GapMind for catabolism of small carbon sources

 

L-proline catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

proY, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proY proline:H+ symporter
put1 proline dehydrogenase DvMF_2146
putA L-glutamate 5-semialdeyde dehydrogenase DvMF_2146
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DvMF_3152
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DvMF_2786
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DvMF_2788 DvMF_3151
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase
AZOBR_RS08235 proline ABC transporter, permease component 1 DvMF_2751 DvMF_2608
AZOBR_RS08240 proline ABC transporter, permease component 2 DvMF_2609 DvMF_2752
AZOBR_RS08245 proline ABC transporter, ATPase component 1 DvMF_2610 DvMF_1481
AZOBR_RS08250 proline ABC transporter, ATPase component 2 DvMF_2611 DvMF_2754
AZOBR_RS08260 proline ABC transporter, substrate-binding component DvMF_2607 DvMF_2750
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase DvMF_2146
davT 5-aminovalerate aminotransferase DvMF_1002 DvMF_3149
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component DvMF_2750
HSERO_RS00885 proline ABC transporter, permease component 1 DvMF_2608 DvMF_2751
HSERO_RS00890 proline ABC transporter, permease component 2 DvMF_2609 DvMF_1164
HSERO_RS00895 proline ABC transporter, ATPase component 1 DvMF_2610 DvMF_2753
HSERO_RS00900 proline ABC transporter, ATPase component 2 DvMF_2754 DvMF_2611
hutV proline ABC transporter, ATPase component HutV DvMF_1045 DvMF_1960
hutW proline ABC transporter, permease component HutW DvMF_1044
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) DvMF_2753 DvMF_1163
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) DvMF_2609
natD proline ABC transporter, permease component 2 (NatD) DvMF_2751 DvMF_2608
natE proline ABC transporter, ATPase component 2 (NatE) DvMF_2754 DvMF_2611
opuBA proline ABC transporter, ATPase component OpuBA/BusAA DvMF_1045 DvMF_0655
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 DvMF_1045 DvMF_1960
proW proline ABC transporter, permease component ProW DvMF_1044
proX proline ABC transporter, substrate-binding component ProX
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.

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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