GapMind for catabolism of small carbon sources

 

L-proline catabolism in Chromobacterium vaccinii MWU205

Best path

HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, 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
HSERO_RS00870 proline ABC transporter, substrate-binding component VL52_RS09675 VL52_RS22490
HSERO_RS00885 proline ABC transporter, permease component 1 VL52_RS15500
HSERO_RS00890 proline ABC transporter, permease component 2 VL52_RS15495
HSERO_RS00895 proline ABC transporter, ATPase component 1 VL52_RS15490 VL52_RS03360
HSERO_RS00900 proline ABC transporter, ATPase component 2 VL52_RS15485 VL52_RS03360
put1 proline dehydrogenase VL52_RS18890
putA L-glutamate 5-semialdeyde dehydrogenase VL52_RS18890 VL52_RS20940
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) VL52_RS08850 VL52_RS19745
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP VL52_RS19750 VL52_RS06130
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) VL52_RS19740 VL52_RS19745
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase VL52_RS14225 VL52_RS21005
AZOBR_RS08235 proline ABC transporter, permease component 1 VL52_RS15500
AZOBR_RS08240 proline ABC transporter, permease component 2 VL52_RS15495
AZOBR_RS08245 proline ABC transporter, ATPase component 1 VL52_RS15490 VL52_RS03360
AZOBR_RS08250 proline ABC transporter, ATPase component 2 VL52_RS15485 VL52_RS15490
AZOBR_RS08260 proline ABC transporter, substrate-binding component VL52_RS09675 VL52_RS22490
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS VL52_RS15675
CCNA_00435 proline transporter VL52_RS03530
davD glutarate semialdehyde dehydrogenase VL52_RS20940 VL52_RS07105
davT 5-aminovalerate aminotransferase VL52_RS20935 VL52_RS15525
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase VL52_RS18865 VL52_RS21030
ectP proline transporter EctP VL52_RS15675
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase VL52_RS10360 VL52_RS21015
gcdG succinyl-CoA:glutarate CoA-transferase VL52_RS20890
gcdH glutaryl-CoA dehydrogenase VL52_RS20895 VL52_RS19965
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV VL52_RS12370 VL52_RS00410
hutW proline ABC transporter, permease component HutW
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) VL52_RS05540
N515DRAFT_2924 proline transporter VL52_RS03530
natA proline ABC transporter, ATPase component 1 (NatA) VL52_RS15490 VL52_RS03360
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) VL52_RS15495
natD proline ABC transporter, permease component 2 (NatD) VL52_RS15500
natE proline ABC transporter, ATPase component 2 (NatE) VL52_RS15485 VL52_RS03360
opuBA proline ABC transporter, ATPase component OpuBA/BusAA VL52_RS12370 VL52_RS00410
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 VL52_RS09515
proP proline:H+ symporter ProP VL52_RS11320 VL52_RS08400
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV VL52_RS12370 VL52_RS00410
proW proline ABC transporter, permease component ProW VL52_RS12375 VL52_RS00405
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter VL52_RS13800 VL52_RS00290
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