GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas fluorescens FW300-N2E3

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter AO353_12815
put1 proline dehydrogenase AO353_12810
putA L-glutamate 5-semialdeyde dehydrogenase AO353_12810 AO353_05300
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ AO353_04615
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) AO353_04605 AO353_12325
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AO353_04600 AO353_16275
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AO353_04610
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase AO353_25685 AO353_27945
AZOBR_RS08235 proline ABC transporter, permease component 1 AO353_13345 AO353_17120
AZOBR_RS08240 proline ABC transporter, permease component 2 AO353_17115 AO353_13350
AZOBR_RS08245 proline ABC transporter, ATPase component 1 AO353_17110 AO353_13355
AZOBR_RS08250 proline ABC transporter, ATPase component 2 AO353_13360 AO353_17105
AZOBR_RS08260 proline ABC transporter, substrate-binding component AO353_13340 AO353_17125
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS AO353_11690 AO353_07795
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase AO353_11505 AO353_28230
davT 5-aminovalerate aminotransferase AO353_11510 AO353_28215
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO353_25675 AO353_00510
ectP proline transporter EctP AO353_11690 AO353_07795
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO353_00510 AO353_27535
gcdG succinyl-CoA:glutarate CoA-transferase AO353_11105 AO353_23060
gcdH glutaryl-CoA dehydrogenase AO353_11100 AO353_20350
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component AO353_13340 AO353_17125
HSERO_RS00885 proline ABC transporter, permease component 1 AO353_13345 AO353_17120
HSERO_RS00890 proline ABC transporter, permease component 2 AO353_17115 AO353_13350
HSERO_RS00895 proline ABC transporter, ATPase component 1 AO353_17110 AO353_13355
HSERO_RS00900 proline ABC transporter, ATPase component 2 AO353_17105 AO353_13360
hutV proline ABC transporter, ATPase component HutV AO353_12265 AO353_07790
hutW proline ABC transporter, permease component HutW AO353_12260 AO353_07785
hutX proline ABC transporter, substrate-binding component HutX AO353_21435
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) AO353_17110 AO353_13530
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) AO353_17120
natE proline ABC transporter, ATPase component 2 (NatE) AO353_17105 AO353_13360
opuBA proline ABC transporter, ATPase component OpuBA/BusAA AO353_05440 AO353_07265
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 AO353_14925 AO353_14880
proP proline:H+ symporter ProP AO353_05775 AO353_04405
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV AO353_07790 AO353_12265
proW proline ABC transporter, permease component ProW AO353_12260 AO353_07785
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter AO353_12275 AO353_16120
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