GapMind for catabolism of small carbon sources

 

L-proline catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

aapJ, aapQ, aapM, aapP, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ CEV31_RS09895
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) CEV31_RS09900 CEV31_RS19045
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) CEV31_RS09905 CEV31_RS08815
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CEV31_RS09910 CEV31_RS19030
put1 proline dehydrogenase CEV31_RS15250 CEV31_RS01735
putA L-glutamate 5-semialdeyde dehydrogenase CEV31_RS15250 CEV31_RS01730
Alternative steps:
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase CEV31_RS03605 CEV31_RS02650
AZOBR_RS08235 proline ABC transporter, permease component 1 CEV31_RS03685 CEV31_RS14835
AZOBR_RS08240 proline ABC transporter, permease component 2 CEV31_RS03680 CEV31_RS14830
AZOBR_RS08245 proline ABC transporter, ATPase component 1 CEV31_RS03675 CEV31_RS14825
AZOBR_RS08250 proline ABC transporter, ATPase component 2 CEV31_RS03670 CEV31_RS14820
AZOBR_RS08260 proline ABC transporter, substrate-binding component CEV31_RS03660 CEV31_RS03655
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS CEV31_RS18345
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase CEV31_RS02995 CEV31_RS17495
davT 5-aminovalerate aminotransferase CEV31_RS07275 CEV31_RS17075
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CEV31_RS05620 CEV31_RS09090
ectP proline transporter EctP CEV31_RS18345
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CEV31_RS15760 CEV31_RS04315
gcdG succinyl-CoA:glutarate CoA-transferase CEV31_RS11730 CEV31_RS09080
gcdH glutaryl-CoA dehydrogenase CEV31_RS11735 CEV31_RS05790
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component CEV31_RS03655 CEV31_RS03660
HSERO_RS00885 proline ABC transporter, permease component 1 CEV31_RS03685 CEV31_RS13110
HSERO_RS00890 proline ABC transporter, permease component 2 CEV31_RS03680 CEV31_RS13105
HSERO_RS00895 proline ABC transporter, ATPase component 1 CEV31_RS14825 CEV31_RS03675
HSERO_RS00900 proline ABC transporter, ATPase component 2 CEV31_RS03670 CEV31_RS14820
hutV proline ABC transporter, ATPase component HutV CEV31_RS20565 CEV31_RS15405
hutW proline ABC transporter, permease component HutW CEV31_RS15400 CEV31_RS20560
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CEV31_RS17795 CEV31_RS18945
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) CEV31_RS14825 CEV31_RS03675
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) CEV31_RS03680
natD proline ABC transporter, permease component 2 (NatD) CEV31_RS14835 CEV31_RS02700
natE proline ABC transporter, ATPase component 2 (NatE) CEV31_RS03670 CEV31_RS17005
opuBA proline ABC transporter, ATPase component OpuBA/BusAA CEV31_RS15405 CEV31_RS20565
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB CEV31_RS15400
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase CEV31_RS03690
proP proline:H+ symporter ProP CEV31_RS15175 CEV31_RS16665
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV CEV31_RS15405 CEV31_RS20565
proW proline ABC transporter, permease component ProW CEV31_RS15400 CEV31_RS02285
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter CEV31_RS20665 CEV31_RS18290
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