GapMind for catabolism of small carbon sources

 

L-proline catabolism in Cupriavidus basilensis 4G11

Best path

HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS00870 proline ABC transporter, substrate-binding component RR42_RS16980 RR42_RS20120
HSERO_RS00885 proline ABC transporter, permease component 1 RR42_RS16975 RR42_RS14420
HSERO_RS00890 proline ABC transporter, permease component 2 RR42_RS16970 RR42_RS14415
HSERO_RS00895 proline ABC transporter, ATPase component 1 RR42_RS16965 RR42_RS34795
HSERO_RS00900 proline ABC transporter, ATPase component 2 RR42_RS16960 RR42_RS14405
put1 proline dehydrogenase RR42_RS20125
putA L-glutamate 5-semialdeyde dehydrogenase RR42_RS20125 RR42_RS27350
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) RR42_RS27120 RR42_RS09485
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RR42_RS16370 RR42_RS02590
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RR42_RS31740 RR42_RS16450
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
AZOBR_RS08235 proline ABC transporter, permease component 1 RR42_RS14420 RR42_RS16975
AZOBR_RS08240 proline ABC transporter, permease component 2 RR42_RS14415 RR42_RS16970
AZOBR_RS08245 proline ABC transporter, ATPase component 1 RR42_RS14410 RR42_RS16965
AZOBR_RS08250 proline ABC transporter, ATPase component 2 RR42_RS14405 RR42_RS16960
AZOBR_RS08260 proline ABC transporter, substrate-binding component RR42_RS14425 RR42_RS16980
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter RR42_RS01585
davD glutarate semialdehyde dehydrogenase RR42_RS21760 RR42_RS24555
davT 5-aminovalerate aminotransferase RR42_RS26160 RR42_RS26240
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RR42_RS18250 RR42_RS23710
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RR42_RS02510 RR42_RS36415
gcdG succinyl-CoA:glutarate CoA-transferase RR42_RS15155 RR42_RS36540
gcdH glutaryl-CoA dehydrogenase RR42_RS15400 RR42_RS28565
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV RR42_RS04555 RR42_RS04825
hutW proline ABC transporter, permease component HutW RR42_RS10790 RR42_RS04820
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RR42_RS06495
N515DRAFT_2924 proline transporter RR42_RS01585
natA proline ABC transporter, ATPase component 1 (NatA) RR42_RS14410 RR42_RS16965
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) RR42_RS34785 RR42_RS14420
natE proline ABC transporter, ATPase component 2 (NatE) RR42_RS20235 RR42_RS14405
opuBA proline ABC transporter, ATPase component OpuBA/BusAA RR42_RS04825 RR42_RS27800
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 RR42_RS36345
proP proline:H+ symporter ProP RR42_RS29835 RR42_RS19610
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV RR42_RS04825 RR42_RS12250
proW proline ABC transporter, permease component ProW RR42_RS10790 RR42_RS04820
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter RR42_RS33780 RR42_RS14635
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