GapMind for catabolism of small carbon sources

 

L-proline catabolism in Paucidesulfovibrio gracilis DSM 16080

Best path

betS, put1, putA

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

53 steps (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
betS proline transporter BetS B5D49_RS07505 B5D49_RS09365
put1 proline dehydrogenase B5D49_RS04205
putA L-glutamate 5-semialdeyde dehydrogenase B5D49_RS04205 B5D49_RS13965
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) B5D49_RS05280
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP B5D49_RS04740 B5D49_RS05290
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) B5D49_RS04750
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase B5D49_RS03160
AZOBR_RS08235 proline ABC transporter, permease component 1 B5D49_RS00090 B5D49_RS04225
AZOBR_RS08240 proline ABC transporter, permease component 2 B5D49_RS00085 B5D49_RS04230
AZOBR_RS08245 proline ABC transporter, ATPase component 1 B5D49_RS00080 B5D49_RS00870
AZOBR_RS08250 proline ABC transporter, ATPase component 2 B5D49_RS00075 B5D49_RS04235
AZOBR_RS08260 proline ABC transporter, substrate-binding component B5D49_RS00095 B5D49_RS04220
BAC2 basic amino acid carrier BAC2
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
davT 5-aminovalerate aminotransferase B5D49_RS03155 B5D49_RS12615
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
ectP proline transporter EctP B5D49_RS07505 B5D49_RS09365
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B5D49_RS01965
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component B5D49_RS04220
HSERO_RS00885 proline ABC transporter, permease component 1 B5D49_RS00090 B5D49_RS04225
HSERO_RS00890 proline ABC transporter, permease component 2 B5D49_RS04230 B5D49_RS00085
HSERO_RS00895 proline ABC transporter, ATPase component 1 B5D49_RS04215 B5D49_RS00080
HSERO_RS00900 proline ABC transporter, ATPase component 2 B5D49_RS04235 B5D49_RS00075
hutV proline ABC transporter, ATPase component HutV B5D49_RS02895 B5D49_RS10250
hutW proline ABC transporter, permease component HutW B5D49_RS02890
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) B5D49_RS12670
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) B5D49_RS04215 B5D49_RS00870
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) B5D49_RS00085
natD proline ABC transporter, permease component 2 (NatD) B5D49_RS04225 B5D49_RS00880
natE proline ABC transporter, ATPase component 2 (NatE) B5D49_RS00075 B5D49_RS04235
opuBA proline ABC transporter, ATPase component OpuBA/BusAA B5D49_RS02895 B5D49_RS03200
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase B5D49_RS03205
proP proline:H+ symporter ProP B5D49_RS00840
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV B5D49_RS02895 B5D49_RS03200
proW proline ABC transporter, permease component ProW B5D49_RS02890
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
putP proline:Na+ symporter
SLC6A7 proline:Na+ symporter

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