GapMind for catabolism of small carbon sources

 

L-proline catabolism in Xanthobacter autotrophicus Py2

Best path

AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, 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
AZOBR_RS08235 proline ABC transporter, permease component 1 XAUT_RS19735 XAUT_RS05260
AZOBR_RS08240 proline ABC transporter, permease component 2 XAUT_RS19740 XAUT_RS20530
AZOBR_RS08245 proline ABC transporter, ATPase component 1 XAUT_RS19745 XAUT_RS09335
AZOBR_RS08250 proline ABC transporter, ATPase component 2 XAUT_RS19750 XAUT_RS03220
AZOBR_RS08260 proline ABC transporter, substrate-binding component XAUT_RS19760
put1 proline dehydrogenase XAUT_RS17390
putA L-glutamate 5-semialdeyde dehydrogenase XAUT_RS17390 XAUT_RS13655
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ XAUT_RS23020 XAUT_RS08225
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) XAUT_RS23030 XAUT_RS10440
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP XAUT_RS23035 XAUT_RS12270
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) XAUT_RS23025
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase XAUT_RS23630 XAUT_RS15615
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase XAUT_RS16460 XAUT_RS13655
davT 5-aminovalerate aminotransferase XAUT_RS21405 XAUT_RS06110
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase XAUT_RS16635 XAUT_RS04570
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase XAUT_RS04535 XAUT_RS04610
gcdG succinyl-CoA:glutarate CoA-transferase XAUT_RS23885 XAUT_RS06250
gcdH glutaryl-CoA dehydrogenase XAUT_RS23880 XAUT_RS21625
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component XAUT_RS19760 XAUT_RS07820
HSERO_RS00885 proline ABC transporter, permease component 1 XAUT_RS19735 XAUT_RS05260
HSERO_RS00890 proline ABC transporter, permease component 2 XAUT_RS19740 XAUT_RS20530
HSERO_RS00895 proline ABC transporter, ATPase component 1 XAUT_RS20495 XAUT_RS25540
HSERO_RS00900 proline ABC transporter, ATPase component 2 XAUT_RS19750 XAUT_RS20500
hutV proline ABC transporter, ATPase component HutV XAUT_RS12990 XAUT_RS10810
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) XAUT_RS14090
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) XAUT_RS20495 XAUT_RS04455
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) XAUT_RS03235 XAUT_RS08110
natE proline ABC transporter, ATPase component 2 (NatE) XAUT_RS19750 XAUT_RS20500
opuBA proline ABC transporter, ATPase component OpuBA/BusAA XAUT_RS12990 XAUT_RS04305
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 XAUT_RS23680 XAUT_RS04685
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV XAUT_RS22330 XAUT_RS14810
proW proline ABC transporter, permease component ProW XAUT_RS20475 XAUT_RS05740
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
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