GapMind for catabolism of small carbon sources

 

L-proline catabolism in Magnetospirillum magneticum AMB-1

Best path

AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AZOBR_RS08235 proline ABC transporter, permease component 1 AMB_RS09135 AMB_RS08455
AZOBR_RS08240 proline ABC transporter, permease component 2 AMB_RS09130 AMB_RS14460
AZOBR_RS08245 proline ABC transporter, ATPase component 1 AMB_RS09125 AMB_RS08465
AZOBR_RS08250 proline ABC transporter, ATPase component 2 AMB_RS09120 AMB_RS10230
AZOBR_RS08260 proline ABC transporter, substrate-binding component AMB_RS15010
put1 proline dehydrogenase AMB_RS12610
putA L-glutamate 5-semialdeyde dehydrogenase AMB_RS12610 AMB_RS04115
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 AMB_RS10565 AMB_RS05625
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase AMB_RS18210 AMB_RS04295
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04160
davT 5-aminovalerate aminotransferase AMB_RS01605 AMB_RS04150
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMB_RS03265 AMB_RS13070
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
gcdG succinyl-CoA:glutarate CoA-transferase AMB_RS08365 AMB_RS07510
gcdH glutaryl-CoA dehydrogenase AMB_RS16315 AMB_RS03480
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component AMB_RS15010
HSERO_RS00885 proline ABC transporter, permease component 1 AMB_RS09135 AMB_RS08455
HSERO_RS00890 proline ABC transporter, permease component 2 AMB_RS09130 AMB_RS08460
HSERO_RS00895 proline ABC transporter, ATPase component 1 AMB_RS08465 AMB_RS18160
HSERO_RS00900 proline ABC transporter, ATPase component 2 AMB_RS18185 AMB_RS08470
hutV proline ABC transporter, ATPase component HutV AMB_RS06730 AMB_RS13205
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) AMB_RS19325
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) AMB_RS08465 AMB_RS12355
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) AMB_RS09130
natD proline ABC transporter, permease component 2 (NatD) AMB_RS08455 AMB_RS14465
natE proline ABC transporter, ATPase component 2 (NatE) AMB_RS10230 AMB_RS09120
opuBA proline ABC transporter, ATPase component OpuBA/BusAA AMB_RS13205 AMB_RS06730
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 AMB_RS08370
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV AMB_RS13205 AMB_RS06730
proW proline ABC transporter, permease component ProW
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
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