GapMind for catabolism of small carbon sources

 

L-proline catabolism in Stutzerimonas stutzeri A1501

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP proline:Na+ symporter PST_RS06325 PST_RS06340
put1 proline dehydrogenase PST_RS06320
putA L-glutamate 5-semialdeyde dehydrogenase PST_RS06320 PST_RS00500
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) PST_RS20440
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PST_RS20430 PST_RS11850
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase PST_RS03530 PST_RS16155
AZOBR_RS08235 proline ABC transporter, permease component 1 PST_RS14955 PST_RS02160
AZOBR_RS08240 proline ABC transporter, permease component 2 PST_RS14960
AZOBR_RS08245 proline ABC transporter, ATPase component 1 PST_RS14965 PST_RS16095
AZOBR_RS08250 proline ABC transporter, ATPase component 2 PST_RS14970 PST_RS18540
AZOBR_RS08260 proline ABC transporter, substrate-binding component PST_RS14950
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS PST_RS02575 PST_RS20425
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase PST_RS00500 PST_RS03775
davT 5-aminovalerate aminotransferase PST_RS03780 PST_RS08350
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PST_RS09740 PST_RS06175
ectP proline transporter EctP PST_RS02575 PST_RS20425
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PST_RS08735 PST_RS00510
gcdG succinyl-CoA:glutarate CoA-transferase PST_RS02290 PST_RS08605
gcdH glutaryl-CoA dehydrogenase PST_RS02285 PST_RS09725
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component PST_RS14950
HSERO_RS00885 proline ABC transporter, permease component 1 PST_RS14955 PST_RS02160
HSERO_RS00890 proline ABC transporter, permease component 2 PST_RS14960 PST_RS16075
HSERO_RS00895 proline ABC transporter, ATPase component 1 PST_RS14965 PST_RS16095
HSERO_RS00900 proline ABC transporter, ATPase component 2 PST_RS14970 PST_RS18540
hutV proline ABC transporter, ATPase component HutV PST_RS00360 PST_RS00200
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) PST_RS19980
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) PST_RS14965 PST_RS16095
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) PST_RS14960
natD proline ABC transporter, permease component 2 (NatD) PST_RS16080 PST_RS02160
natE proline ABC transporter, ATPase component 2 (NatE) PST_RS14970 PST_RS16090
opuBA proline ABC transporter, ATPase component OpuBA/BusAA PST_RS03755 PST_RS00360
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 PST_RS00360 PST_RS12250
proW proline ABC transporter, permease component ProW
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter PST_RS13100
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 Apr 09 2024. 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