GapMind for catabolism of small carbon sources

 

L-proline catabolism in Rhodanobacter denitrificans 2APBS1

Best path

CCNA_00435, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
CCNA_00435 proline transporter R2APBS1_RS06770 R2APBS1_RS06765
put1 proline dehydrogenase R2APBS1_RS01300
putA L-glutamate 5-semialdeyde dehydrogenase R2APBS1_RS01300 R2APBS1_RS03885
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP R2APBS1_RS13010 R2APBS1_RS11520
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase R2APBS1_RS12475 R2APBS1_RS08710
AZOBR_RS08235 proline ABC transporter, permease component 1
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 R2APBS1_RS15240 R2APBS1_RS13570
AZOBR_RS08250 proline ABC transporter, ATPase component 2 R2APBS1_RS15240 R2APBS1_RS10335
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
davD glutarate semialdehyde dehydrogenase R2APBS1_RS05730 R2APBS1_RS00470
davT 5-aminovalerate aminotransferase R2APBS1_RS03870 R2APBS1_RS01840
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase R2APBS1_RS12580 R2APBS1_RS10950
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase R2APBS1_RS08705 R2APBS1_RS10950
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase R2APBS1_RS06240 R2APBS1_RS06205
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component
HSERO_RS00885 proline ABC transporter, permease component 1
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 R2APBS1_RS15240 R2APBS1_RS13270
HSERO_RS00900 proline ABC transporter, ATPase component 2 R2APBS1_RS15240 R2APBS1_RS19035
hutV proline ABC transporter, ATPase component HutV R2APBS1_RS13010 R2APBS1_RS12060
hutW proline ABC transporter, permease component HutW R2APBS1_RS12065
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter R2APBS1_RS06765 R2APBS1_RS17625
natA proline ABC transporter, ATPase component 1 (NatA) R2APBS1_RS15240 R2APBS1_RS14330
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD)
natE proline ABC transporter, ATPase component 2 (NatE) R2APBS1_RS15240 R2APBS1_RS12020
opuBA proline ABC transporter, ATPase component OpuBA/BusAA R2APBS1_RS13010 R2APBS1_RS19035
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
proP proline:H+ symporter ProP R2APBS1_RS00080 R2APBS1_RS10450
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV R2APBS1_RS13010 R2APBS1_RS19035
proW proline ABC transporter, permease component ProW R2APBS1_RS12065
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter R2APBS1_RS05445 R2APBS1_RS12170
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