GapMind for catabolism of small carbon sources

 

Definition of L-proline catabolism

As rules and steps, or see full text

Rules

Overview: Proline degradation in GapMind is based on MetaCyc pathway I via glutamate semialdehyde dehydrogenase (link) and pathway II via 5-aminopentanoate (link). (MetaCyc describes 5-aminopentanoate, also known as 5-aminovalerate, as a fermentative end product, but it is further degraded

Steps

proV: proline ABC transporter, ATPase component ProV

proW: proline ABC transporter, permease component ProW

proX: proline ABC transporter, substrate-binding component ProX

opuBA: proline ABC transporter, ATPase component OpuBA/BusAA

opuBB: proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB

natA: proline ABC transporter, ATPase component 1 (NatA)

natB: proline ABC transporter, substrate-binding component NatB

natC: proline ABC transporter, permease component 1 (NatC)

natD: proline ABC transporter, permease component 2 (NatD)

natE: proline ABC transporter, ATPase component 2 (NatE)

hutV: proline ABC transporter, ATPase component HutV

hutW: proline ABC transporter, permease component HutW

hutX: proline ABC transporter, substrate-binding component HutX

AZOBR_RS08235: proline ABC transporter, permease component 1

AZOBR_RS08240: proline ABC transporter, permease component 2

AZOBR_RS08245: proline ABC transporter, ATPase component 1

AZOBR_RS08250: proline ABC transporter, ATPase component 2

AZOBR_RS08260: proline ABC transporter, substrate-binding component

HSERO_RS00870: proline ABC transporter, substrate-binding component

HSERO_RS00885: proline ABC transporter, permease component 1

HSERO_RS00890: proline ABC transporter, permease component 2

HSERO_RS00895: proline ABC transporter, ATPase component 1

HSERO_RS00900: proline ABC transporter, ATPase component 2

aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ

aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)

aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)

aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP

proY: proline:H+ symporter

putP: proline:Na+ symporter

PROT1: proline transporter

SLC6A7: proline:Na+ symporter

proP: proline:H+ symporter ProP

ectP: proline transporter EctP

betS: proline transporter BetS

BAC2: basic amino acid carrier BAC2

AAT20.2: proline transporter

CCNA_00435: proline transporter

N515DRAFT_2924: proline transporter

put1: proline dehydrogenase

putA: L-glutamate 5-semialdeyde dehydrogenase

prdF: proline racemase

prdA: D-proline reductase, prdA component

prdB: D-proline reductase, prdB component

prdC: D-proline reductase, electron transfer component PrdC

atoB: acetyl-CoA C-acetyltransferase

gcdH: glutaryl-CoA dehydrogenase

ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase

fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase

glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)

lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)

gcdG: succinyl-CoA:glutarate CoA-transferase

davT: 5-aminovalerate aminotransferase

davD: glutarate semialdehyde dehydrogenase

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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