GapMind for catabolism of small carbon sources

 

L-proline catabolism in Williamsia sterculiae CPCC 203464

Best path

proY, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proY proline:H+ symporter BW971_RS09675 BW971_RS07675
put1 proline dehydrogenase BW971_RS03110
putA L-glutamate 5-semialdeyde dehydrogenase BW971_RS03115 BW971_RS04825
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) BW971_RS15735
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BW971_RS05930 BW971_RS17350
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase BW971_RS20375 BW971_RS04170
AZOBR_RS08235 proline ABC transporter, permease component 1 BW971_RS17395
AZOBR_RS08240 proline ABC transporter, permease component 2 BW971_RS17390
AZOBR_RS08245 proline ABC transporter, ATPase component 1 BW971_RS17385 BW971_RS06860
AZOBR_RS08250 proline ABC transporter, ATPase component 2 BW971_RS17380 BW971_RS17385
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS BW971_RS03825
CCNA_00435 proline transporter BW971_RS15225 BW971_RS14700
davD glutarate semialdehyde dehydrogenase BW971_RS02050 BW971_RS04825
davT 5-aminovalerate aminotransferase BW971_RS02060 BW971_RS04810
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BW971_RS12060 BW971_RS00105
ectP proline transporter EctP BW971_RS03825
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BW971_RS08035 BW971_RS03020
gcdG succinyl-CoA:glutarate CoA-transferase BW971_RS08680 BW971_RS09930
gcdH glutaryl-CoA dehydrogenase BW971_RS08610 BW971_RS19425
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 BW971_RS17395
HSERO_RS00890 proline ABC transporter, permease component 2 BW971_RS17390
HSERO_RS00895 proline ABC transporter, ATPase component 1 BW971_RS17385 BW971_RS00080
HSERO_RS00900 proline ABC transporter, ATPase component 2 BW971_RS17380 BW971_RS17385
hutV proline ABC transporter, ATPase component HutV BW971_RS13015 BW971_RS18650
hutW proline ABC transporter, permease component HutW BW971_RS13020
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter BW971_RS15225 BW971_RS14700
natA proline ABC transporter, ATPase component 1 (NatA) BW971_RS17385 BW971_RS19660
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) BW971_RS17380 BW971_RS17385
opuBA proline ABC transporter, ATPase component OpuBA/BusAA BW971_RS13015 BW971_RS18650
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 BW971_RS16640 BW971_RS01235
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV BW971_RS13015 BW971_RS12525
proW proline ABC transporter, permease component ProW BW971_RS13020 BW971_RS18655
proX proline ABC transporter, substrate-binding component ProX
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.

Links

Downloads

Related tools

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