GapMind for catabolism of small carbon sources

 

L-proline catabolism in Azohydromonas australica DSM 1124

Best path

HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS00870 proline ABC transporter, substrate-binding component H537_RS0112015 H537_RS0124915
HSERO_RS00885 proline ABC transporter, permease component 1 H537_RS0121280 H537_RS0113285
HSERO_RS00890 proline ABC transporter, permease component 2 H537_RS0121275 H537_RS0113280
HSERO_RS00895 proline ABC transporter, ATPase component 1 H537_RS0121270 H537_RS0108415
HSERO_RS00900 proline ABC transporter, ATPase component 2 H537_RS0121265 H537_RS0108410
put1 proline dehydrogenase H537_RS0124445 H537_RS44845
putA L-glutamate 5-semialdeyde dehydrogenase H537_RS0124445 H537_RS44845
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ H537_RS0104885
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H537_RS41215 H537_RS0107730
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H537_RS41220 H537_RS0128690
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H537_RS41215
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase H537_RS0122115 H537_RS0129600
AZOBR_RS08235 proline ABC transporter, permease component 1 H537_RS0121280 H537_RS0124595
AZOBR_RS08240 proline ABC transporter, permease component 2 H537_RS0121275 H537_RS0113280
AZOBR_RS08245 proline ABC transporter, ATPase component 1 H537_RS0124590 H537_RS0128195
AZOBR_RS08250 proline ABC transporter, ATPase component 2 H537_RS0121265 H537_RS0124585
AZOBR_RS08260 proline ABC transporter, substrate-binding component H537_RS0112015 H537_RS0135945
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase H537_RS0138620 H537_RS0120085
davT 5-aminovalerate aminotransferase H537_RS0120050 H537_RS0137245
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H537_RS0100790 H537_RS0111045
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H537_RS0132195 H537_RS0116855
gcdG succinyl-CoA:glutarate CoA-transferase H537_RS0123940 H537_RS44370
gcdH glutaryl-CoA dehydrogenase H537_RS0120055 H537_RS0115055
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV H537_RS0132055 H537_RS0104880
hutW proline ABC transporter, permease component HutW H537_RS0122410 H537_RS0124975
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H537_RS0114715
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) H537_RS0121270 H537_RS0113275
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) H537_RS0121275 H537_RS0113280
natD proline ABC transporter, permease component 2 (NatD) H537_RS0121280 H537_RS0108425
natE proline ABC transporter, ATPase component 2 (NatE) H537_RS0121265 H537_RS0113270
opuBA proline ABC transporter, ATPase component OpuBA/BusAA H537_RS48490 H537_RS0120065
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 H537_RS0106085 H537_RS0123005
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV H537_RS0104880 H537_RS0103160
proW proline ABC transporter, permease component ProW H537_RS0122410 H537_RS0124975
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 Sep 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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