GapMind for catabolism of small carbon sources

 

L-proline catabolism in Endozoicomonas montiporae CL-33

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter EZMO1_RS21675 EZMO1_RS08230
put1 proline dehydrogenase EZMO1_RS21535
putA L-glutamate 5-semialdeyde dehydrogenase EZMO1_RS21535 EZMO1_RS18815
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ EZMO1_RS20815
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) EZMO1_RS20805
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP EZMO1_RS20800 EZMO1_RS08085
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) EZMO1_RS20810
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase EZMO1_RS10775 EZMO1_RS06595
AZOBR_RS08235 proline ABC transporter, permease component 1 EZMO1_RS04590
AZOBR_RS08240 proline ABC transporter, permease component 2 EZMO1_RS04595
AZOBR_RS08245 proline ABC transporter, ATPase component 1 EZMO1_RS04600
AZOBR_RS08250 proline ABC transporter, ATPase component 2 EZMO1_RS04605 EZMO1_RS10810
AZOBR_RS08260 proline ABC transporter, substrate-binding component EZMO1_RS04585
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS EZMO1_RS14435 EZMO1_RS13880
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase EZMO1_RS03095 EZMO1_RS02225
davT 5-aminovalerate aminotransferase EZMO1_RS05155 EZMO1_RS05305
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase EZMO1_RS13400 EZMO1_RS12715
ectP proline transporter EctP EZMO1_RS14435 EZMO1_RS13880
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase EZMO1_RS13400 EZMO1_RS12725
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase EZMO1_RS03345 EZMO1_RS02775
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) EZMO1_RS13545
HSERO_RS00870 proline ABC transporter, substrate-binding component EZMO1_RS04585
HSERO_RS00885 proline ABC transporter, permease component 1 EZMO1_RS04590
HSERO_RS00890 proline ABC transporter, permease component 2 EZMO1_RS04595
HSERO_RS00895 proline ABC transporter, ATPase component 1 EZMO1_RS04600 EZMO1_RS20960
HSERO_RS00900 proline ABC transporter, ATPase component 2 EZMO1_RS04605 EZMO1_RS20960
hutV proline ABC transporter, ATPase component HutV EZMO1_RS14415 EZMO1_RS17780
hutW proline ABC transporter, permease component HutW EZMO1_RS14420
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) EZMO1_RS13540
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) EZMO1_RS04600 EZMO1_RS20960
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) EZMO1_RS04595
natD proline ABC transporter, permease component 2 (NatD)
natE proline ABC transporter, ATPase component 2 (NatE) EZMO1_RS04605 EZMO1_RS20960
opuBA proline ABC transporter, ATPase component OpuBA/BusAA EZMO1_RS14415 EZMO1_RS05725
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 EZMO1_RS17440 EZMO1_RS17450
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV EZMO1_RS14415 EZMO1_RS16205
proW proline ABC transporter, permease component ProW EZMO1_RS14420 EZMO1_RS16200
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.

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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