GapMind for catabolism of small carbon sources

 

L-proline catabolism in Phaeobacter inhibens BS107

Best path

ectP, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ectP proline transporter EctP PGA1_c13880 PGA1_262p01440
put1 proline dehydrogenase PGA1_c11750 PGA1_c23300
putA L-glutamate 5-semialdeyde dehydrogenase PGA1_c11750 PGA1_c05130
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PGA1_c01980
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PGA1_c02000 PGA1_c26600
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PGA1_c02010 PGA1_262p02350
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PGA1_c01990
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
AZOBR_RS08235 proline ABC transporter, permease component 1 PGA1_c02590 PGA1_c16550
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 PGA1_c32620 PGA1_c02610
AZOBR_RS08250 proline ABC transporter, ATPase component 2 PGA1_c02620 PGA1_c32560
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS PGA1_c13880 PGA1_262p01440
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase PGA1_c29650 PGA1_c23170
davT 5-aminovalerate aminotransferase PGA1_c24230 PGA1_c28750
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
gcdG succinyl-CoA:glutarate CoA-transferase PGA1_c27870 PGA1_c12340
gcdH glutaryl-CoA dehydrogenase PGA1_c15710 PGA1_c10280
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component
HSERO_RS00885 proline ABC transporter, permease component 1 PGA1_c02590
HSERO_RS00890 proline ABC transporter, permease component 2 PGA1_c32580
HSERO_RS00895 proline ABC transporter, ATPase component 1 PGA1_c32620 PGA1_c02610
HSERO_RS00900 proline ABC transporter, ATPase component 2 PGA1_c32560 PGA1_c02620
hutV proline ABC transporter, ATPase component HutV PGA1_c25590 PGA1_c33760
hutW proline ABC transporter, permease component HutW PGA1_c25580 PGA1_c22790
hutX proline ABC transporter, substrate-binding component HutX PGA1_c25570 PGA1_c22800
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) PGA1_c15910 PGA1_c02610
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) PGA1_c15940
natE proline ABC transporter, ATPase component 2 (NatE) PGA1_c15920 PGA1_c02620
opuBA proline ABC transporter, ATPase component OpuBA/BusAA PGA1_c33760 PGA1_c23270
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 PGA1_262p00280 PGA1_c05120
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV PGA1_c33760 PGA1_c23270
proW proline ABC transporter, permease component ProW PGA1_c33770 PGA1_c22790
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
putP proline:Na+ symporter
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, 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