GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Rhizobium subbaraonis JC85

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase CRO48_RS14340 CRO48_RS21065
deoC deoxyribose-5-phosphate aldolase CRO48_RS25635 CRO48_RS13775
adh acetaldehyde dehydrogenase (not acylating) CRO48_RS25640 CRO48_RS28755
acs acetyl-CoA synthetase, AMP-forming CRO48_RS06990 CRO48_RS06980
Alternative steps:
aacS acetoacetyl-CoA synthetase CRO48_RS21890 CRO48_RS18840
ackA acetate kinase CRO48_RS28905 CRO48_RS17315
ald-dh-CoA acetaldehyde dehydrogenase, acylating CRO48_RS02530
atoA acetoacetyl-CoA transferase, A subunit CRO48_RS04405
atoB acetyl-CoA C-acetyltransferase CRO48_RS08200 CRO48_RS26975
atoD acetoacetyl-CoA transferase, B subunit CRO48_RS04400
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CRO48_RS15665 CRO48_RS04435
deoxyribonate-transport 2-deoxy-D-ribonate transporter CRO48_RS30260 CRO48_RS20400
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit CRO48_RS08125 CRO48_RS21105
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit CRO48_RS08130
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component CRO48_RS21110 CRO48_RS01760
garK glycerate 2-kinase CRO48_RS18670
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme CRO48_RS12690 CRO48_RS24410
pta phosphate acetyltransferase CRO48_RS28900 CRO48_RS17310

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