GapMind for catabolism of small carbon sources

 

L-proline catabolism in Escherichia coli BW25113

Best path

proV, proW, proX, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proV proline ABC transporter, ATPase component ProV b2677 b2129
proW proline ABC transporter, permease component ProW b2678 b2128
proX proline ABC transporter, substrate-binding component ProX b2679
put1 proline dehydrogenase b1014
putA L-glutamate 5-semialdeyde dehydrogenase b1014 b1415
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) b3270 b1918
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP b3271 b0652
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) b3269
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase b2224 b2844
AZOBR_RS08235 proline ABC transporter, permease component 1 b3457
AZOBR_RS08240 proline ABC transporter, permease component 2 b3456
AZOBR_RS08245 proline ABC transporter, ATPase component 1 b3455
AZOBR_RS08250 proline ABC transporter, ATPase component 2 b3454 b3201
AZOBR_RS08260 proline ABC transporter, substrate-binding component b3460 b3458
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS b0314
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase b2661 b1415
davT 5-aminovalerate aminotransferase b2662 b1302
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
ectP proline transporter EctP b0314
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase b3846 b2341
gcdG succinyl-CoA:glutarate CoA-transferase b2371 b2374
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) b2659
HSERO_RS00870 proline ABC transporter, substrate-binding component b3458 b3460
HSERO_RS00885 proline ABC transporter, permease component 1 b3457
HSERO_RS00890 proline ABC transporter, permease component 2 b3456
HSERO_RS00895 proline ABC transporter, ATPase component 1 b3455 b3201
HSERO_RS00900 proline ABC transporter, ATPase component 2 b3454 b3455
hutV proline ABC transporter, ATPase component HutV b2677 b2129
hutW proline ABC transporter, permease component HutW b2678 b2130
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) b2660
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) b3455 b3201
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) b3457
natE proline ABC transporter, ATPase component 2 (NatE) b3454 b1513
opuBA proline ABC transporter, ATPase component OpuBA/BusAA b2677 b2129
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB b2678
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 b4111 b3523
PROT1 proline transporter
proY proline:H+ symporter b0402 b2663
putP proline:Na+ symporter b1015 b3258
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.

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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