GapMind for catabolism of small carbon sources

 

L-proline catabolism in Nocardiopsis lucentensis DSM 44048

Best path

proY, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proY proline:H+ symporter D471_RS0105135
put1 proline dehydrogenase D471_RS0107565 D471_RS0118925
putA L-glutamate 5-semialdeyde dehydrogenase D471_RS0107560 D471_RS0127260
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP D471_RS0100160 D471_RS0110910
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) D471_RS0110905
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase D471_RS0104595 D471_RS0114985
AZOBR_RS08235 proline ABC transporter, permease component 1 D471_RS0127515 D471_RS0105195
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 D471_RS0129920 D471_RS0102645
AZOBR_RS08250 proline ABC transporter, ATPase component 2 D471_RS0129925 D471_RS0102650
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS D471_RS0115100 D471_RS35115
CCNA_00435 proline transporter D471_RS0115645
davD glutarate semialdehyde dehydrogenase D471_RS0113535 D471_RS0127260
davT 5-aminovalerate aminotransferase D471_RS0113530 D471_RS0100020
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase D471_RS0108630 D471_RS0120405
ectP proline transporter EctP D471_RS0115100 D471_RS0115350
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase D471_RS0120405 D471_RS0123250
gcdG succinyl-CoA:glutarate CoA-transferase D471_RS0120140 D471_RS0124980
gcdH glutaryl-CoA dehydrogenase D471_RS0120145 D471_RS0107015
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component
HSERO_RS00885 proline ABC transporter, permease component 1 D471_RS0105195
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 D471_RS0129920 D471_RS0102645
HSERO_RS00900 proline ABC transporter, ATPase component 2 D471_RS0102650 D471_RS0129925
hutV proline ABC transporter, ATPase component HutV D471_RS0121285 D471_RS0129435
hutW proline ABC transporter, permease component HutW D471_RS0121280 D471_RS0125460
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter D471_RS0115645
natA proline ABC transporter, ATPase component 1 (NatA) D471_RS0102645 D471_RS0129920
natB proline ABC transporter, substrate-binding component NatB D471_RS0102655
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) D471_RS0102635 D471_RS0105195
natE proline ABC transporter, ATPase component 2 (NatE) D471_RS0102650 D471_RS0129925
opuBA proline ABC transporter, ATPase component OpuBA/BusAA D471_RS0121285 D471_RS0129435
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB D471_RS0125460
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
proP proline:H+ symporter ProP D471_RS0128695 D471_RS0103990
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV D471_RS0121285 D471_RS0129435
proW proline ABC transporter, permease component ProW D471_RS0121280 D471_RS0125460
proX proline ABC transporter, substrate-binding component ProX
putP proline:Na+ symporter D471_RS36910
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 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