GapMind for catabolism of small carbon sources

 

L-proline catabolism in Nocardiopsis baichengensis YIM 90130

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proY proline:H+ symporter C892_RS0102390
put1 proline dehydrogenase C892_RS0106300 C892_RS0127070
putA L-glutamate 5-semialdeyde dehydrogenase C892_RS0106295 C892_RS0124010
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 C892_RS0107840 C892_RS0116870
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase C892_RS0103915 C892_RS0127360
AZOBR_RS08235 proline ABC transporter, permease component 1 C892_RS0110665 C892_RS0104280
AZOBR_RS08240 proline ABC transporter, permease component 2 C892_RS0110670
AZOBR_RS08245 proline ABC transporter, ATPase component 1 C892_RS0110655 C892_RS0115130
AZOBR_RS08250 proline ABC transporter, ATPase component 2 C892_RS0110660 C892_RS0115135
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS C892_RS0100635 C892_RS0120225
CCNA_00435 proline transporter C892_RS0120615
davD glutarate semialdehyde dehydrogenase C892_RS0121440 C892_RS0126085
davT 5-aminovalerate aminotransferase C892_RS0108560 C892_RS0121435
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C892_RS0126825 C892_RS0118260
ectP proline transporter EctP C892_RS0111120 C892_RS0120225
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C892_RS0118260 C892_RS0113150
gcdG succinyl-CoA:glutarate CoA-transferase C892_RS0114505 C892_RS0124750
gcdH glutaryl-CoA dehydrogenase C892_RS0114500 C892_RS0127300
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 C892_RS0115120 C892_RS0104280
HSERO_RS00890 proline ABC transporter, permease component 2 C892_RS0115125
HSERO_RS00895 proline ABC transporter, ATPase component 1 C892_RS0110655 C892_RS0115130
HSERO_RS00900 proline ABC transporter, ATPase component 2 C892_RS0110660 C892_RS0115135
hutV proline ABC transporter, ATPase component HutV C892_RS0105220 C892_RS0123290
hutW proline ABC transporter, permease component HutW C892_RS0105215 C892_RS0123285
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) C892_RS0108640
N515DRAFT_2924 proline transporter C892_RS0120615
natA proline ABC transporter, ATPase component 1 (NatA) C892_RS0115130 C892_RS0110655
natB proline ABC transporter, substrate-binding component NatB C892_RS0115140
natC proline ABC transporter, permease component 1 (NatC) C892_RS0115125
natD proline ABC transporter, permease component 2 (NatD) C892_RS0115120 C892_RS0104280
natE proline ABC transporter, ATPase component 2 (NatE) C892_RS0115135 C892_RS0110660
opuBA proline ABC transporter, ATPase component OpuBA/BusAA C892_RS0123290 C892_RS0105220
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB C892_RS0105215
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 C892_RS0102995
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV C892_RS0123290 C892_RS0105220
proW proline ABC transporter, permease component ProW C892_RS0105215 C892_RS0123285
proX proline ABC transporter, substrate-binding component ProX
putP proline:Na+ symporter C892_RS0124260 C892_RS0111495
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