GapMind for catabolism of small carbon sources

 

L-proline catabolism in Amantichitinum ursilacus IGB-41

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AZOBR_RS08235 proline ABC transporter, permease component 1 WG78_RS14895 WG78_RS14720
AZOBR_RS08240 proline ABC transporter, permease component 2 WG78_RS14900 WG78_RS14715
AZOBR_RS08245 proline ABC transporter, ATPase component 1 WG78_RS14905 WG78_RS14710
AZOBR_RS08250 proline ABC transporter, ATPase component 2 WG78_RS14910 WG78_RS14705
AZOBR_RS08260 proline ABC transporter, substrate-binding component WG78_RS14890 WG78_RS14725
put1 proline dehydrogenase WG78_RS17855
putA L-glutamate 5-semialdeyde dehydrogenase WG78_RS17855 WG78_RS16670
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) WG78_RS00050 WG78_RS16140
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP WG78_RS16125 WG78_RS16145
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) WG78_RS16135
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase WG78_RS19070 WG78_RS04410
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter WG78_RS04860
davD glutarate semialdehyde dehydrogenase WG78_RS16670 WG78_RS14820
davT 5-aminovalerate aminotransferase WG78_RS16665 WG78_RS06780
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase WG78_RS04405 WG78_RS04575
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component WG78_RS14725 WG78_RS14890
HSERO_RS00885 proline ABC transporter, permease component 1 WG78_RS14720 WG78_RS14895
HSERO_RS00890 proline ABC transporter, permease component 2 WG78_RS14715 WG78_RS14900
HSERO_RS00895 proline ABC transporter, ATPase component 1 WG78_RS14710 WG78_RS14905
HSERO_RS00900 proline ABC transporter, ATPase component 2 WG78_RS14705 WG78_RS14910
hutV proline ABC transporter, ATPase component HutV WG78_RS21100 WG78_RS15495
hutW proline ABC transporter, permease component HutW WG78_RS15500 WG78_RS15490
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) WG78_RS12675
N515DRAFT_2924 proline transporter WG78_RS04860
natA proline ABC transporter, ATPase component 1 (NatA) WG78_RS14710 WG78_RS14905
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) WG78_RS14900 WG78_RS14715
natD proline ABC transporter, permease component 2 (NatD) WG78_RS14720
natE proline ABC transporter, ATPase component 2 (NatE) WG78_RS14705 WG78_RS14910
opuBA proline ABC transporter, ATPase component OpuBA/BusAA WG78_RS15495 WG78_RS08940
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 WG78_RS13380 WG78_RS12280
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV WG78_RS21100 WG78_RS15495
proW proline ABC transporter, permease component ProW WG78_RS12330
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter WG78_RS03005
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