GapMind for catabolism of small carbon sources

 

L-proline catabolism in Nocardioides dokdonensis FR1436

Best path

natA, natB, natC, natD, natE, 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
natA proline ABC transporter, ATPase component 1 (NatA) I601_RS18175 I601_RS10945
natB proline ABC transporter, substrate-binding component NatB I601_RS18165
natC proline ABC transporter, permease component 1 (NatC) I601_RS18180
natD proline ABC transporter, permease component 2 (NatD) I601_RS18185 I601_RS10450
natE proline ABC transporter, ATPase component 2 (NatE) I601_RS18170 I601_RS10465
put1 proline dehydrogenase I601_RS04105 I601_RS05875
putA L-glutamate 5-semialdeyde dehydrogenase I601_RS10820 I601_RS01590
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) I601_RS07010 I601_RS08985
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP I601_RS09290 I601_RS07015
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) I601_RS07010
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase I601_RS03035 I601_RS19250
AZOBR_RS08235 proline ABC transporter, permease component 1 I601_RS02135 I601_RS10450
AZOBR_RS08240 proline ABC transporter, permease component 2 I601_RS05895 I601_RS19355
AZOBR_RS08245 proline ABC transporter, ATPase component 1 I601_RS19350 I601_RS05910
AZOBR_RS08250 proline ABC transporter, ATPase component 2 I601_RS10465 I601_RS02130
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS I601_RS01370 I601_RS07630
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase I601_RS05735 I601_RS14160
davT 5-aminovalerate aminotransferase I601_RS14155 I601_RS12790
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I601_RS19165 I601_RS05525
ectP proline transporter EctP I601_RS07630 I601_RS01370
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I601_RS04220 I601_RS05790
gcdG succinyl-CoA:glutarate CoA-transferase I601_RS06545 I601_RS10415
gcdH glutaryl-CoA dehydrogenase I601_RS02110 I601_RS10230
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component
HSERO_RS00885 proline ABC transporter, permease component 1 I601_RS05905 I601_RS02135
HSERO_RS00890 proline ABC transporter, permease component 2 I601_RS05895
HSERO_RS00895 proline ABC transporter, ATPase component 1 I601_RS02125 I601_RS09180
HSERO_RS00900 proline ABC transporter, ATPase component 2 I601_RS10465 I601_RS19345
hutV proline ABC transporter, ATPase component HutV I601_RS12915 I601_RS08290
hutW proline ABC transporter, permease component HutW I601_RS12920 I601_RS02535
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
opuBA proline ABC transporter, ATPase component OpuBA/BusAA I601_RS12915 I601_RS02540
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB I601_RS12920
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 I601_RS12915 I601_RS02540
proW proline ABC transporter, permease component ProW I601_RS12920 I601_RS02545
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter
putP proline:Na+ symporter
SLC6A7 proline:Na+ symporter I601_RS18805

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