GapMind for catabolism of small carbon sources

 

L-proline catabolism in Photobacterium gaetbulicola Gung47

Best path

putP, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter H744_RS08290 H744_RS09245
put1 proline dehydrogenase H744_RS08300
putA L-glutamate 5-semialdeyde dehydrogenase H744_RS08300 H744_RS01660
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ H744_RS20715 H744_RS06585
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H744_RS20725 H744_RS06575
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H744_RS20730 H744_RS06570
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H744_RS20720 H744_RS06580
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase H744_RS02875 H744_RS04335
AZOBR_RS08235 proline ABC transporter, permease component 1
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 H744_RS07090
AZOBR_RS08250 proline ABC transporter, ATPase component 2 H744_RS07085 H744_RS12065
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS H744_RS06180 H744_RS03445
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase H744_RS01660 H744_RS03200
davT 5-aminovalerate aminotransferase H744_RS11460 H744_RS16550
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H744_RS10395 H744_RS04320
ectP proline transporter EctP H744_RS19750 H744_RS06180
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H744_RS10395 H744_RS14605
gcdG succinyl-CoA:glutarate CoA-transferase H744_RS02205
gcdH glutaryl-CoA dehydrogenase H744_RS04345 H744_RS04325
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component
HSERO_RS00885 proline ABC transporter, permease component 1 H744_RS07100
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 H744_RS12065 H744_RS07090
HSERO_RS00900 proline ABC transporter, ATPase component 2 H744_RS07085 H744_RS12420
hutV proline ABC transporter, ATPase component HutV H744_RS02715 H744_RS22590
hutW proline ABC transporter, permease component HutW H744_RS02720 H744_RS22595
hutX proline ABC transporter, substrate-binding component HutX H744_RS02725
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H744_RS05515
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) H744_RS07090 H744_RS12065
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD)
natE proline ABC transporter, ATPase component 2 (NatE) H744_RS07085 H744_RS12065
opuBA proline ABC transporter, ATPase component OpuBA/BusAA H744_RS02715 H744_RS22590
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 H744_RS20285
prdF proline racemase
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV H744_RS02715 H744_RS22590
proW proline ABC transporter, permease component ProW H744_RS02720 H744_RS22595
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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