GapMind for catabolism of small carbon sources

 

L-proline catabolism in Bradyrhizobium sp. BTAi1

Best path

aapJ, aapQ, aapM, aapP, 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
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BBTA_RS18350 BBTA_RS03295
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BBTA_RS18355 BBTA_RS37095
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BBTA_RS37100 BBTA_RS18360
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BBTA_RS37105 BBTA_RS18365
put1 proline dehydrogenase BBTA_RS28060
putA L-glutamate 5-semialdeyde dehydrogenase BBTA_RS28060 BBTA_RS18005
Alternative steps:
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase BBTA_RS33375 BBTA_RS35630
AZOBR_RS08235 proline ABC transporter, permease component 1 BBTA_RS24905 BBTA_RS28620
AZOBR_RS08240 proline ABC transporter, permease component 2 BBTA_RS24910 BBTA_RS28615
AZOBR_RS08245 proline ABC transporter, ATPase component 1 BBTA_RS24915 BBTA_RS26710
AZOBR_RS08250 proline ABC transporter, ATPase component 2 BBTA_RS24920 BBTA_RS33155
AZOBR_RS08260 proline ABC transporter, substrate-binding component BBTA_RS24925
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter
davD glutarate semialdehyde dehydrogenase BBTA_RS00155 BBTA_RS07435
davT 5-aminovalerate aminotransferase BBTA_RS20045 BBTA_RS03550
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BBTA_RS14030 BBTA_RS08325
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BBTA_RS19915 BBTA_RS33140
gcdG succinyl-CoA:glutarate CoA-transferase BBTA_RS23895 BBTA_RS26930
gcdH glutaryl-CoA dehydrogenase BBTA_RS11430 BBTA_RS31195
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
HSERO_RS00870 proline ABC transporter, substrate-binding component BBTA_RS24925
HSERO_RS00885 proline ABC transporter, permease component 1 BBTA_RS24905 BBTA_RS26720
HSERO_RS00890 proline ABC transporter, permease component 2 BBTA_RS24910 BBTA_RS33165
HSERO_RS00895 proline ABC transporter, ATPase component 1 BBTA_RS33150 BBTA_RS15200
HSERO_RS00900 proline ABC transporter, ATPase component 2 BBTA_RS24920 BBTA_RS33155
hutV proline ABC transporter, ATPase component HutV BBTA_RS11265 BBTA_RS33705
hutW proline ABC transporter, permease component HutW
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BBTA_RS32020 BBTA_RS02930
N515DRAFT_2924 proline transporter
natA proline ABC transporter, ATPase component 1 (NatA) BBTA_RS28610 BBTA_RS28010
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) BBTA_RS28615
natD proline ABC transporter, permease component 2 (NatD) BBTA_RS17480 BBTA_RS28620
natE proline ABC transporter, ATPase component 2 (NatE) BBTA_RS28605 BBTA_RS24920
opuBA proline ABC transporter, ATPase component OpuBA/BusAA BBTA_RS28380 BBTA_RS07485
opuBB proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB BBTA_RS28385
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 BBTA_RS20690 BBTA_RS33450
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV BBTA_RS08550 BBTA_RS30475
proW proline ABC transporter, permease component ProW BBTA_RS11825 BBTA_RS15360
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