GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

putP, 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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter AO356_09010
put1 proline dehydrogenase AO356_09015
putA L-glutamate 5-semialdeyde dehydrogenase AO356_09015 AO356_07180
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ AO356_17380
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) AO356_17390 AO356_29675
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AO356_17395 AO356_18215
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AO356_17385
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
AZOBR_RS08235 proline ABC transporter, permease component 1 AO356_08495 AO356_05325
AZOBR_RS08240 proline ABC transporter, permease component 2 AO356_05330 AO356_08490
AZOBR_RS08245 proline ABC transporter, ATPase component 1 AO356_05335 AO356_28390
AZOBR_RS08250 proline ABC transporter, ATPase component 2 AO356_08480 AO356_05340
AZOBR_RS08260 proline ABC transporter, substrate-binding component AO356_08500 AO356_05320
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS AO356_10225
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase AO356_10720 AO356_29070
davT 5-aminovalerate aminotransferase AO356_10715 AO356_26715
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO356_26360 AO356_02330
ectP proline transporter EctP AO356_10225
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO356_02330 AO356_29995
gcdG succinyl-CoA:glutarate CoA-transferase AO356_10845 AO356_06355
gcdH glutaryl-CoA dehydrogenase AO356_10850 AO356_01580
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component AO356_08500 AO356_05320
HSERO_RS00885 proline ABC transporter, permease component 1 AO356_08495 AO356_05325
HSERO_RS00890 proline ABC transporter, permease component 2 AO356_05330 AO356_08490
HSERO_RS00895 proline ABC transporter, ATPase component 1 AO356_05335 AO356_08485
HSERO_RS00900 proline ABC transporter, ATPase component 2 AO356_05340 AO356_08480
hutV proline ABC transporter, ATPase component HutV AO356_09610 AO356_09255
hutW proline ABC transporter, permease component HutW AO356_09615 AO356_13810
hutX proline ABC transporter, substrate-binding component HutX AO356_09620 AO356_23245
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AO356_26445
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) AO356_05335 AO356_29020
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) AO356_05330
natD proline ABC transporter, permease component 2 (NatD) AO356_08495 AO356_08345
natE proline ABC transporter, ATPase component 2 (NatE) AO356_05340 AO356_08480
opuBA proline ABC transporter, ATPase component OpuBA/BusAA AO356_09255 AO356_00615
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 AO356_09240 AO356_24960
proP proline:H+ symporter ProP AO356_22475 AO356_06425
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV AO356_09255 AO356_13805
proW proline ABC transporter, permease component ProW AO356_09615 AO356_00610
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter AO356_17670 AO356_11625
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