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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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