GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pontibacter ramchanderi LP43

Best path

proY, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proY proline:H+ symporter
put1 proline dehydrogenase BD749_RS15585 BD749_RS12830
putA L-glutamate 5-semialdeyde dehydrogenase BD749_RS16740 BD749_RS10835
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 BD749_RS18690 BD749_RS09725
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase BD749_RS13705 BD749_RS18285
AZOBR_RS08235 proline ABC transporter, permease component 1
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 BD749_RS11320
AZOBR_RS08250 proline ABC transporter, ATPase component 2 BD749_RS11320 BD749_RS06110
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase BD749_RS10835 BD749_RS05780
davT 5-aminovalerate aminotransferase BD749_RS13990 BD749_RS02630
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BD749_RS07655 BD749_RS17005
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BD749_RS18290 BD749_RS03200
gcdG succinyl-CoA:glutarate CoA-transferase BD749_RS06625
gcdH glutaryl-CoA dehydrogenase BD749_RS08765 BD749_RS11220
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
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 BD749_RS11320 BD749_RS17540
HSERO_RS00900 proline ABC transporter, ATPase component 2 BD749_RS11320
hutV proline ABC transporter, ATPase component HutV BD749_RS05320 BD749_RS07915
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) BD749_RS05420
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) BD749_RS11320 BD749_RS14880
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) BD749_RS11320 BD749_RS12890
opuBA proline ABC transporter, ATPase component OpuBA/BusAA BD749_RS11320 BD749_RS07915
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 BD749_RS00760
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV BD749_RS07915 BD749_RS05320
proW proline ABC transporter, permease component ProW
proX proline ABC transporter, substrate-binding component ProX
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