Definition of L-citrulline catabolism

As rules and steps, or see full text

Rules

Overview: 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.

• all:
  • citrulline-transport, arcB, arcC and ornithine-degradation
  • or citrulline-transport, citrullinase and ornithine-degradation
  • Comment: 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. Alternatively, a putative citrullinase hydrolyzes citrulline; the product is probably ornithine.
• ornithine-degradation:
  • aruF, aruG, astC, astD and astE
  • or rocD and rocA
  • or rocD, PRO3 and proline-degradation
  • or ocd and proline-degradation
  • or odc and putrescine-degradation
  • or orr, oraS, oraE, ord, ortA and ortB
  • Comment: Ornithine is a common intermediate. It can be succinylated by aruFG and then catabolized by the later steps of the arginine succinyltransferase pathway, via aminotransferase, dehydrogenase, and desuccinylase reactions (see PMC179677 and PMID:7523119). Or as part of L-arginine degradation I, the aminotransferase rocD converts ornithine to glutamate 5-semialdehyde, which spontaneously converts to 1-pyrroline-5-carboxylate. A dehydrogenase converts this to glutamate. Or 1-pyrroline-5-carboxylate can be reduced to proline by PRO3, as in L-arginine degradation VI. Alternatively, ornithine can be converted directly to proline by ornithine cyclodeaminase (ocd). Or ornithine can be decarboxylated to putrescine by odc (link). Or ornithine can be catabolized via D-ornithine, as in L-arginine degradation XIV. A racemase converts L-ornithine to D-ornithine; an aminomutase forms (2R,4S) 2,4-diaminopentanoate; a dehydrogenase forms (2R)-2-amino-4-oxopentanoate, and a thiolase cleaves it to D-alanine and acetyl-CoA. D-alanine could be oxidized to pyruvate or perhaps secreted; this is not described here.
• proline-degradation:
  • put1 and putA
  • or prdF, D-proline-reductase and 5-aminovalerate-degradation
  • Comment: In pathway I, proline dehydrogenase (put1) forms (S)-1-pyrroline-5-carboxylate, which spontaneously hydrates to L-glutamate 5-semialdehyde, and a dehydrogenase (putA) to glutamate. Glutamate can be transaminated to 2-oxoglutarate, which is an intermediate in central metabolism (not represented). In pathway II, proline racemase (prdF) forms D-proline, and a reductase forms 5-aminovalerate.
• D-proline-reductase: prdA, prdB and prdC
  • Comment: D-proline reductase includes components PrdA and PrdB and electron transfer protein PrdC
• 5-aminovalerate-degradation: davT, davD and glutarate-degradation
  • Comment: 5-aminovalerate is an intermediate in L-lysine degradation (link, link). It is transaminated to glutarate semialdehyde and oxidized to glutarate. (A fermentative pathway via 5-hydroxyvalerate has also been reported, but does not seem to be fully linked to sequence; see pathway 5 of PMID:11759672.)
• glutarate-degradation:
  • glaH and lhgD
  • or gcdG and glutaryl-CoA-degradation
  • Comment: Glutarate is an intermediate in L-lysine degradation. As part of MetaCyc pathway L-lysine degradation I (link), gluratate is hydroxylated to L-2-hydroxyglutarate (also known as (S)-2-hydroxyglutarate) by a 2-oxoglutarate-dependent oxidase. This reaction releases succinate (a TCA cycle intermediate) and CO2. A dehydrogenase then oxidizes to L-2-hydroxyglutarate to regenerate 2-oxoglutarate. Alternatively, as part of pathway IV (link), glutarate can be activated to glutaryl-CoA by a CoA-transferase. Glutaryl-CoA degradation (link) involves glutaryl-CoA dehydrogenase (decarboxylating) to crotonyl-CoA (trans-but-2-enoyl-CoA), hydration to (S)-hydroxybutanoyl-CoA, oxidization to acetoacetyl-CoA, and cleavage by a C-acetyltransferase to two acetyl-CoA.
• glutaryl-CoA-degradation: gcdH, ech, fadB and atoB
  • Comment: In MetaCyc pathway glutaryl-CoA degradation (link), glutaryl-CoA is oxidized to (E)-glutaconyl-CoA and oxidatively decarboxylated to crotonyl-CoA (both by the same enzyme), hydrated to 3-hydroxybutanoyl-CoA, oxidized to acetoacetyl-CoA, and cleaved to two acetyl-CoA.
• putrescine-degradation: putrescine-to-GABA and GABA-degradation
  • Comment: Gamma-aminobutyrate is a common intermediate.
• GABA-degradation: gabT and gabD
  • Comment: GABA (4-aminobutanoate) is consumed by an aminotransferase (known as gabT or puuE), which forms succinate semialdehyde, and dehydrogenase gabD, which forms succinate.
• putrescine-to-GABA:
  • patA and patD
  • or puuA, puuB, puuC and puuD
  • or puo and patD
  • Comment: In pathway I or pathway V, putrescine aminotransferase (patA or spuC) forms 4-aminobutanal, and dehydrogenase patD forms GABA. In pathway II, putrescine is converted to GABA with glutamylated intermedates: puuA forms gamma-glutamyl-putrescine, an oxidase forms 4-(gamma-glutaminylamino)butanal, a dehydrogenase forms 4-(gamma-glutamylamino)butanoate, and a hydrolase releases glutamate and GABA. As part of pathway IV, putrescine oxidase (puo) forms 4-aminobutanal, which is probably converted to GABA by dehydrogenase patD.
• citrulline-transport:
  • AO353_03055, AO353_03050, AO353_03045 and AO353_03040
  • or PS417_17590, PS417_17595, PS417_17600 and PS417_17605
  • Comment: Transporters were identified using query: transporter:citrulline:L-citrulline

Steps

AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component

• Curated sequence Pf1N1B4_3431: ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component
• Curated sequence AO353_03055: ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component
• Ignore hits to AO356_18700 when looking for 'other' hits (L-Arginine ABC transporter, periplasmic substrate-binding component)
• Ignore hits to Pf6N2E2_5660 when looking for 'other' hits (L-Arginine ABC transporter, periplasmic substrate-binding component)
• Ignore hits to GFF4245 when looking for 'other' hits (ABC transporter for L-Arginine, substrate-binding component)
• Ignore hits to O50181 when looking for 'other' hits (AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter)
• Comment: 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).
• Total: 2 characterized proteins

AO353_03050: ABC transporter for L-Citrulline, permease component 1

• Curated sequence Pf1N1B4_3432: ABC transporter for L-Arginine and L-Citrulline, permease component 1
• Curated sequence AO353_03050: ABC transporter for L-Arginine and L-Citrulline, permease component 2
• Ignore hits to GFF4244 when looking for 'other' hits (ABC transporter for L-Arginine, permease component 1)
• Ignore hits to AO356_18705 when looking for 'other' hits (L-Arginine ABC transporter, permease component 2)
• Ignore hits to Pf6N2E2_5661 when looking for 'other' hits (L-Arginine ABC transporter, permease protein AotQ)
• Ignore hits to CH_107317 when looking for 'other' hits (arginine/ornithine transport protein. AotQ, component of Arginine/ornithine (but not lysine) porter)
• Total: 2 characterized proteins

AO353_03045: ABC transporter for L-Citrulline, permease component 2

• Curated sequence Pf1N1B4_3433: ABC transporter for L-Arginine and L-Citrulline, permease component 2
• Curated sequence AO353_03045: ABC transporter for L-Arginine and L-Citrulline, permease component 1
• Ignore hits to AO356_18710 when looking for 'other' hits (L-Arginine ABC transporter, permease component 1)
• Ignore hits to Pf6N2E2_5662 when looking for 'other' hits (L-Arginine ABC transporter, permease protein AotM)
• Ignore hits to GFF4243 when looking for 'other' hits (ABC transporter for L-Arginine, permease component 2)
• Ignore hits to O50183 when looking for 'other' hits (AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter)
• Total: 2 characterized proteins

AO353_03040: ABC transporter for L-Citrulline, ATPase component

• Curated sequence Pf1N1B4_3435: ABC transporter for L-Arginine and L-Citrulline, ATPase component
• Curated sequence AO353_03040: ABC transporter for L-Arginine and L-Citrulline, ATPase component
• Ignore hits to AO356_18715 when looking for 'other' hits (L-Arginine ABC transporter, ATPase component)
• Ignore hits to Pf6N2E2_5663 when looking for 'other' hits (L-Arginine ABC transporter, ATPase component)
• Ignore hits to O30506 when looking for 'other' hits (AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter)
• Total: 2 characterized proteins

PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component

• UniProt sequence A0A1N7UK26: SubName: Full=ABC transporter substrate-binding protein {ECO:0000313|EMBL:AIB37363.1}; SubName: Full=Histidine transport system substrate-binding protein {ECO:0000313|EMBL:SFA85898.1};
• Comment: 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.)
• Total: 1 characterized proteins

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

• UniProt sequence A0A1N7UBU2: SubName: Full=ABC transporter permease subunit {ECO:0000313|EMBL:NVH62211.1}; SubName: Full=Amino acid ABC transporter permease {ECO:0000313|EMBL:AIB37364.1}; SubName: Full=Histidine transport system permease protein {ECO:0000313|EMBL:SFA85886.1};
• Total: 1 characterized proteins

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

• UniProt sequence A0A1N7U128: SubName: Full=ABC transporter permease {ECO:0000313|EMBL:NVH62212.1}; SubName: Full=Amino acid ABC transporter permease {ECO:0000313|EMBL:AIB37365.1}; SubName: Full=Histidine ABC transporter permease HisM {ECO:0000313|EMBL:PRW89156.1}; SubName: Full=Histidine transport system permease protein {ECO:0000313|EMBL:SFA85870.1}; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM {ECO:0000313|EMBL:ERH51948.1};
• Total: 1 characterized proteins

PS417_17605: ABC transporter for L-Citrulline, ATPase component

• UniProt sequence A0A1N7U8S3: SubName: Full=ATP-binding cassette domain-containing protein {ECO:0000313|EMBL:NVH62213.1}; SubName: Full=Amino acid transporter {ECO:0000313|EMBL:AIB37366.1}; SubName: Full=Histidine ABC transporter ATP-binding protein {ECO:0000313|EMBL:ERH51949.1}; SubName: Full=Histidine transport system ATP-binding protein {ECO:0000313|EMBL:SFA85852.1};
• Total: 1 characterized proteins

patA: putrescine aminotransferase (PatA/SpuC)

• Curated proteins or TIGRFams with EC 2.6.1.82
• Curated sequence MONOMER-17: putrescine-pyruvate transaminase (EC 2.6.1.113). Putrescine--pyruvate aminotransferase; PATase; Putrescine--pyruvate transaminase; EC 2.6.1.113. putrescine aminotransferase (EC 2.6.1.113)
• Curated proteins or TIGRFams with EC 2.6.1.113
• Ignore hits to items matching 2.6.1.19 when looking for 'other' hits
• Comment: Since patA and putrescine-pyruvate transaminase (spuC) perform similar reactions and produce gamma-aminobutyraldehyde (4-aminobutanal), they are listed together. Many close homologs of patA are GABA aminotransferases (EC 2.6.1.19), so ignore those.
• Total: 1 HMMs and 2 characterized proteins

patD: gamma-aminobutyraldehyde dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.19
• Total: 1 HMMs and 14 characterized proteins

puuA: glutamate-putrescine ligase

• Curated proteins or TIGRFams with EC 6.3.1.11
• Total: 11 characterized proteins

puuB: gamma-glutamylputrescine oxidase

• Curated proteins matching glutamylputrescine oxidase
• Comment: MetaCyc uses EC 1.4.3.M3; other resources uses 1.4.3.-
• Total: 3 characterized proteins

puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.99
• Curated sequence MONOMER-11560: 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)
• Curated sequence PfGW456L13_805: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
• Curated sequence Pf6N2E2_4383: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
• Curated sequence AO356_12580: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
• Curated sequence GFF5420: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
• Comment: The putative kauB (4-guanidinobutyraldehyde dehydrogenase) from P. putida (metacyc::MONOMER-11560) is included because it is closely related to P. aeruginosa kauB (PA5312), which acts on gamma-glutamyl-gamma-aminobutyraldehyde as well (PMID:3141581). Some other P. fluorescens kauB-type proteins seem to be acting in this pathway but were annotated with EC 1.2.1.54 instead, so these were added manually.
• Total: 6 characterized proteins

puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase

• Curated proteins or TIGRFams with EC 3.5.1.94
• Total: 8 characterized proteins

puo: putrescine oxidase

• Curated proteins or TIGRFams with EC 1.4.3.10
• Total: 2 characterized proteins

gabT: gamma-aminobutyrate transaminase

• Curated proteins or TIGRFams with EC 2.6.1.19
• Curated proteins or TIGRFams with EC 2.6.1.96
• UniProt sequence A1S8Y2: SubName: Full=4-aminobutyrate aminotransferase {ECO:0000313|EMBL:ABM00839.1}; EC=2.6.1.19 {ECO:0000313|EMBL:ABM00839.1};
• Comment: Sama_2636 (A1S8Y2) was added because it is a transaminase involved in putrescine utilization
• Total: 2 HMMs and 28 characterized proteins

gabD: succinate semialdehyde dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.79
• Curated proteins or TIGRFams with EC 1.2.1.24
• Curated proteins or TIGRFams with EC 1.2.1.16
• Ignore hits to Q8BUF0 when looking for 'other' hits (succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24))
• Ignore hits to items matching 1.2.1.20 when looking for 'other' hits
• Ignore hits to items matching 1.2.1.3 when looking for 'other' hits
• Ignore hits to Q9I6M5 when looking for 'other' hits (Glutarate-semialdehyde dehydrogenase; EC 1.2.1.-. glutarate semialdehyde dehydrogenase)
• Comment: This may be either NADH or NADPH dependent, forming succinate in either case. Close homologs in Pseudomonas or Klebsiella are annotated as glutarate-semialdehyde dehydrogenases (1.2.1.20) or aldehyde dehydrogenases (1.2.1.3); Q9I6M5 is annotated as glutarate-semialdehyde dehydrogenase but with no EC number. Q8BUF0 appears to be misannotated in BRENDA.
• Total: 37 characterized proteins

atoB: acetyl-CoA C-acetyltransferase

• Curated proteins or TIGRFams with EC 2.3.1.9
• Ignore hits to items matching 2.3.1.16 when looking for 'other' hits
• Ignore hits to P07256 when looking for 'other' hits (acetyl-CoA C-acetyltransferase (EC 2.3.1.9). Cytochrome b-c1 complex subunit 1, mitochondrial; Complex III subunit 1; Core protein I; Ubiquinol-cytochrome c oxidoreductase core protein 1; Ubiquinol-cytochrome c reductase 44 kDa protein)
• Ignore hits to I3R3D0 when looking for 'other' hits (acetyl-CoA C-acetyltransferase (subunit 1/2) (EC 2.3.1.9))
• Ignore hits to I3RA71 when looking for 'other' hits (acetyl-CoA C-acetyltransferase (subunit 1/2) (EC 2.3.1.9))
• Ignore hits to items matching similar to acetyl-CoA acetyltransferase when looking for 'other' hits
• Comment: Produces two acetyl-CoA from acetoacetyl-CoA and CoA. EC 2.3.1.16 describes a broader range of beta-ketothiolases. This enzyme is usually homomeric, but I3R3D0 and I3RA71 are non-catalytic subunits of an enzyme from Haloferax mediterranei that also contains a "normal" catalytic subunit (I3R3D1, I3RA72). Inclusion of P07256 was an error in BRENDA. And CharProtDB includes an odd annotation of the form "similar to acetyl-CoA acetyltransferase"
• Total: 36 characterized proteins

gcdH: glutaryl-CoA dehydrogenase

• Curated proteins or TIGRFams with EC 1.3.8.6
• Total: 6 characterized proteins

ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase

• Curated proteins or TIGRFams with EC 4.2.1.150
• Ignore hits to Q97MS7 when looking for 'other' hits (short-chain-enoyl-CoA hydratase (EC 4.2.1.150))
• Curated sequence BPHYT_RS17335: trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17)
• Curated sequence GFF2389: Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
• Ignore hits to items matching 4.2.1.17 when looking for 'other' hits
• Comment: Psest_2437 (GFF2389) is the enoyl-CoA hydrotase for both isoleucine and valine degradation, which implies that (S)-3-hydroxybutanoyl-CoA is a substrate. Q97MS7 is misannotated in BRENDA. BPHYT_RS17335 was misannotated as paaF; it is very similar to the ech H16_A3307, which is a different explanation for its role in phenylacetate utilization. Short-chain enoyl-CoA hydratases are sometimes given EC 4.2.1.17 instead, so those are ignored.
• Total: 8 characterized proteins

fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase

• Curated proteins or TIGRFams with EC 1.1.1.35
• Ignore hits to GFF1550 when looking for 'other' hits (Enoyl-CoA hydratase (EC 4.2.1.17))
• Comment: HP15_1512 (GFF1550) is annotated as enoyl-CoA hydratase but likely does this as well
• Total: 36 characterized proteins

glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)

• Curated proteins or TIGRFams with EC 1.14.11.64
• Total: 2 characterized proteins

lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)

• Curated proteins or TIGRFams with EC 1.1.5.13
• Curated sequence G1G01-3089-MONOMER: (S)-2-hydroxyglutarate oxidase
• Curated proteins or TIGRFams with EC 1.1.99.2
• Comment: As discussed in the MetaCyc page for lhgO (G1G01-3089-MONOMER), there is some controversy as to whether the E. coli enzyme (lhgD) uses quinone or oxygen as its acceptor; the Pseudomonas protein (G1G01-3089-MONOMER) does use oxygen.
• Total: 4 characterized proteins

gcdG: succinyl-CoA:glutarate CoA-transferase

• Curated proteins or TIGRFams with EC 2.8.3.13
• Total: 2 characterized proteins

davT: 5-aminovalerate aminotransferase

• Curated proteins or TIGRFams with EC 2.6.1.48
• Ignore hits to MONOMER-11537 when looking for 'other' hits (4-aminobutyrate transaminase subunit (EC 2.6.1.19))
• Ignore hits to Q0K2K2 when looking for 'other' hits (4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19). 4-aminobutyrate aminotransferase monomer (EC 2.6.1.19))
• Comment: Ignore some very-similar 4-aminobutyrate transaminases
• Total: 6 characterized proteins

davD: glutarate semialdehyde dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.20
• Ignore hits to AO353_11505 when looking for 'other' hits (succinate-semialdehyde dehydrogenase (EC 1.2.1.16))
• Ignore hits to MONOMER-15736 when looking for 'other' hits (NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16))
• Curated sequence Q9I6M5: Glutarate-semialdehyde dehydrogenase; EC 1.2.1.-. glutarate semialdehyde dehydrogenase
• Ignore hits to P25526 when looking for 'other' hits (succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79). succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16. Succinate-semialdehyde dehydrogenase [NADP(+)] GabD; SSDH; Glutarate-semialdehyde dehydrogenase; EC 1.2.1.79; EC 1.2.1.-. succinate-semialdehyde dehydrogenase (NADP⁺) GabD (EC 1.2.1.79). succinate-semialdehyde dehydrogenase (NADP⁺) GabD (EC 1.2.1.79))
• Ignore hits to MONOMER-20455 when looking for 'other' hits (succinate-semialdehyde dehydrogenase (NAD⁺) (EC 1.2.1.24))
• Ignore hits to 200453 when looking for 'other' hits (succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16])
• Comment: Ignore some very-similar succinate-semialdehyde dehydrogenases
• Total: 3 characterized proteins

prdA: D-proline reductase, prdA component

• Curated sequence CH_013105: D-proline reductase, PrdA proprotein; EC 1.21.4.1
• Curated sequence Q9Z4P6: D-proline reductase proprotein PrdA; EC 1.21.4.1. proprotein PrdA
• Ignore hits to items matching 1.21.4.1 when looking for 'other' hits
• Total: 2 characterized proteins

prdB: D-proline reductase, prdB component

• Curated sequence Q17ZY6: D-proline reductase (EC 1.21.4.1)
• Curated sequence CH_013103: D-proline reductase, PrdB subunit, selenocysteine-containing; EC 1.21.4.1. D-proline reductase subunit gamma; D-proline reductase 26 kDa subunit; EC 1.21.4.1. 26-kDa subunit
• Ignore hits to items matching 1.21.4.1 when looking for 'other' hits
• Total: 2 characterized proteins

prdC: D-proline reductase, electron transfer component PrdC

• UniProt sequence E3PU00: SubName: Full=Electron transfer protein {ECO:0000313|EMBL:CBH22354.1};
• Comment: PrdC is identified as CLOST_2236 (E3PU00) by PMC3091704
• Total: 1 characterized proteins

put1: proline dehydrogenase

• Curated proteins or TIGRFams with EC 1.5.5.2
• Curated proteins or TIGRFams with EC 1.5.99.8
• Comment: formerly EC 1.5.99.8
• Total: 39 characterized proteins

putA: L-glutamate 5-semialdeyde dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.88
• Curated proteins or TIGRFams with EC 1.5.1.12
• Comment: formerly known as 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
• Total: 3 HMMs and 23 characterized proteins

prdF: proline racemase

• Curated proteins or TIGRFams with EC 5.1.1.4
• Ignore hits to Q4D480 when looking for 'other' hits (proline racemase (EC 5.1.1.4))
• Comment: Q4D480 is misannotated in BRENDA.
• Total: 8 characterized proteins

aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF)

• Curated sequence CH_107315: arginine N-succinyltransferase; EC 2.3.1.109
• Comment: Pseudomonas aeruginsa has a heteromeric succinyltransferase (AruFG) that is active on both arginine and ornithine (PMID:7523119, PMID:9393691).
• Total: 1 characterized proteins

aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG)

• Curated sequence P80358: arginine N-succinyltransferase (EC 2.3.1.109). arginine N-succinyltransferase, beta subunit
• Total: 1 characterized proteins

astC: succinylornithine transaminase

• Curated proteins or TIGRFams with EC 2.6.1.81
• Curated sequence GFF3099: acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17]
• Comment: Marinobacter adhaerens HP15_3042 (GFF3099) is important for arginine biosynthesis as well as catabolism, suggesting it is succinylornithine transaminase and acetylornithine transaminase (similar to P. aeruginosa aruC)
• Total: 1 HMMs and 8 characterized proteins

astD: succinylglutamate semialdehyde dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.71
• Total: 1 HMMs and 6 characterized proteins

astE: succinylglutamate desuccinylase

• Curated proteins or TIGRFams with EC 3.5.1.96
• Total: 1 HMMs and 5 characterized proteins

rocD: ornithine aminotransferase

• Curated proteins or TIGRFams with EC 2.6.1.13
• Total: 1 HMMs and 17 characterized proteins

rocA: 1-pyrroline-5-carboxylate dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.88
• Total: 3 HMMs and 22 characterized proteins

PRO3: pyrroline-5-carboxylate reductase

• Curated proteins or TIGRFams with EC 1.5.1.2
• Total: 1 HMMs and 19 characterized proteins

ocd: ornithine cyclodeaminase

• Curated proteins or TIGRFams with EC 4.3.1.12
• Total: 4 characterized proteins

odc: L-ornithine decarboxylase

• Curated proteins or TIGRFams with EC 4.1.1.17
• Total: 1 HMMs and 31 characterized proteins

orr: ornithine racemase

• Curated proteins or TIGRFams with EC 5.1.1.12
• Total: 4 characterized proteins

oraS: D-ornithine 4,5-aminomutase, alpha (S) subunit

• Curated sequence E3PY96: D-ornithine 4,5-aminomutase subunit alpha; D-ornithine aminomutase S component; OAM-S; EC 5.4.3.5. D-ornithine 4,5-aminomutase (subunit 1/2) (EC 5.4.3.5). D-ornithine aminomutase component S subunit (EC 5.4.3.5)
• Ignore hits to items matching 5.4.3.5 when looking for 'other' hits
• Comment: D-ornithine aminomutase (5.4.3.5) is heteromeric
• Total: 1 characterized proteins

oraE: D-ornithine 4,5-aminomutase, beta (E) subunit

• Curated sequence E3PY95: D-ornithine 4,5-aminomutase subunit beta; D-ornithine aminomutase E component; OAM-E; EC 5.4.3.5. D-ornithine 4,5-aminomutase (EC 5.4.3.5). D-ornithine aminomutase component E subunit (EC 5.4.3.5)
• Ignore hits to items matching 5.4.3.5 when looking for 'other' hits
• Total: 1 characterized proteins

ord: 2,4-diaminopentanoate dehydrogenase

• Curated proteins or TIGRFams with EC 1.4.1.12
• Total: 2 characterized proteins

ortA: 2-amino-4-oxopentanoate thiolase, alpha subunit

• Curated sequence C1FW06: 2-amino-4-ketopentanoate thiolase alpha subunit; AKP thiolase; AKPT; EC 2.3.1.263. 2-amino-4-oxopentanoate thiolase (subunit 1/2) (EC 2.3.1.263). AKP thiolase α subunit (EC 2.3.1.263)
• Curated sequence E3PY98: 2-amino-4-ketopentanoate thiolase alpha subunit; AKP thiolase; AKPT; EC 2.3.1.263
• Ignore hits to items matching 2.3.1.263 when looking for 'other' hits
• Comment: 2-amino-4-oxopentanoate thiolase (2.3.1.263) is heteromeric
• Total: 2 characterized proteins

ortB: 2-amino-4-oxopentanoate thiolase, beta subunit

• Curated sequence C1FW07: 2-amino-4-ketopentanoate thiolase beta subunit; AKP thiolase; AKPT; EC 2.3.1.263. 2-amino-4-oxopentanoate thiolase (subunit 2/2) (EC 2.3.1.263). AKP thiolase β subunit (EC 2.3.1.263)
• Curated sequence E3PY97: 2-amino-4-ketopentanoate thiolase beta subunit; AKP thiolase; AKPT; EC 2.3.1.263
• Ignore hits to items matching 2.3.1.263 when looking for 'other' hits
• Total: 2 characterized proteins

arcB: ornithine carbamoyltransferase

• Curated proteins or TIGRFams with EC 2.1.3.3
• Comment: arcB forms carbamoyl-phosphate and ornithine
• Total: 1 HMMs and 29 characterized proteins

arcC: carbamate kinase

• Curated proteins or TIGRFams with EC 2.7.2.2
• UniProt sequence P13982: RecName: Full=Carbamate kinase; EC=2.7.2.2;
• Comment: arcC from P. aeruginosa (P13982) was studied both biochemically and genetically and linked to sequence by PMID:2537202
• Total: 1 HMMs and 9 characterized proteins

citrullinase: putative citrullinase

• Curated proteins or TIGRFams with EC 3.5.1.20
• UniProt sequence Q5NHL7_FRATT: SubName: Full=Carbon-nitrogen hydrolase family protein {ECO:0000313|EMBL:CAG45068.1}; EC=3.5.-.- {ECO:0000313|EMBL:CAG45068.1};
• Curated sequence GFF1616: arginine deiminase (EC 3.5.3.6)
• Curated sequence AO353_25635: arginine deiminase (EC 3.5.3.6)
• Curated sequence GFF3434: arginine deiminase (EC 3.5.3.6)
• Comment: 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.
• Total: 4 characterized proteins