GapMind for catabolism of small carbon sources

 

L-proline catabolism in Mesorhizobium ciceri WSM1271

Best path

aapJ, aapQ, aapM, aapP, put1, putA

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 Mesci_4657 Mesci_2581
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Mesci_4656 Mesci_2580
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Mesci_4655 Mesci_2579
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Mesci_4654 Mesci_2578
put1 proline dehydrogenase Mesci_3431
putA L-glutamate 5-semialdeyde dehydrogenase Mesci_3431 Mesci_0274
Alternative steps:
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase Mesci_1329 Mesci_1095
AZOBR_RS08235 proline ABC transporter, permease component 1 Mesci_1234 Mesci_6236
AZOBR_RS08240 proline ABC transporter, permease component 2 Mesci_1235 Mesci_6237
AZOBR_RS08245 proline ABC transporter, ATPase component 1 Mesci_1236 Mesci_6238
AZOBR_RS08250 proline ABC transporter, ATPase component 2 Mesci_1237 Mesci_0560
AZOBR_RS08260 proline ABC transporter, substrate-binding component Mesci_4851 Mesci_1239
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase Mesci_3425 Mesci_5665
davT 5-aminovalerate aminotransferase Mesci_0044 Mesci_5987
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Mesci_6037 Mesci_4665
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Mesci_1071 Mesci_6001
gcdG succinyl-CoA:glutarate CoA-transferase Mesci_3113 Mesci_0263
gcdH glutaryl-CoA dehydrogenase Mesci_1983 Mesci_4845
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component Mesci_6235 Mesci_1239
HSERO_RS00885 proline ABC transporter, permease component 1 Mesci_1234 Mesci_6236
HSERO_RS00890 proline ABC transporter, permease component 2 Mesci_6237 Mesci_1235
HSERO_RS00895 proline ABC transporter, ATPase component 1 Mesci_6238 Mesci_1236
HSERO_RS00900 proline ABC transporter, ATPase component 2 Mesci_1237 Mesci_0560
hutV proline ABC transporter, ATPase component HutV Mesci_0079 Mesci_2119
hutW proline ABC transporter, permease component HutW Mesci_0080 Mesci_2118
hutX proline ABC transporter, substrate-binding component HutX Mesci_0081
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Mesci_2427
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) Mesci_5232 Mesci_6238
natB proline ABC transporter, substrate-binding component NatB Mesci_5226
natC proline ABC transporter, permease component 1 (NatC) Mesci_5235 Mesci_6237
natD proline ABC transporter, permease component 2 (NatD) Mesci_5234 Mesci_6236
natE proline ABC transporter, ATPase component 2 (NatE) Mesci_5233 Mesci_1237
opuBA proline ABC transporter, ATPase component OpuBA/BusAA Mesci_0079 Mesci_2119
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB Mesci_5139
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Mesci_1233 Mesci_0177
proP proline:H+ symporter ProP Mesci_3660
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV Mesci_0079 Mesci_2119
proW proline ABC transporter, permease component ProW Mesci_0080 Mesci_2118
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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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