GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas fluorescens GW456-L13

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter PfGW456L13_221
put1 proline dehydrogenase PfGW456L13_223
putA L-glutamate 5-semialdeyde dehydrogenase PfGW456L13_223 PfGW456L13_5044
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PfGW456L13_1698
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PfGW456L13_1700 PfGW456L13_4772
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PfGW456L13_1701 PfGW456L13_4773
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PfGW456L13_1699
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
AZOBR_RS08235 proline ABC transporter, permease component 1 PfGW456L13_4608 PfGW456L13_123
AZOBR_RS08240 proline ABC transporter, permease component 2 PfGW456L13_4609 PfGW456L13_122
AZOBR_RS08245 proline ABC transporter, ATPase component 1 PfGW456L13_4610 PfGW456L13_121
AZOBR_RS08250 proline ABC transporter, ATPase component 2 PfGW456L13_120 PfGW456L13_4611
AZOBR_RS08260 proline ABC transporter, substrate-binding component PfGW456L13_124 PfGW456L13_4606
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS PfGW456L13_439 PfGW456L13_1085
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase PfGW456L13_495 PfGW456L13_3737
davT 5-aminovalerate aminotransferase PfGW456L13_494 PfGW456L13_4982
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PfGW456L13_2984 PfGW456L13_2434
ectP proline transporter EctP PfGW456L13_439 PfGW456L13_1085
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_3873
gcdG succinyl-CoA:glutarate CoA-transferase PfGW456L13_553 PfGW456L13_3635
gcdH glutaryl-CoA dehydrogenase PfGW456L13_554 PfGW456L13_2591
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component PfGW456L13_4606 PfGW456L13_124
HSERO_RS00885 proline ABC transporter, permease component 1 PfGW456L13_123 PfGW456L13_4608
HSERO_RS00890 proline ABC transporter, permease component 2 PfGW456L13_4609 PfGW456L13_122
HSERO_RS00895 proline ABC transporter, ATPase component 1 PfGW456L13_4610 PfGW456L13_121
HSERO_RS00900 proline ABC transporter, ATPase component 2 PfGW456L13_4611 PfGW456L13_120
hutV proline ABC transporter, ATPase component HutV PfGW456L13_322 PfGW456L13_3150
hutW proline ABC transporter, permease component HutW PfGW456L13_323 PfGW456L13_1087
hutX proline ABC transporter, substrate-binding component HutX PfGW456L13_324 PfGW456L13_3631
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) PfGW456L13_4610 PfGW456L13_84
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) PfGW456L13_4609
natD proline ABC transporter, permease component 2 (NatD) PfGW456L13_4608
natE proline ABC transporter, ATPase component 2 (NatE) PfGW456L13_4611 PfGW456L13_120
opuBA proline ABC transporter, ATPase component OpuBA/BusAA PfGW456L13_3150 PfGW456L13_5065
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 PfGW456L13_3147 PfGW456L13_3583
proP proline:H+ symporter ProP PfGW456L13_3155 PfGW456L13_2328
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV PfGW456L13_3150 PfGW456L13_1086
proW proline ABC transporter, permease component ProW PfGW456L13_323 PfGW456L13_1087
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter PfGW456L13_318 PfGW456L13_4790
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