ackA acetate kinase B5X82_RS10990
acs acetyl-CoA synthetase, AMP-forming B5X82_RS24705 B5X82_RS19755
adh acetaldehyde dehydrogenase (not acylating) B5X82_RS24620 B5X82_RS22235
ald-dh-CoA acetaldehyde dehydrogenase, acylating B5X82_RS20945
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase B5X82_RS14625
deoP deoxyribose transporter
pta phosphate acetyltransferase B5X82_RS16895

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