GapMind for catabolism of small carbon sources

 

L-proline catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA

Also see fitness data for the top candidates

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS00870 proline ABC transporter, substrate-binding component H281DRAFT_02161 H281DRAFT_04063
HSERO_RS00885 proline ABC transporter, permease component 1 H281DRAFT_04062 H281DRAFT_06397
HSERO_RS00890 proline ABC transporter, permease component 2 H281DRAFT_04061
HSERO_RS00895 proline ABC transporter, ATPase component 1 H281DRAFT_04060 H281DRAFT_02383
HSERO_RS00900 proline ABC transporter, ATPase component 2 H281DRAFT_04059 H281DRAFT_02384
put1 proline dehydrogenase H281DRAFT_02404 H281DRAFT_06542
putA L-glutamate 5-semialdeyde dehydrogenase H281DRAFT_02404 H281DRAFT_03016
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) H281DRAFT_05402 H281DRAFT_04268
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H281DRAFT_04267 H281DRAFT_02565
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H281DRAFT_03349 H281DRAFT_04269
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
AZOBR_RS08235 proline ABC transporter, permease component 1 H281DRAFT_04062 H281DRAFT_06397
AZOBR_RS08240 proline ABC transporter, permease component 2 H281DRAFT_04061
AZOBR_RS08245 proline ABC transporter, ATPase component 1 H281DRAFT_04060 H281DRAFT_02383
AZOBR_RS08250 proline ABC transporter, ATPase component 2 H281DRAFT_04059 H281DRAFT_02384
AZOBR_RS08260 proline ABC transporter, substrate-binding component H281DRAFT_02161 H281DRAFT_02405
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter H281DRAFT_02180
davD glutarate semialdehyde dehydrogenase H281DRAFT_03178 H281DRAFT_03540
davT 5-aminovalerate aminotransferase H281DRAFT_03179 H281DRAFT_06478
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H281DRAFT_05725 H281DRAFT_02514
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
gcdG succinyl-CoA:glutarate CoA-transferase H281DRAFT_04444 H281DRAFT_01169
gcdH glutaryl-CoA dehydrogenase H281DRAFT_04737 H281DRAFT_01204
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV H281DRAFT_00987 H281DRAFT_02450
hutW proline ABC transporter, permease component HutW H281DRAFT_02451 H281DRAFT_00988
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H281DRAFT_02167
N515DRAFT_2924 proline transporter H281DRAFT_02180
natA proline ABC transporter, ATPase component 1 (NatA) H281DRAFT_04060 H281DRAFT_02383
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) H281DRAFT_04452
natD proline ABC transporter, permease component 2 (NatD) H281DRAFT_06397 H281DRAFT_04062
natE proline ABC transporter, ATPase component 2 (NatE) H281DRAFT_02384 H281DRAFT_04059
opuBA proline ABC transporter, ATPase component OpuBA/BusAA H281DRAFT_02450 H281DRAFT_00987
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB H281DRAFT_00988
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase H281DRAFT_01193
proP proline:H+ symporter ProP H281DRAFT_00442 H281DRAFT_04917
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV H281DRAFT_00987 H281DRAFT_02450
proW proline ABC transporter, permease component ProW H281DRAFT_00988 H281DRAFT_02451
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter H281DRAFT_01668 H281DRAFT_04042
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 Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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