GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas putida KT2440

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter PP_4946
put1 proline dehydrogenase PP_4947
putA L-glutamate 5-semialdeyde dehydrogenase PP_4947 PP_2694
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PP_1297
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PP_1299 PP_1069
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PP_1300 PP_3597
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PP_1298 PP_5023
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
AZOBR_RS08235 proline ABC transporter, permease component 1 PP_4866 PP_1140
AZOBR_RS08240 proline ABC transporter, permease component 2 PP_1139 PP_4865
AZOBR_RS08245 proline ABC transporter, ATPase component 1 PP_4864 PP_1138
AZOBR_RS08250 proline ABC transporter, ATPase component 2 PP_4863 PP_1137
AZOBR_RS08260 proline ABC transporter, substrate-binding component PP_4867 PP_1141
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS PP_3957 PP_0229
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase PP_0213 PP_4422
davT 5-aminovalerate aminotransferase PP_0214 PP_4108
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PP_2217 PP_3284
ectP proline transporter EctP PP_3957 PP_5374
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PP_2136 PP_3755
gcdG succinyl-CoA:glutarate CoA-transferase PP_0159 PP_3001
gcdH glutaryl-CoA dehydrogenase PP_0158 PP_4064
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) PP_2909
HSERO_RS00870 proline ABC transporter, substrate-binding component PP_4867 PP_1141
HSERO_RS00885 proline ABC transporter, permease component 1 PP_4866 PP_1140
HSERO_RS00890 proline ABC transporter, permease component 2 PP_1139 PP_4865
HSERO_RS00895 proline ABC transporter, ATPase component 1 PP_1138 PP_2767
HSERO_RS00900 proline ABC transporter, ATPase component 2 PP_1137 PP_4863
hutV proline ABC transporter, ATPase component HutV PP_0294 PP_2774
hutW proline ABC transporter, permease component HutW PP_3559 PP_2774
hutX proline ABC transporter, substrate-binding component HutX PP_3558
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) PP_2910
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) PP_1138 PP_2767
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) PP_4865
natD proline ABC transporter, permease component 2 (NatD) PP_1140 PP_0618
natE proline ABC transporter, ATPase component 2 (NatE) PP_1137 PP_0615
opuBA proline ABC transporter, ATPase component OpuBA/BusAA PP_0294 PP_0868
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 PP_1258
proP proline:H+ symporter ProP PP_2914 PP_4433
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV PP_0294 PP_2774
proW proline ABC transporter, permease component ProW PP_3559 PP_2774
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter PP_5031 PP_1059
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