GapMind for catabolism of small carbon sources

 

L-proline catabolism in Cereibacter sphaeroides ATCC 17029

Best path

ectP, 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
ectP proline transporter EctP RSPH17029_RS19240
put1 proline dehydrogenase RSPH17029_RS04265 RSPH17029_RS07235
putA L-glutamate 5-semialdeyde dehydrogenase RSPH17029_RS04265 RSPH17029_RS16005
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ RSPH17029_RS18145 RSPH17029_RS02000
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) RSPH17029_RS18135 RSPH17029_RS02010
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RSPH17029_RS02015 RSPH17029_RS18130
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RSPH17029_RS18140 RSPH17029_RS02005
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase RSPH17029_RS12120 RSPH17029_RS19805
AZOBR_RS08235 proline ABC transporter, permease component 1 RSPH17029_RS17970 RSPH17029_RS09815
AZOBR_RS08240 proline ABC transporter, permease component 2 RSPH17029_RS17975 RSPH17029_RS14870
AZOBR_RS08245 proline ABC transporter, ATPase component 1 RSPH17029_RS04855 RSPH17029_RS17980
AZOBR_RS08250 proline ABC transporter, ATPase component 2 RSPH17029_RS04835 RSPH17029_RS07940
AZOBR_RS08260 proline ABC transporter, substrate-binding component
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS RSPH17029_RS19240
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase RSPH17029_RS13480 RSPH17029_RS04350
davT 5-aminovalerate aminotransferase RSPH17029_RS04315 RSPH17029_RS17535
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RSPH17029_RS00050 RSPH17029_RS17990
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RSPH17029_RS16015 RSPH17029_RS04435
gcdG succinyl-CoA:glutarate CoA-transferase RSPH17029_RS00595
gcdH glutaryl-CoA dehydrogenase RSPH17029_RS14905 RSPH17029_RS05935
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 RSPH17029_RS17970 RSPH17029_RS20325
HSERO_RS00890 proline ABC transporter, permease component 2 RSPH17029_RS17975 RSPH17029_RS04845
HSERO_RS00895 proline ABC transporter, ATPase component 1 RSPH17029_RS04855 RSPH17029_RS17980
HSERO_RS00900 proline ABC transporter, ATPase component 2 RSPH17029_RS04835 RSPH17029_RS07940
hutV proline ABC transporter, ATPase component HutV RSPH17029_RS19130 RSPH17029_RS04330
hutW proline ABC transporter, permease component HutW RSPH17029_RS19135 RSPH17029_RS04335
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RSPH17029_RS10685
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) RSPH17029_RS07935 RSPH17029_RS14865
natB proline ABC transporter, substrate-binding component NatB RSPH17029_RS07930
natC proline ABC transporter, permease component 1 (NatC)
natD proline ABC transporter, permease component 2 (NatD) RSPH17029_RS07945 RSPH17029_RS17970
natE proline ABC transporter, ATPase component 2 (NatE) RSPH17029_RS07940 RSPH17029_RS04835
opuBA proline ABC transporter, ATPase component OpuBA/BusAA RSPH17029_RS19130 RSPH17029_RS02690
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 RSPH17029_RS15945
proP proline:H+ symporter ProP
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV RSPH17029_RS19130 RSPH17029_RS04330
proW proline ABC transporter, permease component ProW RSPH17029_RS19135 RSPH17029_RS04335
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 Apr 10 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