GapMind for catabolism of small carbon sources

 

L-proline catabolism in Herbaspirillum seropedicae SmR1

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS00870 proline ABC transporter, substrate-binding component HSERO_RS00870 HSERO_RS17350
HSERO_RS00885 proline ABC transporter, permease component 1 HSERO_RS05960 HSERO_RS00885
HSERO_RS00890 proline ABC transporter, permease component 2 HSERO_RS00890 HSERO_RS05965
HSERO_RS00895 proline ABC transporter, ATPase component 1 HSERO_RS05970 HSERO_RS00895
HSERO_RS00900 proline ABC transporter, ATPase component 2 HSERO_RS05975 HSERO_RS00900
put1 proline dehydrogenase HSERO_RS00905 HSERO_RS05695
putA L-glutamate 5-semialdeyde dehydrogenase HSERO_RS00905 HSERO_RS11260
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) HSERO_RS07530 HSERO_RS23030
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HSERO_RS19240 HSERO_RS17555
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) HSERO_RS19340 HSERO_RS17565
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase HSERO_RS01180 HSERO_RS04635
AZOBR_RS08235 proline ABC transporter, permease component 1 HSERO_RS08275 HSERO_RS05960
AZOBR_RS08240 proline ABC transporter, permease component 2 HSERO_RS08280 HSERO_RS00890
AZOBR_RS08245 proline ABC transporter, ATPase component 1 HSERO_RS08285 HSERO_RS05970
AZOBR_RS08250 proline ABC transporter, ATPase component 2 HSERO_RS08290 HSERO_RS05975
AZOBR_RS08260 proline ABC transporter, substrate-binding component HSERO_RS08270 HSERO_RS00870
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase HSERO_RS05395 HSERO_RS05645
davT 5-aminovalerate aminotransferase HSERO_RS05420 HSERO_RS19685
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HSERO_RS19405 HSERO_RS20665
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HSERO_RS01260 HSERO_RS04630
gcdG succinyl-CoA:glutarate CoA-transferase HSERO_RS18350 HSERO_RS14050
gcdH glutaryl-CoA dehydrogenase HSERO_RS23440 HSERO_RS04640
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV HSERO_RS07850 HSERO_RS08545
hutW proline ABC transporter, permease component HutW HSERO_RS08540
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) HSERO_RS21645
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) HSERO_RS14705 HSERO_RS08285
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) HSERO_RS14700
natD proline ABC transporter, permease component 2 (NatD) HSERO_RS05960 HSERO_RS00885
natE proline ABC transporter, ATPase component 2 (NatE) HSERO_RS08290 HSERO_RS08925
opuBA proline ABC transporter, ATPase component OpuBA/BusAA HSERO_RS08545 HSERO_RS03005
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 HSERO_RS00875
proP proline:H+ symporter ProP HSERO_RS01150 HSERO_RS00050
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV HSERO_RS08545 HSERO_RS08240
proW proline ABC transporter, permease component ProW HSERO_RS08530 HSERO_RS08540
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