GapMind for catabolism of small carbon sources

 

L-proline catabolism in Methylocystis bryophila S285

Best path

N515DRAFT_2924, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
N515DRAFT_2924 proline transporter B1812_RS04230 B1812_RS03615
put1 proline dehydrogenase B1812_RS02885
putA L-glutamate 5-semialdeyde dehydrogenase B1812_RS02885 B1812_RS01610
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ B1812_RS21010 B1812_RS19680
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 B1812_RS18275 B1812_RS21530
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase B1812_RS02620 B1812_RS16320
AZOBR_RS08235 proline ABC transporter, permease component 1
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 B1812_RS04380 B1812_RS12645
AZOBR_RS08250 proline ABC transporter, ATPase component 2 B1812_RS04360 B1812_RS12645
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter B1812_RS04230 B1812_RS03615
davD glutarate semialdehyde dehydrogenase B1812_RS10880 B1812_RS13395
davT 5-aminovalerate aminotransferase B1812_RS21480 B1812_RS12405
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B1812_RS05255 B1812_RS13170
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B1812_RS19300 B1812_RS13170
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase B1812_RS16285 B1812_RS14765
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 B1812_RS04375
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 B1812_RS04380 B1812_RS12645
HSERO_RS00900 proline ABC transporter, ATPase component 2 B1812_RS04360 B1812_RS13145
hutV proline ABC transporter, ATPase component HutV B1812_RS01630 B1812_RS18275
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) B1812_RS08345 B1812_RS21390
natA proline ABC transporter, ATPase component 1 (NatA) B1812_RS04380 B1812_RS12645
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) B1812_RS04360 B1812_RS12645
opuBA proline ABC transporter, ATPase component OpuBA/BusAA B1812_RS01630 B1812_RS15290
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB B1812_RS15295
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 B1812_RS09575
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV B1812_RS01630 B1812_RS18275
proW proline ABC transporter, permease component ProW
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
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