GapMind for catabolism of small carbon sources

 

L-proline catabolism in Desulfobacter vibrioformis DSM 8776

Best path

proV, proW, proX, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proV proline ABC transporter, ATPase component ProV Q366_RS03735 Q366_RS06100
proW proline ABC transporter, permease component ProW Q366_RS03740
proX proline ABC transporter, substrate-binding component ProX Q366_RS03745
put1 proline dehydrogenase Q366_RS04815
putA L-glutamate 5-semialdeyde dehydrogenase Q366_RS11500 Q366_RS10385
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 Q366_RS06100 Q366_RS03735
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase Q366_RS09305 Q366_RS02505
AZOBR_RS08235 proline ABC transporter, permease component 1 Q366_RS13525 Q366_RS04655
AZOBR_RS08240 proline ABC transporter, permease component 2 Q366_RS04650
AZOBR_RS08245 proline ABC transporter, ATPase component 1 Q366_RS04645 Q366_RS13535
AZOBR_RS08250 proline ABC transporter, ATPase component 2 Q366_RS04640 Q366_RS13540
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase Q366_RS17050 Q366_RS13505
davT 5-aminovalerate aminotransferase Q366_RS13500 Q366_RS12820
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q366_RS18135 Q366_RS13010
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q366_RS00865 Q366_RS00395
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Q366_RS06780 Q366_RS11450
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 Q366_RS04655 Q366_RS13525
HSERO_RS00890 proline ABC transporter, permease component 2 Q366_RS04650
HSERO_RS00895 proline ABC transporter, ATPase component 1 Q366_RS04645 Q366_RS13535
HSERO_RS00900 proline ABC transporter, ATPase component 2 Q366_RS04640 Q366_RS13540
hutV proline ABC transporter, ATPase component HutV Q366_RS03735 Q366_RS06100
hutW proline ABC transporter, permease component HutW Q366_RS03740
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) Q366_RS04645 Q366_RS13535
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) Q366_RS04655
natE proline ABC transporter, ATPase component 2 (NatE) Q366_RS13540 Q366_RS04640
opuBA proline ABC transporter, ATPase component OpuBA/BusAA Q366_RS03735 Q366_RS06100
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
proP proline:H+ symporter ProP
PROT1 proline transporter
proY proline:H+ symporter
putP proline:Na+ symporter
SLC6A7 proline:Na+ symporter Q366_RS14330

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