GapMind for catabolism of small carbon sources

 

L-proline catabolism in Dyella japonica UNC79MFTsu3.2

Best path

N515DRAFT_2924, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
N515DRAFT_2924 proline transporter N515DRAFT_2924 N515DRAFT_2925
put1 proline dehydrogenase N515DRAFT_4232 N515DRAFT_0956
putA L-glutamate 5-semialdeyde dehydrogenase N515DRAFT_4232 N515DRAFT_3729
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 N515DRAFT_1085 N515DRAFT_1562
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase N515DRAFT_0938 N515DRAFT_2688
AZOBR_RS08235 proline ABC transporter, permease component 1
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 N515DRAFT_3950
AZOBR_RS08250 proline ABC transporter, ATPase component 2 N515DRAFT_3950 N515DRAFT_4159
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter N515DRAFT_2924 N515DRAFT_0606
davD glutarate semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
davT 5-aminovalerate aminotransferase N515DRAFT_3308 N515DRAFT_1751
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase N515DRAFT_1164 N515DRAFT_0416
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
gcdG succinyl-CoA:glutarate CoA-transferase N515DRAFT_3223
gcdH glutaryl-CoA dehydrogenase N515DRAFT_0484 N515DRAFT_0492
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 N515DRAFT_3950 N515DRAFT_1562
HSERO_RS00900 proline ABC transporter, ATPase component 2 N515DRAFT_3950 N515DRAFT_4159
hutV proline ABC transporter, ATPase component HutV N515DRAFT_1085 N515DRAFT_1562
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)
natA proline ABC transporter, ATPase component 1 (NatA) N515DRAFT_3950 N515DRAFT_1687
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) N515DRAFT_3950 N515DRAFT_1687
opuBA proline ABC transporter, ATPase component OpuBA/BusAA N515DRAFT_4212 N515DRAFT_1562
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 N515DRAFT_0959
proP proline:H+ symporter ProP N515DRAFT_1367 N515DRAFT_0011
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV N515DRAFT_1562 N515DRAFT_1085
proW proline ABC transporter, permease component ProW
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter N515DRAFT_2630 N515DRAFT_3653
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