GapMind for catabolism of small carbon sources

 

L-proline catabolism in Maridesulfovibrio zosterae DSM 11974

Best path

putP, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter H589_RS0113975
put1 proline dehydrogenase H589_RS0114955 H589_RS0107295
putA L-glutamate 5-semialdeyde dehydrogenase H589_RS0107295 H589_RS0109990
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ H589_RS0105860
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H589_RS0105870 H589_RS0100760
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H589_RS0105875 H589_RS0112205
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H589_RS0105865
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase
AZOBR_RS08235 proline ABC transporter, permease component 1 H589_RS0112345 H589_RS0101630
AZOBR_RS08240 proline ABC transporter, permease component 2 H589_RS0112350 H589_RS0101625
AZOBR_RS08245 proline ABC transporter, ATPase component 1 H589_RS0112355 H589_RS0101640
AZOBR_RS08250 proline ABC transporter, ATPase component 2 H589_RS0112360 H589_RS0101620
AZOBR_RS08260 proline ABC transporter, substrate-binding component H589_RS0101635 H589_RS0112340
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase H589_RS0109990 H589_RS0118155
davT 5-aminovalerate aminotransferase H589_RS0118185 H589_RS0104130
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H589_RS0116710
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 H589_RS0101635
HSERO_RS00885 proline ABC transporter, permease component 1 H589_RS0101630 H589_RS0112345
HSERO_RS00890 proline ABC transporter, permease component 2 H589_RS0112350 H589_RS0101625
HSERO_RS00895 proline ABC transporter, ATPase component 1 H589_RS0101640 H589_RS0112355
HSERO_RS00900 proline ABC transporter, ATPase component 2 H589_RS0101620 H589_RS0112360
hutV proline ABC transporter, ATPase component HutV H589_RS0117235 H589_RS0110275
hutW proline ABC transporter, permease component HutW H589_RS0117230
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H589_RS0100555
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) H589_RS0101640 H589_RS0108450
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) H589_RS0112350 H589_RS0101625
natD proline ABC transporter, permease component 2 (NatD) H589_RS0101630 H589_RS0118175
natE proline ABC transporter, ATPase component 2 (NatE) H589_RS0101620 H589_RS0112360
opuBA proline ABC transporter, ATPase component OpuBA/BusAA H589_RS0117235 H589_RS0116465
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 H589_RS0116275
prdF proline racemase
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV H589_RS0117235 H589_RS0110275
proW proline ABC transporter, permease component ProW H589_RS0117230
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
SLC6A7 proline:Na+ symporter H589_RS0103040

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