GapMind for catabolism of small carbon sources

 

L-proline catabolism in Marinobacter guineae M3B

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter CLH62_RS03100
put1 proline dehydrogenase CLH62_RS05435
putA L-glutamate 5-semialdeyde dehydrogenase CLH62_RS05435 CLH62_RS11815
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ CLH62_RS02950
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) CLH62_RS02940
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CLH62_RS02935 CLH62_RS06600
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) CLH62_RS02945
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase CLH62_RS07455 CLH62_RS15420
AZOBR_RS08235 proline ABC transporter, permease component 1 CLH62_RS07845 CLH62_RS05535
AZOBR_RS08240 proline ABC transporter, permease component 2 CLH62_RS07850 CLH62_RS05530
AZOBR_RS08245 proline ABC transporter, ATPase component 1 CLH62_RS07855 CLH62_RS05525
AZOBR_RS08250 proline ABC transporter, ATPase component 2 CLH62_RS07860 CLH62_RS05520
AZOBR_RS08260 proline ABC transporter, substrate-binding component CLH62_RS07840
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS CLH62_RS07110 CLH62_RS15035
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase CLH62_RS09265 CLH62_RS11930
davT 5-aminovalerate aminotransferase CLH62_RS11925 CLH62_RS11500
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CLH62_RS15970 CLH62_RS10205
ectP proline transporter EctP CLH62_RS15035 CLH62_RS07110
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CLH62_RS18530 CLH62_RS10205
gcdG succinyl-CoA:glutarate CoA-transferase CLH62_RS09260 CLH62_RS14995
gcdH glutaryl-CoA dehydrogenase CLH62_RS10225 CLH62_RS15440
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component CLH62_RS07840
HSERO_RS00885 proline ABC transporter, permease component 1 CLH62_RS07845 CLH62_RS05535
HSERO_RS00890 proline ABC transporter, permease component 2 CLH62_RS07850 CLH62_RS09240
HSERO_RS00895 proline ABC transporter, ATPase component 1 CLH62_RS05525 CLH62_RS09250
HSERO_RS00900 proline ABC transporter, ATPase component 2 CLH62_RS05520 CLH62_RS07860
hutV proline ABC transporter, ATPase component HutV CLH62_RS13425 CLH62_RS10425
hutW proline ABC transporter, permease component HutW CLH62_RS13430
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) CLH62_RS05525 CLH62_RS12085
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) CLH62_RS07850
natD proline ABC transporter, permease component 2 (NatD) CLH62_RS07845 CLH62_RS15915
natE proline ABC transporter, ATPase component 2 (NatE) CLH62_RS05520 CLH62_RS07860
opuBA proline ABC transporter, ATPase component OpuBA/BusAA CLH62_RS13425 CLH62_RS01400
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
proV proline ABC transporter, ATPase component ProV CLH62_RS13425 CLH62_RS10425
proW proline ABC transporter, permease component ProW CLH62_RS13430
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ 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 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