GapMind for catabolism of small carbon sources

 

L-proline catabolism in Oleispira antarctica

Best path

proV, proW, proX, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proV proline ABC transporter, ATPase component ProV OLEAN_RS14330 OLEAN_RS18015
proW proline ABC transporter, permease component ProW OLEAN_RS14325 OLEAN_RS18020
proX proline ABC transporter, substrate-binding component ProX OLEAN_RS14320
put1 proline dehydrogenase OLEAN_RS17490
putA L-glutamate 5-semialdeyde dehydrogenase OLEAN_RS17490 OLEAN_RS18035
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 OLEAN_RS14330 OLEAN_RS18015
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase OLEAN_RS17915 OLEAN_RS18075
AZOBR_RS08235 proline ABC transporter, permease component 1 OLEAN_RS18860 OLEAN_RS03235
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 OLEAN_RS03225 OLEAN_RS18850
AZOBR_RS08250 proline ABC transporter, ATPase component 2 OLEAN_RS18845 OLEAN_RS03220
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS OLEAN_RS13920 OLEAN_RS14025
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase OLEAN_RS18035 OLEAN_RS05680
davT 5-aminovalerate aminotransferase OLEAN_RS06405 OLEAN_RS15795
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase OLEAN_RS07250 OLEAN_RS13050
ectP proline transporter EctP OLEAN_RS13920 OLEAN_RS14025
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase OLEAN_RS07250 OLEAN_RS16520
gcdG succinyl-CoA:glutarate CoA-transferase OLEAN_RS16530
gcdH glutaryl-CoA dehydrogenase OLEAN_RS16500 OLEAN_RS16525
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 OLEAN_RS18860
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 OLEAN_RS03225 OLEAN_RS18850
HSERO_RS00900 proline ABC transporter, ATPase component 2 OLEAN_RS18845 OLEAN_RS03220
hutV proline ABC transporter, ATPase component HutV OLEAN_RS14330 OLEAN_RS18015
hutW proline ABC transporter, permease component HutW OLEAN_RS14325 OLEAN_RS18020
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) OLEAN_RS04990
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) OLEAN_RS02280 OLEAN_RS18850
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) OLEAN_RS18860
natE proline ABC transporter, ATPase component 2 (NatE) OLEAN_RS03220 OLEAN_RS03225
opuBA proline ABC transporter, ATPase component OpuBA/BusAA OLEAN_RS14330 OLEAN_RS18015
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 OLEAN_RS05770
prdF proline racemase
proP proline:H+ symporter ProP
PROT1 proline transporter
proY proline:H+ symporter
putP proline:Na+ symporter OLEAN_RS17495
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