GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas fluorescens FW300-N2E2

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter Pf6N2E2_3684
put1 proline dehydrogenase Pf6N2E2_3685
putA L-glutamate 5-semialdeyde dehydrogenase Pf6N2E2_3685 Pf6N2E2_3298
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf6N2E2_5402
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf6N2E2_5404 Pf6N2E2_1799
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf6N2E2_5405 Pf6N2E2_5567
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf6N2E2_5403
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
AZOBR_RS08235 proline ABC transporter, permease component 1 Pf6N2E2_3579 Pf6N2E2_2923
AZOBR_RS08240 proline ABC transporter, permease component 2 Pf6N2E2_2924 Pf6N2E2_3578
AZOBR_RS08245 proline ABC transporter, ATPase component 1 Pf6N2E2_2925 Pf6N2E2_1433
AZOBR_RS08250 proline ABC transporter, ATPase component 2 Pf6N2E2_3576 Pf6N2E2_2926
AZOBR_RS08260 proline ABC transporter, substrate-binding component Pf6N2E2_3580 Pf6N2E2_2921
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS Pf6N2E2_3917
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase Pf6N2E2_4014 Pf6N2E2_368
davT 5-aminovalerate aminotransferase Pf6N2E2_4013 Pf6N2E2_373
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
ectP proline transporter EctP Pf6N2E2_3917
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
gcdG succinyl-CoA:glutarate CoA-transferase Pf6N2E2_4035 Pf6N2E2_3139
gcdH glutaryl-CoA dehydrogenase Pf6N2E2_4036 Pf6N2E2_2191
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component Pf6N2E2_3580 Pf6N2E2_2921
HSERO_RS00885 proline ABC transporter, permease component 1 Pf6N2E2_3579 Pf6N2E2_2923
HSERO_RS00890 proline ABC transporter, permease component 2 Pf6N2E2_2924 Pf6N2E2_3578
HSERO_RS00895 proline ABC transporter, ATPase component 1 Pf6N2E2_1433 Pf6N2E2_2925
HSERO_RS00900 proline ABC transporter, ATPase component 2 Pf6N2E2_2926 Pf6N2E2_3576
hutV proline ABC transporter, ATPase component HutV Pf6N2E2_3801 Pf6N2E2_4681
hutW proline ABC transporter, permease component HutW Pf6N2E2_3802 Pf6N2E2_4682
hutX proline ABC transporter, substrate-binding component HutX Pf6N2E2_3803 Pf6N2E2_530
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf6N2E2_261
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) Pf6N2E2_2925 Pf6N2E2_1705
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) Pf6N2E2_2924
natD proline ABC transporter, permease component 2 (NatD) Pf6N2E2_3579 Pf6N2E2_3548
natE proline ABC transporter, ATPase component 2 (NatE) Pf6N2E2_2926 Pf6N2E2_3576
opuBA proline ABC transporter, ATPase component OpuBA/BusAA Pf6N2E2_3333 Pf6N2E2_240
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 Pf6N2E2_681 Pf6N2E2_671
proP proline:H+ symporter ProP Pf6N2E2_388 Pf6N2E2_1930
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV Pf6N2E2_4681 Pf6N2E2_3801
proW proline ABC transporter, permease component ProW Pf6N2E2_3802 Pf6N2E2_4682
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter Pf6N2E2_5459 Pf6N2E2_4195
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 17 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 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, the preprint on GapMind for carbon sources, 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