GapMind for catabolism of small carbon sources

 

L-proline catabolism in Marivita geojedonensis DPG-138

Best path

ectP, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ectP proline transporter EctP MGEO_RS09375
put1 proline dehydrogenase MGEO_RS16525
putA L-glutamate 5-semialdeyde dehydrogenase MGEO_RS16525 MGEO_RS17260
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ MGEO_RS16990
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) MGEO_RS17000 MGEO_RS10180
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP MGEO_RS17005 MGEO_RS07775
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) MGEO_RS16995
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase MGEO_RS09905 MGEO_RS17560
AZOBR_RS08235 proline ABC transporter, permease component 1 MGEO_RS18500 MGEO_RS10635
AZOBR_RS08240 proline ABC transporter, permease component 2 MGEO_RS14470
AZOBR_RS08245 proline ABC transporter, ATPase component 1 MGEO_RS04005 MGEO_RS05255
AZOBR_RS08250 proline ABC transporter, ATPase component 2 MGEO_RS05250 MGEO_RS04030
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS MGEO_RS09375
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase MGEO_RS15320 MGEO_RS02345
davT 5-aminovalerate aminotransferase MGEO_RS15340 MGEO_RS10195
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase MGEO_RS17480 MGEO_RS15835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase MGEO_RS15835 MGEO_RS14675
gcdG succinyl-CoA:glutarate CoA-transferase MGEO_RS11950 MGEO_RS18005
gcdH glutaryl-CoA dehydrogenase MGEO_RS11945 MGEO_RS05735
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 MGEO_RS04010 MGEO_RS19850
HSERO_RS00890 proline ABC transporter, permease component 2
HSERO_RS00895 proline ABC transporter, ATPase component 1 MGEO_RS04005 MGEO_RS05255
HSERO_RS00900 proline ABC transporter, ATPase component 2 MGEO_RS04030 MGEO_RS05250
hutV proline ABC transporter, ATPase component HutV MGEO_RS10720 MGEO_RS18525
hutW proline ABC transporter, permease component HutW MGEO_RS18520 MGEO_RS17245
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) MGEO_RS19860 MGEO_RS14455
natB proline ABC transporter, substrate-binding component NatB MGEO_RS14450
natC proline ABC transporter, permease component 1 (NatC) MGEO_RS14470
natD proline ABC transporter, permease component 2 (NatD) MGEO_RS14465 MGEO_RS19850
natE proline ABC transporter, ATPase component 2 (NatE) MGEO_RS14460 MGEO_RS19855
opuBA proline ABC transporter, ATPase component OpuBA/BusAA MGEO_RS18525 MGEO_RS10720
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 MGEO_RS01160
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV MGEO_RS10720 MGEO_RS18525
proW proline ABC transporter, permease component ProW MGEO_RS18520 MGEO_RS10725
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