GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1487
put1 proline dehydrogenase Pf1N1B4_1489
putA L-glutamate 5-semialdeyde dehydrogenase Pf1N1B4_1489 Pf1N1B4_1109
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf1N1B4_917
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf1N1B4_915 Pf1N1B4_4805
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf1N1B4_914 Pf1N1B4_774
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf1N1B4_916 Pf1N1B4_772
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
AZOBR_RS08235 proline ABC transporter, permease component 1 Pf1N1B4_3217 Pf1N1B4_1381
AZOBR_RS08240 proline ABC transporter, permease component 2 Pf1N1B4_3216 Pf1N1B4_1380
AZOBR_RS08245 proline ABC transporter, ATPase component 1 Pf1N1B4_3215 Pf1N1B4_1379
AZOBR_RS08250 proline ABC transporter, ATPase component 2 Pf1N1B4_1378 Pf1N1B4_3214
AZOBR_RS08260 proline ABC transporter, substrate-binding component Pf1N1B4_1382 Pf1N1B4_3218
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS Pf1N1B4_1689 Pf1N1B4_2419
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase Pf1N1B4_1734 Pf1N1B4_4931
davT 5-aminovalerate aminotransferase Pf1N1B4_1733 Pf1N1B4_4910
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf1N1B4_4788 Pf1N1B4_3903
ectP proline transporter EctP Pf1N1B4_1689 Pf1N1B4_2419
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
gcdG succinyl-CoA:glutarate CoA-transferase Pf1N1B4_1815 Pf1N1B4_5611
gcdH glutaryl-CoA dehydrogenase Pf1N1B4_1816 Pf1N1B4_3987
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component Pf1N1B4_3218 Pf1N1B4_1382
HSERO_RS00885 proline ABC transporter, permease component 1 Pf1N1B4_1381 Pf1N1B4_3217
HSERO_RS00890 proline ABC transporter, permease component 2 Pf1N1B4_3216 Pf1N1B4_1380
HSERO_RS00895 proline ABC transporter, ATPase component 1 Pf1N1B4_3215 Pf1N1B4_1379
HSERO_RS00900 proline ABC transporter, ATPase component 2 Pf1N1B4_3214 Pf1N1B4_1378
hutV proline ABC transporter, ATPase component HutV Pf1N1B4_1583 Pf1N1B4_2420
hutW proline ABC transporter, permease component HutW Pf1N1B4_1584 Pf1N1B4_2421
hutX proline ABC transporter, substrate-binding component HutX Pf1N1B4_1585 Pf1N1B4_4296
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf1N1B4_4264
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) Pf1N1B4_3215 Pf1N1B4_1346
natB proline ABC transporter, substrate-binding component NatB Pf1N1B4_1382
natC proline ABC transporter, permease component 1 (NatC) Pf1N1B4_3216
natD proline ABC transporter, permease component 2 (NatD)
natE proline ABC transporter, ATPase component 2 (NatE) Pf1N1B4_3214 Pf1N1B4_1378
opuBA proline ABC transporter, ATPase component OpuBA/BusAA Pf1N1B4_1134 Pf1N1B4_2538
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 Pf1N1B4_5964 Pf1N1B4_5975
proP proline:H+ symporter ProP Pf1N1B4_5977 Pf1N1B4_180
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV Pf1N1B4_2420 Pf1N1B4_1583
proW proline ABC transporter, permease component ProW Pf1N1B4_1584 Pf1N1B4_2421
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter Pf1N1B4_1580 Pf1N1B4_801
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 Aug 02 2021. The underlying query database was built on Aug 02 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