GapMind for catabolism of small carbon sources

 

L-proline catabolism in Herbaspirillum autotrophicum IAM 14942

Best path

HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS00870 proline ABC transporter, substrate-binding component AKL27_RS04835 AKL27_RS25150
HSERO_RS00885 proline ABC transporter, permease component 1 AKL27_RS04820 AKL27_RS09915
HSERO_RS00890 proline ABC transporter, permease component 2 AKL27_RS04815 AKL27_RS09910
HSERO_RS00895 proline ABC transporter, ATPase component 1 AKL27_RS04810 AKL27_RS06300
HSERO_RS00900 proline ABC transporter, ATPase component 2 AKL27_RS04805 AKL27_RS23280
put1 proline dehydrogenase AKL27_RS04800 AKL27_RS00520
putA L-glutamate 5-semialdeyde dehydrogenase AKL27_RS04800 AKL27_RS26270
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) AKL27_RS00255 AKL27_RS23090
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AKL27_RS02440 AKL27_RS21660
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AKL27_RS21650
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase AKL27_RS04650 AKL27_RS00755
AZOBR_RS08235 proline ABC transporter, permease component 1 AKL27_RS04820 AKL27_RS09915
AZOBR_RS08240 proline ABC transporter, permease component 2 AKL27_RS09910 AKL27_RS18995
AZOBR_RS08245 proline ABC transporter, ATPase component 1 AKL27_RS09905 AKL27_RS18995
AZOBR_RS08250 proline ABC transporter, ATPase component 2 AKL27_RS09900 AKL27_RS19000
AZOBR_RS08260 proline ABC transporter, substrate-binding component AKL27_RS09920 AKL27_RS06845
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase AKL27_RS02365 AKL27_RS01645
davT 5-aminovalerate aminotransferase AKL27_RS02370 AKL27_RS14040
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AKL27_RS10475 AKL27_RS23795
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AKL27_RS04630 AKL27_RS20445
gcdG succinyl-CoA:glutarate CoA-transferase AKL27_RS00360 AKL27_RS22965
gcdH glutaryl-CoA dehydrogenase AKL27_RS00355 AKL27_RS20495
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV AKL27_RS02135 AKL27_RS09775
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) AKL27_RS06090
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) AKL27_RS23275 AKL27_RS18995
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) AKL27_RS09910 AKL27_RS23270
natD proline ABC transporter, permease component 2 (NatD) AKL27_RS04820 AKL27_RS15590
natE proline ABC transporter, ATPase component 2 (NatE) AKL27_RS15575 AKL27_RS09900
opuBA proline ABC transporter, ATPase component OpuBA/BusAA AKL27_RS09775 AKL27_RS23420
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 AKL27_RS04830
proP proline:H+ symporter ProP AKL27_RS19275 AKL27_RS20200
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV AKL27_RS09775 AKL27_RS23420
proW proline ABC transporter, permease component ProW AKL27_RS09780 AKL27_RS18335
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter AKL27_RS21895 AKL27_RS05855
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 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