GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pantoea rwandensis LMG 26275

Best path

deoP, deoK, deoC, adh, ackA, pta

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter HA51_RS07045 HA51_RS22420
deoK deoxyribokinase HA51_RS05175 HA51_RS07040
deoC deoxyribose-5-phosphate aldolase HA51_RS12395
adh acetaldehyde dehydrogenase (not acylating) HA51_RS23475 HA51_RS08520
ackA acetate kinase HA51_RS11240 HA51_RS10465
pta phosphate acetyltransferase HA51_RS11235 HA51_RS26220
Alternative steps:
aacS acetoacetyl-CoA synthetase HA51_RS10660
acs acetyl-CoA synthetase, AMP-forming
ald-dh-CoA acetaldehyde dehydrogenase, acylating HA51_RS08520
atoA acetoacetyl-CoA transferase, A subunit HA51_RS19820
atoB acetyl-CoA C-acetyltransferase HA51_RS19810 HA51_RS26555
atoD acetoacetyl-CoA transferase, B subunit HA51_RS19815
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase HA51_RS00225 HA51_RS02190
deoxyribonate-transport 2-deoxy-D-ribonate transporter HA51_RS26595 HA51_RS19860
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit HA51_RS13115 HA51_RS01575
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit HA51_RS13110 HA51_RS01570
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component HA51_RS13105 HA51_RS25125
garK glycerate 2-kinase HA51_RS26585
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme

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