GapMind for catabolism of small carbon sources

 

L-proline catabolism in Azospirillum brasilense Sp245

Best path

AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AZOBR_RS08235 proline ABC transporter, permease component 1 AZOBR_RS08235 AZOBR_RS03565
AZOBR_RS08240 proline ABC transporter, permease component 2 AZOBR_RS08240 AZOBR_RS32410
AZOBR_RS08245 proline ABC transporter, ATPase component 1 AZOBR_RS08245 AZOBR_RS13290
AZOBR_RS08250 proline ABC transporter, ATPase component 2 AZOBR_RS08250 AZOBR_RS29685
AZOBR_RS08260 proline ABC transporter, substrate-binding component AZOBR_RS08260
put1 proline dehydrogenase AZOBR_RS23695
putA L-glutamate 5-semialdeyde dehydrogenase AZOBR_RS23695 AZOBR_RS29185
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ AZOBR_RS08655 AZOBR_RS00530
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) AZOBR_RS08665 AZOBR_RS18065
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AZOBR_RS08670 AZOBR_RS15690
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AZOBR_RS08660 AZOBR_RS15675
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS AZOBR_RS23220
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
davT 5-aminovalerate aminotransferase AZOBR_RS19630 AZOBR_RS19025
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AZOBR_RS01260 AZOBR_RS26485
ectP proline transporter EctP AZOBR_RS23220
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
gcdG succinyl-CoA:glutarate CoA-transferase AZOBR_RS19675 AZOBR_RS29180
gcdH glutaryl-CoA dehydrogenase AZOBR_RS19670 AZOBR_RS22310
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component AZOBR_RS25645 AZOBR_RS08260
HSERO_RS00885 proline ABC transporter, permease component 1 AZOBR_RS08235 AZOBR_RS13300
HSERO_RS00890 proline ABC transporter, permease component 2 AZOBR_RS08240 AZOBR_RS25635
HSERO_RS00895 proline ABC transporter, ATPase component 1 AZOBR_RS22350 AZOBR_RS32405
HSERO_RS00900 proline ABC transporter, ATPase component 2 AZOBR_RS29685 AZOBR_RS20990
hutV proline ABC transporter, ATPase component HutV AZOBR_RS23480 AZOBR_RS15760
hutW proline ABC transporter, permease component HutW AZOBR_RS23475 AZOBR_RS15765
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AZOBR_RS33525
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) AZOBR_RS32405 AZOBR_RS04130
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) AZOBR_RS29675
natD proline ABC transporter, permease component 2 (NatD) AZOBR_RS29670 AZOBR_RS21005
natE proline ABC transporter, ATPase component 2 (NatE) AZOBR_RS19790 AZOBR_RS29685
opuBA proline ABC transporter, ATPase component OpuBA/BusAA AZOBR_RS23480 AZOBR_RS15760
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 AZOBR_RS27830
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV AZOBR_RS23480 AZOBR_RS15760
proW proline ABC transporter, permease component ProW AZOBR_RS23475 AZOBR_RS15765
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 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