GapMind for catabolism of small carbon sources

 

L-proline catabolism in Streptacidiphilus oryzae TH49

Best path

proY, 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
proY proline:H+ symporter BS73_RS16535 BS73_RS25710
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase BS73_RS12295 BS73_RS24175
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 BS73_RS32880 BS73_RS15740
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase BS73_RS10365 BS73_RS08675
AZOBR_RS08235 proline ABC transporter, permease component 1 BS73_RS29125 BS73_RS13625
AZOBR_RS08240 proline ABC transporter, permease component 2 BS73_RS29120
AZOBR_RS08245 proline ABC transporter, ATPase component 1 BS73_RS29115 BS73_RS00335
AZOBR_RS08250 proline ABC transporter, ATPase component 2 BS73_RS29110 BS73_RS13620
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter BS73_RS12665 BS73_RS17340
davD glutarate semialdehyde dehydrogenase BS73_RS19435 BS73_RS01225
davT 5-aminovalerate aminotransferase BS73_RS14180 BS73_RS19430
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BS73_RS14910 BS73_RS05650
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BS73_RS08975 BS73_RS07230
gcdG succinyl-CoA:glutarate CoA-transferase BS73_RS32920 BS73_RS15390
gcdH glutaryl-CoA dehydrogenase BS73_RS32915 BS73_RS25270
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component BS73_RS29130
HSERO_RS00885 proline ABC transporter, permease component 1 BS73_RS29125 BS73_RS13625
HSERO_RS00890 proline ABC transporter, permease component 2 BS73_RS29120
HSERO_RS00895 proline ABC transporter, ATPase component 1 BS73_RS29115 BS73_RS00335
HSERO_RS00900 proline ABC transporter, ATPase component 2 BS73_RS29110 BS73_RS13620
hutV proline ABC transporter, ATPase component HutV BS73_RS09120 BS73_RS28185
hutW proline ABC transporter, permease component HutW BS73_RS09115 BS73_RS28180
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BS73_RS18665
N515DRAFT_2924 proline transporter BS73_RS12665 BS73_RS16585
natA proline ABC transporter, ATPase component 1 (NatA) BS73_RS00335 BS73_RS29115
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) BS73_RS29120
natD proline ABC transporter, permease component 2 (NatD) BS73_RS29125
natE proline ABC transporter, ATPase component 2 (NatE) BS73_RS00340 BS73_RS29110
opuBA proline ABC transporter, ATPase component OpuBA/BusAA BS73_RS28185 BS73_RS21095
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB BS73_RS09115
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 BS73_RS02840 BS73_RS02825
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV BS73_RS28185 BS73_RS09120
proW proline ABC transporter, permease component ProW BS73_RS09115 BS73_RS28180
proX proline ABC transporter, substrate-binding component ProX
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