GapMind for catabolism of small carbon sources

 

L-proline catabolism in Dinoroseobacter shibae DFL-12

Best path

aapJ, aapQ, aapM, aapP, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Dshi_0318
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Dshi_0319
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Dshi_0320
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Dshi_0321 Dshi_2221
put1 proline dehydrogenase Dshi_2311
putA L-glutamate 5-semialdeyde dehydrogenase Dshi_2311 Dshi_0577
Alternative steps:
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
AZOBR_RS08235 proline ABC transporter, permease component 1 Dshi_3725 Dshi_0861
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 Dshi_0375 Dshi_3727
AZOBR_RS08250 proline ABC transporter, ATPase component 2 Dshi_0381 Dshi_1400
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS Dshi_2119 Dshi_0579
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase Dshi_2887 Dshi_0577
davT 5-aminovalerate aminotransferase Dshi_1446 Dshi_0798
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dshi_3370 Dshi_0835
ectP proline transporter EctP Dshi_2119 Dshi_0579
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dshi_3826 Dshi_0835
gcdG succinyl-CoA:glutarate CoA-transferase Dshi_3269 Dshi_1057
gcdH glutaryl-CoA dehydrogenase Dshi_2357 Dshi_1297
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 Dshi_1979 Dshi_0861
HSERO_RS00890 proline ABC transporter, permease component 2 Dshi_1978
HSERO_RS00895 proline ABC transporter, ATPase component 1 Dshi_0375 Dshi_1981
HSERO_RS00900 proline ABC transporter, ATPase component 2 Dshi_0381 Dshi_1520
hutV proline ABC transporter, ATPase component HutV Dshi_1437 Dshi_1055
hutW proline ABC transporter, permease component HutW Dshi_1436
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) Dshi_1521 Dshi_1981
natB proline ABC transporter, substrate-binding component NatB Dshi_1977
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) Dshi_1518 Dshi_1979
natE proline ABC transporter, ATPase component 2 (NatE) Dshi_1520 Dshi_1980
opuBA proline ABC transporter, ATPase component OpuBA/BusAA Dshi_1437 Dshi_2120
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
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV Dshi_1437 Dshi_0546
proW proline ABC transporter, permease component ProW Dshi_1436
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 Aug 02 2021. The underlying query database was built on Aug 02 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