GapMind for catabolism of small carbon sources

 

L-proline catabolism in Sinorhizobium meliloti 1021

Best path

aapJ, aapQ, aapM, aapP, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ SMc02118 SMc00676
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) SMc02119 SMc03865
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) SMc02120 SMc03865
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP SMc02121 SMc03135
put1 proline dehydrogenase SMc02181
putA L-glutamate 5-semialdeyde dehydrogenase SMc02181 SM_b20891
Alternative steps:
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
AZOBR_RS08235 proline ABC transporter, permease component 1 SMc01951 SMc02359
AZOBR_RS08240 proline ABC transporter, permease component 2 SMc01950
AZOBR_RS08245 proline ABC transporter, ATPase component 1 SMc01949 SMc02357
AZOBR_RS08250 proline ABC transporter, ATPase component 2 SMc01948 SMc02358
AZOBR_RS08260 proline ABC transporter, substrate-binding component SMa0576 SMc01946
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS SM_b20333
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase SMc02780 SMa0805
davT 5-aminovalerate aminotransferase SM_b21186 SMc02413
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SMc01153 SMc01669
ectP proline transporter EctP SM_b20333
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SMc02227 SMc00727
gcdG succinyl-CoA:glutarate CoA-transferase SM_b21182 SM_b21089
gcdH glutaryl-CoA dehydrogenase SM_b21181 SM_b21121
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component SMc01946 SMc00078
HSERO_RS00885 proline ABC transporter, permease component 1 SMc01951 SMc02359
HSERO_RS00890 proline ABC transporter, permease component 2 SMc01950 SMa0217
HSERO_RS00895 proline ABC transporter, ATPase component 1 SMc02357 SMc01949
HSERO_RS00900 proline ABC transporter, ATPase component 2 SMc02358 SMc01948
hutV proline ABC transporter, ATPase component HutV SMc00670 SMc04439
hutW proline ABC transporter, permease component HutW SMc00671 SMc02379
hutX proline ABC transporter, substrate-binding component HutX SMc00672 SMc02378
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) SM_b20101
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) SMc03120 SMc02357
natB proline ABC transporter, substrate-binding component NatB SMc01946
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) SM_b20604 SMc03118
natE proline ABC transporter, ATPase component 2 (NatE) SMc01948 SMc02358
opuBA proline ABC transporter, ATPase component OpuBA/BusAA SMa1466 SMc02739
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 SM_b20268 SM_b20270
proP proline:H+ symporter ProP SMc01869 SMa1328
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV SMc02739 SMc04439
proW proline ABC transporter, permease component ProW SMc00671 SMc02379
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 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