GapMind for catabolism of small carbon sources

 

L-proline catabolism in Jannaschia aquimarina GSW-M26

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ectP proline transporter EctP jaqu_RS11040
put1 proline dehydrogenase jaqu_RS06790 jaqu_RS08505
putA L-glutamate 5-semialdeyde dehydrogenase jaqu_RS06790 jaqu_RS19035
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ jaqu_RS19390
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) jaqu_RS19380 jaqu_RS18165
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP jaqu_RS19375 jaqu_RS02055
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) jaqu_RS19385
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase jaqu_RS08040 jaqu_RS12590
AZOBR_RS08235 proline ABC transporter, permease component 1 jaqu_RS07820 jaqu_RS03105
AZOBR_RS08240 proline ABC transporter, permease component 2
AZOBR_RS08245 proline ABC transporter, ATPase component 1 jaqu_RS14580 jaqu_RS18390
AZOBR_RS08250 proline ABC transporter, ATPase component 2 jaqu_RS14620 jaqu_RS18395
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS jaqu_RS11040
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase jaqu_RS19035 jaqu_RS05710
davT 5-aminovalerate aminotransferase jaqu_RS05750 jaqu_RS08900
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase jaqu_RS12650 jaqu_RS00375
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase jaqu_RS01850 jaqu_RS00375
gcdG succinyl-CoA:glutarate CoA-transferase jaqu_RS05760 jaqu_RS12220
gcdH glutaryl-CoA dehydrogenase jaqu_RS01820 jaqu_RS05745
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 jaqu_RS07820
HSERO_RS00890 proline ABC transporter, permease component 2 jaqu_RS04945
HSERO_RS00895 proline ABC transporter, ATPase component 1 jaqu_RS14580 jaqu_RS18390
HSERO_RS00900 proline ABC transporter, ATPase component 2 jaqu_RS14620 jaqu_RS04925
hutV proline ABC transporter, ATPase component HutV jaqu_RS03655 jaqu_RS05725
hutW proline ABC transporter, permease component HutW jaqu_RS03650
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) jaqu_RS04915 jaqu_RS14580
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) jaqu_RS07825
natD proline ABC transporter, permease component 2 (NatD) jaqu_RS04940 jaqu_RS14600
natE proline ABC transporter, ATPase component 2 (NatE) jaqu_RS04925 jaqu_RS14620
opuBA proline ABC transporter, ATPase component OpuBA/BusAA jaqu_RS06985 jaqu_RS18640
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
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV jaqu_RS03655 jaqu_RS05725
proW proline ABC transporter, permease component ProW jaqu_RS03650
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