GapMind for catabolism of small carbon sources

 

L-proline catabolism in Sinorhizobium fredii NGR234

Best path

aapJ, aapQ, aapM, aapP, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ NGR_RS17855
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) NGR_RS17850 NGR_RS02885
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) NGR_RS17845 NGR_RS23815
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP NGR_RS17840 NGR_RS10540
put1 proline dehydrogenase NGR_RS11860 NGR_RS21360
putA L-glutamate 5-semialdeyde dehydrogenase NGR_RS11860 NGR_RS21360
Alternative steps:
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase NGR_RS27475 NGR_RS26100
AZOBR_RS08235 proline ABC transporter, permease component 1 NGR_RS23745 NGR_RS21540
AZOBR_RS08240 proline ABC transporter, permease component 2 NGR_RS23740 NGR_RS28285
AZOBR_RS08245 proline ABC transporter, ATPase component 1 NGR_RS23735 NGR_RS07020
AZOBR_RS08250 proline ABC transporter, ATPase component 2 NGR_RS23730 NGR_RS21555
AZOBR_RS08260 proline ABC transporter, substrate-binding component NGR_RS07325 NGR_RS23720
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS NGR_RS24265
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase NGR_RS27930 NGR_RS06520
davT 5-aminovalerate aminotransferase NGR_RS06525 NGR_RS12135
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase NGR_RS29675 NGR_RS12210
ectP proline transporter EctP NGR_RS24265
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase NGR_RS24175 NGR_RS12210
gcdG succinyl-CoA:glutarate CoA-transferase NGR_RS06375 NGR_RS02365
gcdH glutaryl-CoA dehydrogenase NGR_RS06370 NGR_RS05525
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component NGR_RS23720 NGR_RS14075
HSERO_RS00885 proline ABC transporter, permease component 1 NGR_RS23745 NGR_RS10925
HSERO_RS00890 proline ABC transporter, permease component 2 NGR_RS23740 NGR_RS10930
HSERO_RS00895 proline ABC transporter, ATPase component 1 NGR_RS07890 NGR_RS07020
HSERO_RS00900 proline ABC transporter, ATPase component 2 NGR_RS07025 NGR_RS07885
hutV proline ABC transporter, ATPase component HutV NGR_RS24855 NGR_RS02380
hutW proline ABC transporter, permease component HutW NGR_RS24850 NGR_RS02375
hutX proline ABC transporter, substrate-binding component HutX NGR_RS24845 NGR_RS15275
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) NGR_RS06795
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) NGR_RS10935 NGR_RS28290
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) NGR_RS10930
natD proline ABC transporter, permease component 2 (NatD) NGR_RS28280 NGR_RS10455
natE proline ABC transporter, ATPase component 2 (NatE) NGR_RS10940 NGR_RS23730
opuBA proline ABC transporter, ATPase component OpuBA/BusAA NGR_RS02380 NGR_RS20365
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 NGR_RS26225 NGR_RS11875
proP proline:H+ symporter ProP NGR_RS27720
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV NGR_RS20365 NGR_RS02380
proW proline ABC transporter, permease component ProW NGR_RS24850 NGR_RS15280
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter NGR_RS11085
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 Apr 09 2024. 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