GapMind for catabolism of small carbon sources

 

L-proline catabolism in Rhizobium etli CFN 42

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AZOBR_RS08235 proline ABC transporter, permease component 1 RHE_RS17010 RHE_RS25480
AZOBR_RS08240 proline ABC transporter, permease component 2 RHE_RS17005
AZOBR_RS08245 proline ABC transporter, ATPase component 1 RHE_RS17000 RHE_RS25470
AZOBR_RS08250 proline ABC transporter, ATPase component 2 RHE_RS16995 RHE_RS25475
AZOBR_RS08260 proline ABC transporter, substrate-binding component RHE_RS15140 RHE_RS16985
put1 proline dehydrogenase RHE_RS28430 RHE_RS00450
putA L-glutamate 5-semialdeyde dehydrogenase RHE_RS28430 RHE_RS16180
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ RHE_RS09695
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) RHE_RS09685 RHE_RS27265
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RHE_RS09680 RHE_RS27420
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RHE_RS09690 RHE_RS20265
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase RHE_RS20545 RHE_RS23190
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase RHE_RS23010 RHE_RS00470
davT 5-aminovalerate aminotransferase RHE_RS00475 RHE_RS02610
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RHE_RS01800 RHE_RS02825
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RHE_RS02825 RHE_RS19395
gcdG succinyl-CoA:glutarate CoA-transferase RHE_RS14710
gcdH glutaryl-CoA dehydrogenase RHE_RS25445 RHE_RS23195
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component RHE_RS16985 RHE_RS15820
HSERO_RS00885 proline ABC transporter, permease component 1 RHE_RS17010 RHE_RS25480
HSERO_RS00890 proline ABC transporter, permease component 2 RHE_RS17005
HSERO_RS00895 proline ABC transporter, ATPase component 1 RHE_RS17000 RHE_RS25470
HSERO_RS00900 proline ABC transporter, ATPase component 2 RHE_RS16995 RHE_RS25475
hutV proline ABC transporter, ATPase component HutV RHE_RS28575 RHE_RS28485
hutW proline ABC transporter, permease component HutW RHE_RS28570 RHE_RS15785
hutX proline ABC transporter, substrate-binding component HutX RHE_RS28565
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) RHE_RS17000 RHE_RS25470
natB proline ABC transporter, substrate-binding component NatB RHE_RS15140
natC proline ABC transporter, permease component 1 (NatC) RHE_RS17005
natD proline ABC transporter, permease component 2 (NatD) RHE_RS25480
natE proline ABC transporter, ATPase component 2 (NatE) RHE_RS16995 RHE_RS17625
opuBA proline ABC transporter, ATPase component OpuBA/BusAA RHE_RS28485 RHE_RS28575
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 RHE_RS28470 RHE_RS02295
proP proline:H+ symporter ProP RHE_RS20930
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV RHE_RS28485 RHE_RS28575
proW proline ABC transporter, permease component ProW RHE_RS28570 RHE_RS15785
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter RHE_RS25845
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