GapMind for catabolism of small carbon sources

 

L-proline catabolism in Pseudomonas litoralis 2SM5

Best path

putP, 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
putP proline:Na+ symporter BLU11_RS15570
put1 proline dehydrogenase BLU11_RS15565
putA L-glutamate 5-semialdeyde dehydrogenase BLU11_RS15565 BLU11_RS07260
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLU11_RS14500 BLU11_RS18455
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase BLU11_RS15740 BLU11_RS15515
AZOBR_RS08235 proline ABC transporter, permease component 1 BLU11_RS03765
AZOBR_RS08240 proline ABC transporter, permease component 2 BLU11_RS03760
AZOBR_RS08245 proline ABC transporter, ATPase component 1 BLU11_RS03755 BLU11_RS01725
AZOBR_RS08250 proline ABC transporter, ATPase component 2 BLU11_RS03750 BLU11_RS03755
AZOBR_RS08260 proline ABC transporter, substrate-binding component BLU11_RS03770
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS BLU11_RS00755 BLU11_RS18920
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase BLU11_RS14925 BLU11_RS07285
davT 5-aminovalerate aminotransferase BLU11_RS00885 BLU11_RS10765
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLU11_RS12290 BLU11_RS02050
ectP proline transporter EctP BLU11_RS18920 BLU11_RS00755
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLU11_RS06160 BLU11_RS15910
gcdG succinyl-CoA:glutarate CoA-transferase BLU11_RS06185 BLU11_RS15305
gcdH glutaryl-CoA dehydrogenase BLU11_RS13665 BLU11_RS12305
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component BLU11_RS03770
HSERO_RS00885 proline ABC transporter, permease component 1 BLU11_RS03765
HSERO_RS00890 proline ABC transporter, permease component 2 BLU11_RS03760
HSERO_RS00895 proline ABC transporter, ATPase component 1 BLU11_RS03755 BLU11_RS01420
HSERO_RS00900 proline ABC transporter, ATPase component 2 BLU11_RS03750 BLU11_RS03755
hutV proline ABC transporter, ATPase component HutV BLU11_RS14815 BLU11_RS18455
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) BLU11_RS14525
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) BLU11_RS03755 BLU11_RS01420
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) BLU11_RS03765
natE proline ABC transporter, ATPase component 2 (NatE) BLU11_RS03750 BLU11_RS01420
opuBA proline ABC transporter, ATPase component OpuBA/BusAA BLU11_RS07240 BLU11_RS14815
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 BLU11_RS07275
proP proline:H+ symporter ProP BLU11_RS11460
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV BLU11_RS14815 BLU11_RS18455
proW proline ABC transporter, permease component ProW
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ 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