GapMind for catabolism of small carbon sources

 

L-proline catabolism in Herbaspirillum aquaticum IEH 4430

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 CEJ45_RS22985 CEJ45_RS12295
HSERO_RS00885 proline ABC transporter, permease component 1 CEJ45_RS11220 CEJ45_RS04950
HSERO_RS00890 proline ABC transporter, permease component 2 CEJ45_RS04955 CEJ45_RS05575
HSERO_RS00895 proline ABC transporter, ATPase component 1 CEJ45_RS22550 CEJ45_RS01010
HSERO_RS00900 proline ABC transporter, ATPase component 2 CEJ45_RS22555 CEJ45_RS05580
put1 proline dehydrogenase CEJ45_RS14295 CEJ45_RS11565
putA L-glutamate 5-semialdeyde dehydrogenase CEJ45_RS14295 CEJ45_RS04055
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) CEJ45_RS19655 CEJ45_RS14240
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CEJ45_RS14125 CEJ45_RS21940
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) CEJ45_RS04235
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase CEJ45_RS14415 CEJ45_RS09425
AZOBR_RS08235 proline ABC transporter, permease component 1 CEJ45_RS11220 CEJ45_RS04950
AZOBR_RS08240 proline ABC transporter, permease component 2 CEJ45_RS04955 CEJ45_RS05575
AZOBR_RS08245 proline ABC transporter, ATPase component 1 CEJ45_RS04960 CEJ45_RS15965
AZOBR_RS08250 proline ABC transporter, ATPase component 2 CEJ45_RS04965 CEJ45_RS01005
AZOBR_RS08260 proline ABC transporter, substrate-binding component CEJ45_RS04945 CEJ45_RS12295
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase CEJ45_RS11845 CEJ45_RS11615
davT 5-aminovalerate aminotransferase CEJ45_RS11820 CEJ45_RS14475
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CEJ45_RS16530 CEJ45_RS06410
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CEJ45_RS14455 CEJ45_RS11470
gcdG succinyl-CoA:glutarate CoA-transferase CEJ45_RS11495 CEJ45_RS17765
gcdH glutaryl-CoA dehydrogenase CEJ45_RS11500 CEJ45_RS12595
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV CEJ45_RS04905 CEJ45_RS05205
hutW proline ABC transporter, permease component HutW CEJ45_RS05200
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CEJ45_RS10670
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) CEJ45_RS01010 CEJ45_RS05575
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) CEJ45_RS04955 CEJ45_RS01015
natD proline ABC transporter, permease component 2 (NatD) CEJ45_RS11220 CEJ45_RS04950
natE proline ABC transporter, ATPase component 2 (NatE) CEJ45_RS05580 CEJ45_RS04965
opuBA proline ABC transporter, ATPase component OpuBA/BusAA CEJ45_RS05205 CEJ45_RS18040
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 CEJ45_RS22980
proP proline:H+ symporter ProP CEJ45_RS14385 CEJ45_RS08565
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV CEJ45_RS05205 CEJ45_RS04905
proW proline ABC transporter, permease component ProW CEJ45_RS05200 CEJ45_RS05190
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