Definition of L-proline catabolism

As rules and steps, or see full text

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

• all: proline-transport and proline-degradation
• 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.
• 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.
• D-proline-reductase: prdA, prdB and prdC
  • Comment: D-proline reductase includes components PrdA and PrdB and electron transfer protein PrdC
• proline-transport:
  • proV, proW and proX
  • or opuBA and opuBB
  • or natA, natB, natC, natD and natE
  • or hutV, hutW and hutX
  • or AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250 and AZOBR_RS08260
  • or HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895 and HSERO_RS00900
  • or aapJ, aapQ, aapM and aapP
  • or proY
  • or putP
  • or PROT1
  • or SLC6A7
  • or proP
  • or ectP
  • or betS
  • or BAC2
  • or AAT20.2
  • or CCNA_00435
  • or N515DRAFT_2924
  • Comment: Transporters were identified using query: transporter:proline:L-proline

Steps

proV: proline ABC transporter, ATPase component ProV

• Curated sequence CH_001555: glycine betaine/l-proline transport atp-binding protein prov. Glycine betaine/proline betaine transport system ATP-binding protein ProV. ProV aka B2677, component of Glycine betaine/proline porter, ProU or ProVWX (also transports proline betaine, carnitine, dimethyl proline, homobetaine, γ-butyrobetaine and choline with low affinity). glycine betaine ABC transporter ATP binding subunit ProV (EC 7.6.2.9). glycine betaine ABC transporter ATP binding subunit ProV (EC 7.6.2.9)
• Curated sequence P17328: Glycine betaine/proline betaine transport system ATP-binding protein ProV
• Ignore hits to E0SCY1 when looking for 'other' hits (Glycine betaine/choline transport system ATP-binding protein OusV)
• Comment: E.coli/Salmonella have proVWX (only ProV is curated in S. typhimurium). Ignore a similar system in Dickeya dadantii (or Erwinia chrysanthemi) reported to act on glycine betaine only
• Total: 2 characterized proteins

proW: proline ABC transporter, permease component ProW

• Curated sequence P14176: Glycine betaine/proline betaine transport system permease protein ProW. ProW aka B2678, component of Glycine betaine/proline porter, ProU or ProVWX (also transports proline betaine, carnitine, dimethyl proline, homobetaine, γ-butyrobetaine and choline with low affinity). glycine betaine ABC transporter membrane subunit ProW (EC 7.6.2.9). glycine betaine ABC transporter membrane subunit ProW (EC 7.6.2.9)
• Ignore hits to E0SCY2 when looking for 'other' hits (Glycine betaine/choline transport system permease protein OusW)
• Total: 1 characterized proteins

proX: proline ABC transporter, substrate-binding component ProX

• Curated sequence CH_024698: glycine betaine-binding periplasmic protein. Glycine betaine/proline betaine-binding periplasmic protein; GBBP. ProX aka ProU aka B2679, component of Glycine betaine/proline porter, ProU or ProVWX (also transports proline betaine, carnitine, dimethyl proline, homobetaine, γ-butyrobetaine and choline with low affinity). glycine betaine ABC transporter periplasmic binding protein ProX (EC 7.6.2.9). glycine betaine ABC transporter periplasmic binding protein ProX (EC 7.6.2.9)
• Ignore hits to E0SCY3 when looking for 'other' hits (Glycine betaine-binding periplasmic protein OusX)
• Total: 1 characterized proteins

opuBA: proline ABC transporter, ATPase component OpuBA/BusAA

• Curated sequence Q93A35: BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence)
• Curated sequence Q9RQ06: BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport
• Comment: In Listeria monocytogenes and in Lactococcus lactis, the permease is fused to the substrate-binding component.
• Total: 2 characterized proteins

opuBB: proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB

• Curated sequence Q93A34: BilEB aka OpuBB protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence)
• Curated sequence Q9RQ05: BusAB aka OPUABC, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport
• Ignore hits to Q7DAU8 when looking for 'other' hits (ABC-type quaternary amine transporter (EC 7.6.2.9))
• Comment: Ignore a nearly-identical protein from L. lactis, annotated as a quarternary amine transporter
• Total: 2 characterized proteins

natA: proline ABC transporter, ATPase component 1 (NatA)

• Curated sequence Q55164: NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
• Curated sequence Q7A2H0: NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
• Comment: Synechocystis sp. NatABCDE; also a similar system in Anabaena
• Total: 2 characterized proteins

natB: proline ABC transporter, substrate-binding component NatB

• Curated sequence Q55387: NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
• Curated sequence Q8YVY4: NatB, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
• Total: 2 characterized proteins

natC: proline ABC transporter, permease component 1 (NatC)

• Curated sequence P74455: NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
• Curated sequence Q8YY08: NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
• Total: 2 characterized proteins

natD: proline ABC transporter, permease component 2 (NatD)

• Curated sequence P74318: NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
• Curated sequence Q8YXD0: NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
• Total: 2 characterized proteins

natE: proline ABC transporter, ATPase component 2 (NatE)

• Curated sequence P73650: NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE
• Curated sequence Q8YT15: NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB)
• Total: 2 characterized proteins

hutV: proline ABC transporter, ATPase component HutV

• Curated sequence Q9KKE1: HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine
• Comment: Ensifer meliloti (formerly Rhizobium or Sinorhizobium) hutVWX
• Total: 1 characterized proteins

hutW: proline ABC transporter, permease component HutW

• Curated sequence Q9KKE2: HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine
• Total: 1 characterized proteins

hutX: proline ABC transporter, substrate-binding component HutX

• Curated sequence Q9KKE3: HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine
• Total: 1 characterized proteins

AZOBR_RS08235: proline ABC transporter, permease component 1

• Curated sequence AZOBR_RS08235: L-proline and D-alanine ABC transporter, permease component 1
• Comment: Azospirillum brasilense -- just one component is in the reannotations, but all show up in the fitness data for proline.
• Total: 1 characterized proteins

AZOBR_RS08240: proline ABC transporter, permease component 2

• UniProt sequence G8ALI9: SubName: Full=Leucine/isoleucine/valine ABC transporter,permease component {ECO:0000313|EMBL:CCC98101.1};
• Total: 1 characterized proteins

AZOBR_RS08245: proline ABC transporter, ATPase component 1

• UniProt sequence G8ALJ0: SubName: Full=Leucine/isoleucine/valine ABC transporter,ATPase component {ECO:0000313|EMBL:CCC98102.1}; EC=3.6.3.- {ECO:0000313|EMBL:CCC98102.1};
• Total: 1 characterized proteins

AZOBR_RS08250: proline ABC transporter, ATPase component 2

• UniProt sequence G8ALJ1: SubName: Full=Leucine//isoleucine/valine ABC transporter,ATPase component {ECO:0000313|EMBL:CCC98103.1}; EC=3.6.3.- {ECO:0000313|EMBL:CCC98103.1};
• Total: 1 characterized proteins

AZOBR_RS08260: proline ABC transporter, substrate-binding component

• UniProt sequence G8ALJ3: SubName: Full=Branched-chain amino acid ABC transporter,substrate-binding periplasmic component {ECO:0000313|EMBL:CCC98105.1};
• Total: 1 characterized proteins

HSERO_RS00870: proline ABC transporter, substrate-binding component

• UniProt sequence D8IUY1: SubName: Full=ABC-type branched-chain amino acid transport system, periplasmic component protein {ECO:0000313|EMBL:ADJ61700.1};
• UniProt sequence A0A165KTD4: SubName: Full=Branched chain amino acid ABC transporter substrate-binding protein {ECO:0000313|EMBL:KZT16064.1};
• Comment: 5-part ABC transporter in Herbaspirillum brasilense, identified using fitness data. (This system is distantly related to AZOBR_RS08235:RS08260.) A related system from Acidovorax sp. GW101-3H11 is also important for proline utilization: Ac3H11_2396 (A0A165KTD4), Ac3H11_1695 (A0A165KC95), Ac3H11_1694 (A0A165KER0), Ac3H11_1693 (A0A165KC86), Ac3H11_1692 (A0A165KC78).
• Total: 2 characterized proteins

HSERO_RS00885: proline ABC transporter, permease component 1

• UniProt sequence D8IUY4: SubName: Full=ABC-type branched-chain amino acid transport system, permease component protein {ECO:0000313|EMBL:ADJ61703.1};
• UniProt sequence A0A165KC95: SubName: Full=ABC transporter permease {ECO:0000313|EMBL:KZT15319.1};
• Total: 2 characterized proteins

HSERO_RS00890: proline ABC transporter, permease component 2

• UniProt sequence D8IUY5: SubName: Full=ABC-type branched-chain amino acid transport system, permease component protein {ECO:0000313|EMBL:ADJ61704.1};
• UniProt sequence A0A165KER0: SubName: Full=ABC transporter ATP-binding protein {ECO:0000313|EMBL:KZT15410.1};
• Total: 2 characterized proteins

HSERO_RS00895: proline ABC transporter, ATPase component 1

• UniProt sequence D8J1T6: SubName: Full=ABC-type branched-chain amino acid transport system, ATPase component protein {ECO:0000313|EMBL:ADJ62707.1};
• UniProt sequence A0A165KC86: SubName: Full=ABC transporter ATP-binding protein {ECO:0000313|EMBL:KZT15318.1};
• Total: 2 characterized proteins

HSERO_RS00900: proline ABC transporter, ATPase component 2

• UniProt sequence D8IUY7: SubName: Full=ABC-type branched-chain amino acid transport system, ATPase component protein {ECO:0000313|EMBL:ADJ61706.1};
• UniProt sequence A0A165KC78: SubName: Full=ABC transporter ATP-binding protein {ECO:0000313|EMBL:KZT15317.1};
• Total: 2 characterized proteins

aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ

• Curated sequence Q52812: AapJ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02118 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component)
• Total: 1 characterized proteins

aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)

• Curated sequence Q52813: AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02119 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1)
• Total: 1 characterized proteins

aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)

• Curated sequence Q52814: AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02120 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2)
• Total: 1 characterized proteins

aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP

• Curated sequence Q52815: AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02121 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component)
• Total: 1 characterized proteins

proY: proline:H+ symporter

• Curated sequence Q2VQZ4: Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids)
• Curated sequence CH_091285: proline-specific permease. Proline-specific permease. Proline permease
• Curated sequence CH_122066: proline-specific permease (proline transport protein)
• Curated sequence P46349: GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP. β-alanine/γ-aminobutyrate/proline/3,4-dehydroproline:H+ symporter, GabP
• Curated sequence Q9URZ3: Probable proline-specific permease put4
• Curated sequence P0AAE2: ProY of 457 aas and 12 TMSs
• Curated sequence P37460: Proline-specific permease (ProY)
• Total: 7 characterized proteins

putP: proline:Na+ symporter

• Curated sequence O06493: Osmoregulated proline transporter OpuE; Osmoprotectant uptake; Proline uptake system. Proline uptake porter, OpuE (YerK)
• Curated sequence P07117: Sodium/proline symporter; Proline permease; Propionate transporter. Proline:Na+ symporter, PutP. proline:Na⁺ symporter. proline:Na⁺ symporter
• Curated sequence P94392: High-affinity proline transporter PutP. The high affinity nutritional proline uptake porter, PutP
• Curated sequence Q2FWY7: Sodium/proline symporter; Proline permease. Sodium/proline symporter (Proline permease)
• Curated sequence O24896: High affinity proline-specific Na+:proline symporter, PutP (Rivera-Ordaz et al. 2013).  Proline is a preferred source of energy for this microaerophilic bacterium.  PutP is efficiently inhibited by the proline analogs, 3,4-dehydro-D,L-proline and L-azetidine-2-carboxylic acid
• Curated sequence Q9I5F5: L-proline uptake porter, PutP
• Total: 6 characterized proteins

PROT1: proline transporter

• Curated sequence CH_091590: proline transporter 1. Proline transporter 1; AtPROT1. Proline permease 1
• Curated sequence P92962: Proline transporter 2; AtPROT2
• Curated sequence Q60DN5: Proline transporter 1; OsPROT
• Curated sequence Q9SJP9: Proline transporter 3; AtPROT3
• Curated sequence Q9XE48: Proline/GABA/glycine betaine permease, ProT1
• Total: 5 characterized proteins

SLC6A7: proline:Na+ symporter

• Curated sequence CH_091144: sodium-dependent proline transporter. Proline:Na+ symporter
• Curated sequence Q64093: Sodium- and chloride-dependent transporter XTRP3; Sodium/imino-acid transporter 1; Solute carrier family 6 member 20; Transporter rB21A. sodium- and chloride-dependent transporter XTRP3. Na+/Amino acid transporter 1, SIT1/IMINO (SLC6A20). Transports imino acids such as proline (Km=0.2 mM), pipecolate, and N-methylated amino acids such as MeAIB and sarcosine (Na+-dependent, Cl--stimulated, pH-independent, voltage-dependent) (Li+, but not H+ can substitute for Na+) (Takanaga et al., 2005). It is a 2Na+/1Cl--proline cotransporter
• Curated sequence P48065: Betaine/GABA:Na+ symporter, BGT1. (Substrates include: betaine, GABA, diaminobutyrate, β-alanine, proline, quinidine, dimethylglycine, glycine, and sarcosine with decreasing affinity in that order)
• Curated sequence Q99884: Sodium-dependent proline transporter (Solute carrier family 6 member 7)
• Total: 4 characterized proteins

proP: proline:H+ symporter ProP

• Curated sequence CH_024324: proline porter II. Proline/betaine transporter; Proline porter II; PPII. (Proline/glycine-betaine):(H+/Na+) symporter, ProP (also transports taurine, ectoine, pipecolate, proline-betaine, N,N-dimethylglycine, carnitine, and 1-carboxymethyl-pyridinium) (subject to osmotic activation). Transmembrane helix I and periplasmic loop 1 are involved in osmosensing and osmoprotectant transport. osmolyte:H⁺ symporter ProP. osmolyte:H⁺ symporter ProP
• Curated sequence Q47421: Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A
• Curated sequence Q79VC4: Ectoine/proline transporter ProP
• Total: 3 characterized proteins

ectP: proline transporter EctP

• Curated sequence Q79VE0: Ectoine/glycine betaine/proline transporter EctP. Ectosine/glycine betaine/proline:Na+ symporter
• Curated sequence Q87NZ5: Glycine betaine/proline/choline transporter VP1723
• Curated sequence Q87PP5: Glycine betaine/proline/choline/ectoine transporter VP1456
• Total: 3 characterized proteins

betS: proline transporter BetS

• Curated sequence G3XCN6: Glycine betaine/proline betaine transporter BetS. Glycine-betaine/proline-betaine:Na+ symporter, BetS; BetT, OpuD
• Total: 1 characterized proteins

BAC2: basic amino acid carrier BAC2

• Curated sequence Q9CA93: Mitochondrial arginine transporter BAC2; Mitochondrial basic amino acid carrier 2; AtMBAC2. Basic amino acid carrier2, BAC2 of 296 aas and 6 TMSs
• Total: 1 characterized proteins

AAT20.2: proline transporter

• Curated sequence A4HUI4: Proline/alanine transporter of 488 aas and 10 TMSs, AAP24. The first 18 amino acids of the negatively charged N-terminal LdAAP24 tail are required for alanine transport and may facilitate the electrostatic interactions of the entire negatively charged N-terminal tail with the positively charged internal loops in the transmembrane domain
• Total: 1 characterized proteins

CCNA_00435: proline transporter

• UniProt sequence A0A0H3C3Q5: SubName: Full=Amino acid transporter {ECO:0000313|EMBL:ACL93902.2};
• Comment: Identified using fitness data for Caulobacter crescentus
• Total: 1 characterized proteins

N515DRAFT_2924: proline transporter

• UniProt sequence A0A1I1Y8J0: SubName: Full=Basic amino acid/polyamine antiporter, APA family {ECO:0000313|EMBL:SFE15955.1};
• Comment: Identified using fitness data for Dyella japonica
• 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

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

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