GapMind for catabolism of small carbon sources

 

L-proline catabolism in Burkholderia phytofirmans PsJN

Best path

HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA

Also see fitness data for the top candidates

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
HSERO_RS00870 proline ABC transporter, substrate-binding component BPHYT_RS28270 BPHYT_RS01885
HSERO_RS00885 proline ABC transporter, permease component 1 BPHYT_RS15605 BPHYT_RS31740
HSERO_RS00890 proline ABC transporter, permease component 2 BPHYT_RS15600 BPHYT_RS31745
HSERO_RS00895 proline ABC transporter, ATPase component 1 BPHYT_RS15595 BPHYT_RS31750
HSERO_RS00900 proline ABC transporter, ATPase component 2 BPHYT_RS15590 BPHYT_RS31755
put1 proline dehydrogenase BPHYT_RS19355 BPHYT_RS29290
putA L-glutamate 5-semialdeyde dehydrogenase BPHYT_RS19355 BPHYT_RS28770
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) BPHYT_RS24645 BPHYT_RS34460
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BPHYT_RS16685 BPHYT_RS34455
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BPHYT_RS21915 BPHYT_RS16695
AAT20.2 proline transporter
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
AZOBR_RS08235 proline ABC transporter, permease component 1 BPHYT_RS15605 BPHYT_RS31740
AZOBR_RS08240 proline ABC transporter, permease component 2 BPHYT_RS15600 BPHYT_RS31745
AZOBR_RS08245 proline ABC transporter, ATPase component 1 BPHYT_RS15595 BPHYT_RS31750
AZOBR_RS08250 proline ABC transporter, ATPase component 2 BPHYT_RS15590 BPHYT_RS31755
AZOBR_RS08260 proline ABC transporter, substrate-binding component BPHYT_RS31715 BPHYT_RS01885
BAC2 basic amino acid carrier BAC2
betS proline transporter BetS
CCNA_00435 proline transporter BPHYT_RS01785 BPHYT_RS33230
davD glutarate semialdehyde dehydrogenase BPHYT_RS22430 BPHYT_RS34305
davT 5-aminovalerate aminotransferase BPHYT_RS22435 BPHYT_RS07695
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHYT_RS17335 BPHYT_RS28020
ectP proline transporter EctP
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
gcdG succinyl-CoA:glutarate CoA-transferase BPHYT_RS13985 BPHYT_RS31850
gcdH glutaryl-CoA dehydrogenase BPHYT_RS03780 BPHYT_RS23260
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
hutV proline ABC transporter, ATPase component HutV BPHYT_RS25065 BPHYT_RS11445
hutW proline ABC transporter, permease component HutW BPHYT_RS25070
hutX proline ABC transporter, substrate-binding component HutX
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BPHYT_RS28480 BPHYT_RS01855
N515DRAFT_2924 proline transporter BPHYT_RS33230 BPHYT_RS01785
natA proline ABC transporter, ATPase component 1 (NatA) BPHYT_RS15595 BPHYT_RS04435
natB proline ABC transporter, substrate-binding component NatB
natC proline ABC transporter, permease component 1 (NatC) BPHYT_RS31745
natD proline ABC transporter, permease component 2 (NatD) BPHYT_RS32510 BPHYT_RS31740
natE proline ABC transporter, ATPase component 2 (NatE) BPHYT_RS19445 BPHYT_RS15590
opuBA proline ABC transporter, ATPase component OpuBA/BusAA BPHYT_RS25065 BPHYT_RS11750
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 BPHYT_RS28265 BPHYT_RS22640
proP proline:H+ symporter ProP BPHYT_RS12995 BPHYT_RS08740
PROT1 proline transporter
proV proline ABC transporter, ATPase component ProV BPHYT_RS25065 BPHYT_RS09400
proW proline ABC transporter, permease component ProW BPHYT_RS25070 BPHYT_RS14815
proX proline ABC transporter, substrate-binding component ProX
proY proline:H+ symporter BPHYT_RS21680 BPHYT_RS15500
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 Aug 02 2021. The underlying query database was built on Aug 02 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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