GapMind for catabolism of small carbon sources

 

L-proline catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ectP proline transporter EctP Echvi_0794
put1 proline dehydrogenase Echvi_0119
putA L-glutamate 5-semialdeyde dehydrogenase Echvi_1300 Echvi_0481
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Echvi_1582 Echvi_4044
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase Echvi_3705 Echvi_1071
AZOBR_RS08235 proline ABC transporter, permease component 1
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1
AZOBR_RS08250 proline ABC transporter, ATPase component 2 Echvi_1333 Echvi_2123
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS Echvi_0794
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase Echvi_0481 Echvi_3822
davT 5-aminovalerate aminotransferase Echvi_2919 Echvi_3848
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Echvi_4069 Echvi_0069
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Echvi_1069 Echvi_3304
gcdG succinyl-CoA:glutarate CoA-transferase Echvi_1686 Echvi_1687
gcdH glutaryl-CoA dehydrogenase Echvi_2990 Echvi_0738
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
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 Echvi_1333 Echvi_4539
HSERO_RS00900 proline ABC transporter, ATPase component 2 Echvi_1333 Echvi_1022
hutV proline ABC transporter, ATPase component HutV Echvi_1022 Echvi_1096
hutW proline ABC transporter, permease component HutW
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Echvi_3348
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) Echvi_1333 Echvi_1022
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD)
natE proline ABC transporter, ATPase component 2 (NatE) Echvi_1333 Echvi_4044
opuBA proline ABC transporter, ATPase component OpuBA/BusAA Echvi_3653 Echvi_2123
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 Echvi_3951
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV Echvi_1022 Echvi_3653
proW proline ABC transporter, permease component ProW
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.

Links

Downloads

Related tools

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