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Conserved domains on  [gi|30683266|ref|NP_850088|]
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Aldolase superfamily protein [Arabidopsis thaliana]

Protein Classification

beta/alpha barrel domain-containing protein( domain architecture ID 229392)

beta/alpha barrel domain-containing protein belongs to a large superfamily with a wide variety of enzymatic functions

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TIM super family cl21457
TIM-like beta/alpha barrel domains; A large family of domains similar to triose phosphate ...
122-350 5.47e-151

TIM-like beta/alpha barrel domains; A large family of domains similar to triose phosphate isomerase (TIM) which, in general, share an eight beta/alpha closed barrel structure.


The actual alignment was detected with superfamily member PLN02746:

Pssm-ID: 473867  Cd Length: 347  Bit Score: 428.82  E-value: 5.47e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  122 FAGRTSTVSGTLRESKSFKEQKYSTFSNENGTSHISNKISKGIPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSS 201
Cdd:PLN02746   1 SRGSTSTVSGTLGSSWSFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  202 GLPVVEATSFVSPKWVPQLADAKDVMDAVNTLDGARLPVLTPNLKGFQAAVSAGAKEVAIFASASESFSLSNINCTIEES 281
Cdd:PLN02746  81 GLPVVEATSFVSPKWVPQLADAKDVMAAVRNLEGARFPVLTPNLKGFEAAIAAGAKEVAVFASASESFSKSNINCSIEES 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30683266  282 LLRYRVVATAAKEHSVPVRGYVSCVVGCPVEGPVLPSKVAYVVKELYDMGCFEISLGDTIGIGTPGNFV 350
Cdd:PLN02746 161 LVRYREVALAAKKHSIPVRGYVSCVVGCPIEGPVPPSKVAYVAKELYDMGCYEISLGDTIGVGTPGTVV 229
 
Name Accession Description Interval E-value
PLN02746 PLN02746
hydroxymethylglutaryl-CoA lyase
122-350 5.47e-151

hydroxymethylglutaryl-CoA lyase


Pssm-ID: 178347  Cd Length: 347  Bit Score: 428.82  E-value: 5.47e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  122 FAGRTSTVSGTLRESKSFKEQKYSTFSNENGTSHISNKISKGIPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSS 201
Cdd:PLN02746   1 SRGSTSTVSGTLGSSWSFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  202 GLPVVEATSFVSPKWVPQLADAKDVMDAVNTLDGARLPVLTPNLKGFQAAVSAGAKEVAIFASASESFSLSNINCTIEES 281
Cdd:PLN02746  81 GLPVVEATSFVSPKWVPQLADAKDVMAAVRNLEGARFPVLTPNLKGFEAAIAAGAKEVAVFASASESFSKSNINCSIEES 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30683266  282 LLRYRVVATAAKEHSVPVRGYVSCVVGCPVEGPVLPSKVAYVVKELYDMGCFEISLGDTIGIGTPGNFV 350
Cdd:PLN02746 161 LVRYREVALAAKKHSIPVRGYVSCVVGCPIEGPVPPSKVAYVAKELYDMGCYEISLGDTIGVGTPGTVV 229
DRE_TIM_HMGL cd07938
3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; ...
170-347 2.03e-109

3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; 3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".


Pssm-ID: 163676  Cd Length: 274  Bit Score: 320.49  E-value: 2.03e-109
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266 170 IVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADAKDVMDAVNTLDGARLPVLTPNLKGFQ 249
Cdd:cd07938   1 IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADAEEVLAGLPRRPGVRYSALVPNLRGAE 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266 250 AAVSAGAKEVAIFASASESFSLSNINCTIEESLLRYRVVATAAKEHSVPVRGYVSCVVGCPVEGPVLPSKVAYVVKELYD 329
Cdd:cd07938  81 RALAAGVDEVAVFVSASETFSQKNINCSIAESLERFEPVAELAKAAGLRVRGYVSTAFGCPYEGEVPPERVAEVAERLLD 160
                       170
                ....*....|....*...
gi 30683266 330 MGCFEISLGDTIGIGTPG 347
Cdd:cd07938 161 LGCDEISLGDTIGVATPA 178
HMGL-like pfam00682
HMGL-like; This family contains a diverse set of enzymes. These include various aldolases and ...
168-349 5.96e-24

HMGL-like; This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase.


Pssm-ID: 459902 [Multi-domain]  Cd Length: 264  Bit Score: 98.95  E-value: 5.96e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266   168 VKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEAtsfvspkWVPQL--ADAKDVMDAVNTLDGAR-LPVLTPN 244
Cdd:pfam00682   2 VAICDTTLRDGEQALGVAFSIDEKLAIARALDAAGVDEIEV-------GFPAAseDDFEVVRAIAKVIPHARiLVLCRAR 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266   245 LKGFQAAVS----AGAKEVAIFASASESFSLSNINCTIEESLLRYRVVATAAKEHSVpvrgyvSCVVGCPVEGPVLPSKV 320
Cdd:pfam00682  75 EHDIKAAVEalkgAGAVRVHVFIATSDLHRKYKLGKDREEVAKRAVAAVKAARSRGI------DVEFSPEDASRTDPEFL 148
                         170       180
                  ....*....|....*....|....*....
gi 30683266   321 AYVVKELYDMGCFEISLGDTIGIGTPGNF 349
Cdd:pfam00682 149 AEVVEAAIEAGATRINIPDTVGVLTPNEA 177
 
Name Accession Description Interval E-value
PLN02746 PLN02746
hydroxymethylglutaryl-CoA lyase
122-350 5.47e-151

hydroxymethylglutaryl-CoA lyase


Pssm-ID: 178347  Cd Length: 347  Bit Score: 428.82  E-value: 5.47e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  122 FAGRTSTVSGTLRESKSFKEQKYSTFSNENGTSHISNKISKGIPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSS 201
Cdd:PLN02746   1 SRGSTSTVSGTLGSSWSFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  202 GLPVVEATSFVSPKWVPQLADAKDVMDAVNTLDGARLPVLTPNLKGFQAAVSAGAKEVAIFASASESFSLSNINCTIEES 281
Cdd:PLN02746  81 GLPVVEATSFVSPKWVPQLADAKDVMAAVRNLEGARFPVLTPNLKGFEAAIAAGAKEVAVFASASESFSKSNINCSIEES 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30683266  282 LLRYRVVATAAKEHSVPVRGYVSCVVGCPVEGPVLPSKVAYVVKELYDMGCFEISLGDTIGIGTPGNFV 350
Cdd:PLN02746 161 LVRYREVALAAKKHSIPVRGYVSCVVGCPIEGPVPPSKVAYVAKELYDMGCYEISLGDTIGVGTPGTVV 229
DRE_TIM_HMGL cd07938
3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; ...
170-347 2.03e-109

3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; 3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".


Pssm-ID: 163676  Cd Length: 274  Bit Score: 320.49  E-value: 2.03e-109
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266 170 IVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADAKDVMDAVNTLDGARLPVLTPNLKGFQ 249
Cdd:cd07938   1 IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADAEEVLAGLPRRPGVRYSALVPNLRGAE 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266 250 AAVSAGAKEVAIFASASESFSLSNINCTIEESLLRYRVVATAAKEHSVPVRGYVSCVVGCPVEGPVLPSKVAYVVKELYD 329
Cdd:cd07938  81 RALAAGVDEVAVFVSASETFSQKNINCSIAESLERFEPVAELAKAAGLRVRGYVSTAFGCPYEGEVPPERVAEVAERLLD 160
                       170
                ....*....|....*...
gi 30683266 330 MGCFEISLGDTIGIGTPG 347
Cdd:cd07938 161 LGCDEISLGDTIGVATPA 178
PRK05692 PRK05692
hydroxymethylglutaryl-CoA lyase; Provisional
164-347 5.59e-106

hydroxymethylglutaryl-CoA lyase; Provisional


Pssm-ID: 180206  Cd Length: 287  Bit Score: 312.21  E-value: 5.59e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  164 IPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADAKDVMDAVNTLDGARLPVLTP 243
Cdd:PRK05692   1 LPKRVKIVEVGPRDGLQNEKRFIPTADKIALIDRLSAAGLSYIEVASFVSPKWVPQMADAAEVMAGIQRRPGVTYAALTP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266  244 NLKGFQAAVSAGAKEVAIFASASESFSLSNINCTIEESLLRYRVVATAAKEHSVPVRGYVSCVVGCPVEGPVLPSKVAYV 323
Cdd:PRK05692  81 NLKGLEAALAAGADEVAVFASASEAFSQKNINCSIAESLERFEPVAEAAKQAGVRVRGYVSCVLGCPYEGEVPPEAVADV 160
                        170       180
                 ....*....|....*....|....
gi 30683266  324 VKELYDMGCFEISLGDTIGIGTPG 347
Cdd:PRK05692 161 AERLFALGCYEISLGDTIGVGTPG 184
DRE_TIM_metallolyase cd03174
DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes ...
171-346 1.02e-60

DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".


Pssm-ID: 163674 [Multi-domain]  Cd Length: 265  Bit Score: 195.75  E-value: 1.02e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266 171 VEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADAKDVMDAVNTLD-GARLPVLTPN-LKGF 248
Cdd:cd03174   1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDDWEVLRAIRKLVpNVKLQALVRNrEKGI 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266 249 QAAVSAGAKEVAIFASASESFSLSNINCTIEESLLRYRVVATAAKEHSVPVRGYVSCVVGCPVEgpvlPSKVAYVVKELY 328
Cdd:cd03174  81 ERALEAGVDEVRIFDSASETHSRKNLNKSREEDLENAEEAIEAAKEAGLEVEGSLEDAFGCKTD----PEYVLEVAKALE 156
                       170
                ....*....|....*...
gi 30683266 329 DMGCFEISLGDTIGIGTP 346
Cdd:cd03174 157 EAGADEISLKDTVGLATP 174
HMGL-like pfam00682
HMGL-like; This family contains a diverse set of enzymes. These include various aldolases and ...
168-349 5.96e-24

HMGL-like; This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase.


Pssm-ID: 459902 [Multi-domain]  Cd Length: 264  Bit Score: 98.95  E-value: 5.96e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266   168 VKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEAtsfvspkWVPQL--ADAKDVMDAVNTLDGAR-LPVLTPN 244
Cdd:pfam00682   2 VAICDTTLRDGEQALGVAFSIDEKLAIARALDAAGVDEIEV-------GFPAAseDDFEVVRAIAKVIPHARiLVLCRAR 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30683266   245 LKGFQAAVS----AGAKEVAIFASASESFSLSNINCTIEESLLRYRVVATAAKEHSVpvrgyvSCVVGCPVEGPVLPSKV 320
Cdd:pfam00682  75 EHDIKAAVEalkgAGAVRVHVFIATSDLHRKYKLGKDREEVAKRAVAAVKAARSRGI------DVEFSPEDASRTDPEFL 148
                         170       180
                  ....*....|....*....|....*....
gi 30683266   321 AYVVKELYDMGCFEISLGDTIGIGTPGNF 349
Cdd:pfam00682 149 AEVVEAAIEAGATRINIPDTVGVLTPNEA 177
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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