Definition of L-citrulline catabolism

GapMind for catabolism of small carbon sources

Definition of L-citrulline catabolism

# Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535).
# Genetic evidence suggests that some bacteria use a putative citrullinase (EC:3.5.1.20) to consume citrulline.

# An ABC transporter for citrulline (and arginine) was identified in
# two strains of Pseudomonas fluorescens.
# It is closely related to arginine transporters from other Pseudomonas, which
# are marked ignore.
# It is also related to the arginine/ornithine/lysine transporter of Salmonella and E. coli,
# but citrulline is a poor substrate for the Salmonella system (PMID:1400387).
AO353_03055	ABC transporter for L-Citrulline, periplasmic substrate-binding component	curated:reanno::pseudo1_N1B4:Pf1N1B4_3431	curated:reanno::pseudo3_N2E3:AO353_03055	ignore:reanno::pseudo5_N2C3_1:AO356_18700	ignore:reanno::pseudo6_N2E2:Pf6N2E2_5660	ignore:reanno::WCS417:GFF4245	ignore:TCDB::O50181

AO353_03050	ABC transporter for L-Citrulline, permease component 1	curated:reanno::pseudo1_N1B4:Pf1N1B4_3432	curated:reanno::pseudo3_N2E3:AO353_03050	ignore:reanno::WCS417:GFF4244	ignore:reanno::pseudo5_N2C3_1:AO356_18705	ignore:reanno::pseudo6_N2E2:Pf6N2E2_5661	ignore:CharProtDB::CH_107317

AO353_03045	ABC transporter for L-Citrulline, permease component 2	curated:reanno::pseudo1_N1B4:Pf1N1B4_3433	curated:reanno::pseudo3_N2E3:AO353_03045	ignore:reanno::pseudo5_N2C3_1:AO356_18710	ignore:reanno::pseudo6_N2E2:Pf6N2E2_5662	ignore:reanno::WCS417:GFF4243	ignore:TCDB::O50183

AO353_03040	ABC transporter for L-Citrulline, ATPase component	curated:reanno::pseudo1_N1B4:Pf1N1B4_3435	curated:reanno::pseudo3_N2E3:AO353_03040	ignore:reanno::pseudo5_N2C3_1:AO356_18715	ignore:reanno::pseudo6_N2E2:Pf6N2E2_5663	ignore:TCDB::O30506

# Transporters were identified using
# query: transporter:citrulline:L-citrulline
citrulline-transport: AO353_03055 AO353_03050 AO353_03045 AO353_03040

# Another ABC transporter for citrulline (and ornithine) was identified in
# Pseudomonas simiae WCS417. It is distantly related to
# AO353_0355:AO353_03040 (for instance, the substrate-binding components are only 43% identical).
# (PS417_17590 = A0A1N7UK26; PS417_17595 = A0A1N7UBU2; PS417_17600 = A0A1N7U128; PS417_17605 = A0A1N7U8S3.)
PS417_17590	ABC transporter for L-Citrulline, periplasmic substrate-binding component	uniprot:A0A1N7UK26

PS417_17595	ABC transporter for L-Citrulline, permease component 1	uniprot:A0A1N7UBU2

PS417_17600	ABC transporter for L-Citrulline, permease component 2	uniprot:A0A1N7U128

PS417_17605	ABC transporter for L-Citrulline, ATPase component	uniprot:A0A1N7U8S3

citrulline-transport: PS417_17590 PS417_17595 PS417_17600 PS417_17605

# Mitochondrial ornithine/citrulline exchangers were ignored.

# GABA (gamma-aminobutyrate) is a common intermediate
import putrescine.steps:GABA-degradation putrescine-degradation

import leucine.steps:atoB # acetyl-CoA acetyltransferase is part of glutaryl-CoA degradation
import phenylacetate.steps:glutaryl-CoA-degradation # glutaryl-CoA is part of 5-aminovalerate degradation
import lysine.steps:5-aminovalerate-degradation # 5-aminovalerate-degradation is part of proline degradation
import proline.steps:proline-degradation # proline is an intermediate in ornithine degradation

# arcB = ornithine carbamoyltransferase
# arcC = carbamate kinase
import arginine.steps:ornithine-degradation arcB arcC

# Citrulline is coverted to ornithine by ornithine
# carbamoyltransferase (arcB) in reverse; the
# carbamoyltransferase reaction also yields carbamoyl-phosphate, which
# is consumed by carbamate kinase (arcC) in reverse.
all: citrulline-transport arcB arcC ornithine-degradation

# The characterized enzyme hydrolyzes citrulline to ornithine, carbon dioxide, and ammonia
# (FTT0435 or FTT_0435 or Q5NHL7_FRATT; PMID:19502406).
# Genetic evidence from diverse bacteria shows that a family of putative hydrolases
# is involved in ornithine utilization: PGA1_c16380 (GFF1616) from Phaeobacter inhibens;
# AO353_25635 from Pseudomonas fluorescens FW300-N2E3, and PS417_17580 (GFF3434) from Pseudomonas simiae WCS417.
# These are distantly related to arginine deiminases and were originally reannotated as such
# (operating in reverse), but Equilibrator predicts that the reverse reaction is thermodynamically
# very unfavorable. Also, the guanidino-binding residues are not conserved.
# They are probably citrullinases.
citrullinase	putative citrullinase	EC:3.5.1.20	uniprot:Q5NHL7_FRATT	curated:reanno::Phaeo:GFF1616	curated:reanno::pseudo3_N2E3:AO353_25635	curated:reanno::WCS417:GFF3434

# Alternatively, a putative citrullinase hydrolyzes citrulline; the product
# is probably ornithine.
all: citrulline-transport citrullinase ornithine-degradation

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources