GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas stutzeri RCH2

Best path

putP, put1, putA

Also see fitness data for the top candidates

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter Psest_3075 Psest_3078
put1 proline dehydrogenase Psest_3079
putA L-glutamate 5-semialdeyde dehydrogenase Psest_3079 Psest_0375
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Psest_3163
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Psest_3161 Psest_0018
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Psest_3160 Psest_0139
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Psest_3162
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
AZOBR_RS08235 proline ABC transporter, permease component 1 Psest_1311 Psest_3855
AZOBR_RS08240 proline ABC transporter, permease component 2 Psest_1310
AZOBR_RS08245 proline ABC transporter, ATPase component 1 Psest_1309 Psest_1089
AZOBR_RS08250 proline ABC transporter, ATPase component 2 Psest_1308 Psest_0563
AZOBR_RS08260 proline ABC transporter, substrate-binding component Psest_1312
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS Psest_3776 Psest_0140
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase Psest_4237 Psest_3654
davT 5-aminovalerate aminotransferase Psest_3653 Psest_2719
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Psest_2437 Psest_3109
ectP proline transporter EctP Psest_3776 Psest_0140
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Psest_2654 Psest_4235
gcdG succinyl-CoA:glutarate CoA-transferase Psest_3829 Psest_2660
gcdH glutaryl-CoA dehydrogenase Psest_3830 Psest_2440
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component Psest_1312
HSERO_RS00885 proline ABC transporter, permease component 1 Psest_1311 Psest_3855
HSERO_RS00890 proline ABC transporter, permease component 2 Psest_1310 Psest_1093
HSERO_RS00895 proline ABC transporter, ATPase component 1 Psest_1309 Psest_1089
HSERO_RS00900 proline ABC transporter, ATPase component 2 Psest_1308 Psest_0563
hutV proline ABC transporter, ATPase component HutV Psest_4282 Psest_4314
hutW proline ABC transporter, permease component HutW
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Psest_0232
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) Psest_1309 Psest_1089
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) Psest_1310
natD proline ABC transporter, permease component 2 (NatD) Psest_1311 Psest_1092
natE proline ABC transporter, ATPase component 2 (NatE) Psest_1308 Psest_1090
opuBA proline ABC transporter, ATPase component OpuBA/BusAA Psest_3658 Psest_0871
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 Psest_1584
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV Psest_4282 Psest_4314
proW proline ABC transporter, permease component ProW
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter Psest_1697
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 Aug 02 2021. The underlying query database was built on Aug 02 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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