GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Tistlia consotensis USBA 355

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 B9O00_RS26465 B9O00_RS06075
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit B9O00_RS26470 B9O00_RS10800
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component B9O00_RS25485
deoxyribonate-transport 2-deoxy-D-ribonate transporter
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase B9O00_RS27505 B9O00_RS08765
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme B9O00_RS26395 B9O00_RS08755
garK glycerate 2-kinase B9O00_RS18360
aacS acetoacetyl-CoA synthetase B9O00_RS16180 B9O00_RS21920
atoB acetyl-CoA C-acetyltransferase B9O00_RS02255 B9O00_RS06430
Alternative steps:
ackA acetate kinase
acs acetyl-CoA synthetase, AMP-forming B9O00_RS28395 B9O00_RS29560
adh acetaldehyde dehydrogenase (not acylating) B9O00_RS05420 B9O00_RS20310
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit B9O00_RS13585
atoD acetoacetyl-CoA transferase, B subunit B9O00_RS13580
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase B9O00_RS01300 B9O00_RS16275
deoP deoxyribose transporter
pta phosphate acetyltransferase B9O00_RS18815 B9O00_RS03595

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 Apr 09 2024. 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