GapMind for catabolism of small carbon sources

 

L-proline catabolism in Marinomonas arctica 328

Best path

putP, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter DK187_RS13450
put1 proline dehydrogenase DK187_RS02925
putA L-glutamate 5-semialdeyde dehydrogenase DK187_RS02925 DK187_RS15725
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DK187_RS03070 DK187_RS01945
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DK187_RS03060 DK187_RS01935
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DK187_RS03055 DK187_RS01930
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) DK187_RS03065 DK187_RS01940
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase DK187_RS06190 DK187_RS08790
AZOBR_RS08235 proline ABC transporter, permease component 1 DK187_RS07510
AZOBR_RS08240 proline ABC transporter, permease component 2 DK187_RS07515
AZOBR_RS08245 proline ABC transporter, ATPase component 1 DK187_RS07520 DK187_RS09960
AZOBR_RS08250 proline ABC transporter, ATPase component 2 DK187_RS07525 DK187_RS09965
AZOBR_RS08260 proline ABC transporter, substrate-binding component DK187_RS07505
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS DK187_RS16770 DK187_RS03365
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase DK187_RS02405 DK187_RS15780
davT 5-aminovalerate aminotransferase DK187_RS02410 DK187_RS13600
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DK187_RS04965 DK187_RS08785
ectP proline transporter EctP DK187_RS03365 DK187_RS16770
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DK187_RS08785 DK187_RS04955
gcdG succinyl-CoA:glutarate CoA-transferase DK187_RS07920
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component DK187_RS07505
HSERO_RS00885 proline ABC transporter, permease component 1 DK187_RS07510 DK187_RS18835
HSERO_RS00890 proline ABC transporter, permease component 2 DK187_RS07515
HSERO_RS00895 proline ABC transporter, ATPase component 1 DK187_RS07520 DK187_RS09960
HSERO_RS00900 proline ABC transporter, ATPase component 2 DK187_RS07525 DK187_RS09965
hutV proline ABC transporter, ATPase component HutV DK187_RS01005 DK187_RS00225
hutW proline ABC transporter, permease component HutW DK187_RS01000
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) DK187_RS04730
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) DK187_RS07520 DK187_RS09960
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) DK187_RS07510 DK187_RS18835
natE proline ABC transporter, ATPase component 2 (NatE) DK187_RS07525 DK187_RS18820
opuBA proline ABC transporter, ATPase component OpuBA/BusAA DK187_RS01005 DK187_RS03285
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 DK187_RS02370
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV DK187_RS01005 DK187_RS08910
proW proline ABC transporter, permease component ProW DK187_RS01000
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ 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.

Links

Downloads

Related tools

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