GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas simiae WCS417

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter PS417_02180
put1 proline dehydrogenase PS417_02175
putA L-glutamate 5-semialdeyde dehydrogenase PS417_02175 PS417_04200
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PS417_23345 PS417_04900
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PS417_04910 PS417_01810
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PS417_04915 PS417_26115
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PS417_04905
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
AZOBR_RS08235 proline ABC transporter, permease component 1 PS417_02660 PS417_06610
AZOBR_RS08240 proline ABC transporter, permease component 2 PS417_06605 PS417_02665
AZOBR_RS08245 proline ABC transporter, ATPase component 1 PS417_06600 PS417_16795
AZOBR_RS08250 proline ABC transporter, ATPase component 2 PS417_06595 PS417_02675
AZOBR_RS08260 proline ABC transporter, substrate-binding component PS417_02655 PS417_06615
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS PS417_01120 PS417_26330
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase PS417_00895 PS417_17840
davT 5-aminovalerate aminotransferase PS417_00900 PS417_23355
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PS417_13845 PS417_07575
ectP proline transporter EctP PS417_01120 PS417_26330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PS417_07575 PS417_21215
gcdG succinyl-CoA:glutarate CoA-transferase PS417_00585 PS417_14920
gcdH glutaryl-CoA dehydrogenase PS417_00580 PS417_17015
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component PS417_02655 PS417_06615
HSERO_RS00885 proline ABC transporter, permease component 1 PS417_02660 PS417_06610
HSERO_RS00890 proline ABC transporter, permease component 2 PS417_06605 PS417_02665
HSERO_RS00895 proline ABC transporter, ATPase component 1 PS417_06600 PS417_02670
HSERO_RS00900 proline ABC transporter, ATPase component 2 PS417_06595 PS417_02675
hutV proline ABC transporter, ATPase component HutV PS417_26325 PS417_04010
hutW proline ABC transporter, permease component HutW PS417_01735 PS417_26320
hutX proline ABC transporter, substrate-binding component HutX PS417_01730 PS417_11935
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) PS417_06600 PS417_16795
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) PS417_02665
natD proline ABC transporter, permease component 2 (NatD) PS417_06610 PS417_02660
natE proline ABC transporter, ATPase component 2 (NatE) PS417_06595 PS417_02675
opuBA proline ABC transporter, ATPase component OpuBA/BusAA PS417_26325 PS417_04010
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 PS417_14305
proP proline:H+ symporter ProP PS417_14785 PS417_14575
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV PS417_26325 PS417_04010
proW proline ABC transporter, permease component ProW PS417_01735 PS417_26320
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter PS417_01755 PS417_05405
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