GapMind for catabolism of small carbon sources

 

L-proline catabolism in Marinobacter adhaerens HP15

Best path

putP, 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
putP proline:Na+ symporter HP15_2205
put1 proline dehydrogenase HP15_2688
putA L-glutamate 5-semialdeyde dehydrogenase HP15_2688 HP15_3626
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ HP15_2196
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) HP15_2194
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HP15_2193 HP15_2920
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) HP15_2195
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase HP15_2996 HP15_5
AZOBR_RS08235 proline ABC transporter, permease component 1 HP15_3056 HP15_2706
AZOBR_RS08240 proline ABC transporter, permease component 2 HP15_3057 HP15_4097
AZOBR_RS08245 proline ABC transporter, ATPase component 1 HP15_3058 HP15_4095
AZOBR_RS08250 proline ABC transporter, ATPase component 2 HP15_3059 HP15_2703
AZOBR_RS08260 proline ABC transporter, substrate-binding component HP15_3055
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS HP15_1130 HP15_2795
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase HP15_2020 HP15_3404
davT 5-aminovalerate aminotransferase HP15_3708 HP15_3042
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HP15_908 HP15_12
ectP proline transporter EctP HP15_2795 HP15_1130
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HP15_1512 HP15_3941
gcdG succinyl-CoA:glutarate CoA-transferase HP15_1416 HP15_2609
gcdH glutaryl-CoA dehydrogenase HP15_3936 HP15_2
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component HP15_3055
HSERO_RS00885 proline ABC transporter, permease component 1 HP15_3056 HP15_2706
HSERO_RS00890 proline ABC transporter, permease component 2 HP15_3057 HP15_2705
HSERO_RS00895 proline ABC transporter, ATPase component 1 HP15_2704 HP15_3058
HSERO_RS00900 proline ABC transporter, ATPase component 2 HP15_2703 HP15_3059
hutV proline ABC transporter, ATPase component HutV HP15_3298 HP15_3903
hutW proline ABC transporter, permease component HutW HP15_3297 HP15_995
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) HP15_2488
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) HP15_3058 HP15_2704
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) HP15_3057
natD proline ABC transporter, permease component 2 (NatD) HP15_3056 HP15_2015
natE proline ABC transporter, ATPase component 2 (NatE) HP15_3059 HP15_4099
opuBA proline ABC transporter, ATPase component OpuBA/BusAA HP15_3298 HP15_994
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB HP15_991
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 HP15_1348
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV HP15_3298 HP15_3903
proW proline ABC transporter, permease component ProW HP15_3297
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ 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