GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Phyllobacterium brassicacearum STM 196

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase CU102_RS00810 CU102_RS02690
deoC deoxyribose-5-phosphate aldolase CU102_RS10615
adh acetaldehyde dehydrogenase (not acylating) CU102_RS10620 CU102_RS28215
acs acetyl-CoA synthetase, AMP-forming CU102_RS26175 CU102_RS18670
Alternative steps:
aacS acetoacetyl-CoA synthetase CU102_RS20310
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit CU102_RS22230
atoB acetyl-CoA C-acetyltransferase CU102_RS21705 CU102_RS10795
atoD acetoacetyl-CoA transferase, B subunit CU102_RS22225
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CU102_RS18370 CU102_RS17075
deoxyribonate-transport 2-deoxy-D-ribonate transporter CU102_RS27940
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit CU102_RS21265 CU102_RS24850
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit CU102_RS16690 CU102_RS24855
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component CU102_RS00535
garK glycerate 2-kinase CU102_RS02440
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme CU102_RS11865 CU102_RS07810
pta phosphate acetyltransferase CU102_RS27390 CU102_RS05525

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