2-deoxy-D-ribose catabolism in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

2-deoxy-D-ribose catabolism in Xanthobacter autotrophicus Py2

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).

all:

deoxyribose-transport, deoK, deoC and acetaldehyde-degradation
or deoxyribose-dehyd, deoxyribonate-transport and deoxyribonate-degradation
Comment: The deoxyribose 5-phosphate pathway involves the kinase deoK and the aldolase deoC. The oxidative pathway involves oxidation in the periplasm to deoxyribonate.

deoxyribonate-degradation: deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK and acetoacetate-degradation

Comment: After oxidation of deoxyribonate to 2-deoxy-3-ketoribonate, a cleavage enzyme produces glyceroyl-CoA and acetoacetate; the enzyme for the conversion of glyceroyl-CoA to glycerate is not known; and garK phosphorylates glycerate to 2-phospho-D-glycerate, an intermediate in glycolysis.

acetoacetate-degradation: acetoacetate-activation and atoB

Comment: The acetoacetate is activated to acetoacetyl-CoA, and cleaved by acetyl-CoA acetyltransferase, giving two acetyl-CoA.

acetoacetate-activation:

atoA and atoD
or aacS
Comment: acetyl-CoA:acetoacetyl-CoA transferase (sometimes given EC 2.8.3.9 or EC 2.8.3.8) or succinyl-CoA:acetoacetyl-CoA transferase (EC 2.8.3.5, also known as 3-oxoacid CoA-transferase) can activate acetoacetate. These have an A and B subunit. Alternatively, an ATP-dependent ligase (aacS) can activate acetoacetate (EC 6.2.1.16).

deoxyribose-dehyd: drdehyd-alpha, drdehyd-beta and drdehyd-cytc
acetaldehyde-degradation:

ald-dh-CoA
or adh and acs
or adh, ackA and pta
Comment: Acetaldehyde can be oxidized to acetyl-CoA, or oxidized to acetate and activated to acetyl-CoA by either acetyl-CoA synthetase (acs) or by acetate kinase (ackA) and phosphate acetyltransferase (pta).

deoxyribose-transport: deoP

19 steps (17 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
drdehyd-alpha	2-deoxy-D-ribose dehydrogenase, alpha subunit	XAUT_RS14690	XAUT_RS21310
drdehyd-beta	2-deoxy-D-ribose dehydrogenase, beta subunit	XAUT_RS14685
drdehyd-cytc	2-deoxyribose-D dehydrogenase, cytochrome c component	XAUT_RS05365	XAUT_RS26035
deoxyribonate-transport	2-deoxy-D-ribonate transporter	XAUT_RS05170	XAUT_RS14735
deoxyribonate-dehyd	2-deoxy-D-ribonate 3-dehydrogenase	XAUT_RS02185	XAUT_RS13880
ketodeoxyribonate-cleavage	2-deoxy-3-keto-D-ribonate cleavage enzyme	XAUT_RS02155	XAUT_RS24025
garK	glycerate 2-kinase	XAUT_RS15595
atoA	acetoacetyl-CoA transferase, A subunit	XAUT_RS11815	XAUT_RS05620
atoD	acetoacetyl-CoA transferase, B subunit	XAUT_RS11820	XAUT_RS05615
atoB	acetyl-CoA C-acetyltransferase	XAUT_RS23630	XAUT_RS15615
Alternative steps:
aacS	acetoacetyl-CoA synthetase	XAUT_RS20600	XAUT_RS14125
ackA	acetate kinase	XAUT_RS16350
acs	acetyl-CoA synthetase, AMP-forming	XAUT_RS07400	XAUT_RS12385
adh	acetaldehyde dehydrogenase (not acylating)	XAUT_RS01855	XAUT_RS03370
ald-dh-CoA	acetaldehyde dehydrogenase, acylating	XAUT_RS04720
deoC	deoxyribose-5-phosphate aldolase
deoK	deoxyribokinase	XAUT_RS19115
deoP	deoxyribose transporter
pta	phosphate acetyltransferase	XAUT_RS16345	XAUT_RS15790

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources