GapMind for catabolism of small carbon sources

 

L-proline catabolism in Moritella dasanensis ArB 0140

Best path

ectP, 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
ectP proline transporter EctP A923_RS0106725 A923_RS0106730
put1 proline dehydrogenase A923_RS0115365
putA L-glutamate 5-semialdeyde dehydrogenase A923_RS0115365 A923_RS0108515
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ A923_RS0106870
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) A923_RS0106860 A923_RS0119710
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP A923_RS0106855 A923_RS0109795
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) A923_RS22050
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase A923_RS0119275 A923_RS0119825
AZOBR_RS08235 proline ABC transporter, permease component 1
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 A923_RS0116420
AZOBR_RS08250 proline ABC transporter, ATPase component 2 A923_RS0116415 A923_RS0110810
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS A923_RS0100215 A923_RS0106725
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase A923_RS0105090 A923_RS0108515
davT 5-aminovalerate aminotransferase A923_RS0118545 A923_RS0109340
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A923_RS0104120 A923_RS0110330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A923_RS0119830 A923_RS0104120
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase A923_RS0101015
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 A923_RS0116430
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 A923_RS0116420 A923_RS0110810
HSERO_RS00900 proline ABC transporter, ATPase component 2 A923_RS0116415 A923_RS0116605
hutV proline ABC transporter, ATPase component HutV A923_RS0108545 A923_RS0118395
hutW proline ABC transporter, permease component HutW A923_RS0108540
hutX proline ABC transporter, substrate-binding component HutX A923_RS0108535 A923_RS0100760
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) A923_RS0105505
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) A923_RS0110810 A923_RS0116420
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) A923_RS0116415 A923_RS0106420
opuBA proline ABC transporter, ATPase component OpuBA/BusAA A923_RS0108545 A923_RS0101995
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
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV A923_RS0108545 A923_RS0116010
proW proline ABC transporter, permease component ProW A923_RS0108540
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
putP proline:Na+ symporter A923_RS0118515
SLC6A7 proline:Na+ symporter A923_RS0114590

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