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Conserved domains on  [gi|1962495272|emb|CAD8532760|]
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unnamed protein product, partial [Calcidiscus leptoporus]

Protein Classification

Rossmann-fold NAD(P)-binding domain-containing protein( domain architecture ID 229380)

Rossmann-fold NAD(P)-binding domain-containing protein may function as an oxidoreductase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NADB_Rossmann super family cl21454
Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a ...
 17-104 2.09e-33

Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction.


The actual alignment was detected with superfamily member cd05312:

Pssm-ID: 473865  Cd Length: 279  Bit Score: 116.49  E-value: 2.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272  17 KDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMVKVQEakkhpgRPLVFALSNPKSQAECTAEDAYKFSDGKVIFGSGT 96
Cdd:cd05312    95 KSLLEVVKAVKPTVLIGLSG-VGGAFTEEVVRAMAKSNE------RPIIFALSNPTSKAECTAEDAYKWTDGRALFASGS 167


                  ....*...
gi 1962495272  97 RFSPVKIK 104
Cdd:cd05312   168 PFPPVEYN 175
 
Name Accession Description Interval E-value
NAD_bind_1_malic_enz cd05312
NAD(P) binding domain of malic enzyme (ME), subgroup 1; Malic enzyme (ME), a member of the ...
 17-104 2.09e-33

NAD(P) binding domain of malic enzyme (ME), subgroup 1; Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.


Pssm-ID: 133454  Cd Length: 279  Bit Score: 116.49  E-value: 2.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272  17 KDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMVKVQEakkhpgRPLVFALSNPKSQAECTAEDAYKFSDGKVIFGSGT 96
Cdd:cd05312    95 KSLLEVVKAVKPTVLIGLSG-VGGAFTEEVVRAMAKSNE------RPIIFALSNPTSKAECTAEDAYKWTDGRALFASGS 167


                  ....*...
gi 1962495272  97 RFSPVKIK 104
Cdd:cd05312   168 PFPPVEYN 175
PLN03129 PLN03129
NADP-dependent malic enzyme; Provisional
 17-103 7.17e-32

NADP-dependent malic enzyme; Provisional


Pssm-ID: 215594 [Multi-domain]  Cd Length: 581  Bit Score: 116.55  E-value: 7.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272  17 KDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMVKVQEakkhpgRPLVFALSNPKSQAECTAEDAYKFSDGKVIFGSGT 96
Cdd:PLN03129  391 ASLLEAVKAIKPTVLIGLSG-VGGTFTKEVLEAMASLNE------RPIIFALSNPTSKAECTAEEAYTWTGGRAIFASGS 463


                  ....*..
gi 1962495272  97 RFSPVKI 103
Cdd:PLN03129  464 PFDPVEY 470
Malic_M pfam03949
Malic enzyme, NAD binding domain;
15-104 5.64e-31

Malic enzyme, NAD binding domain;


Pssm-ID: 427608 [Multi-domain]  Cd Length: 257  Bit Score: 109.59  E-value: 5.64e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272  15 DSKDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMvkvqeaKKHPGRPLVFALSNPKSQAECTAEDAYKFSDGKVIFGS 94
Cdd:pfam03949  97 DGITLLEVVRKVKPTVLIGASG-VPGAFTEEIVRAM------AAHTERPIIFPLSNPTSKAEATPEDAYKWTDGRALFAT 169

                          90
                  ....*....|
gi 1962495272  95 GTRFSPVKIK 104
Cdd:pfam03949 170 GSPFPPVEYN 179
Malic_M smart00919
Malic enzyme, NAD binding domain; Malic enzymes (malate oxidoreductases) catalyse the ...
 2-100 3.22e-19

Malic enzyme, NAD binding domain; Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate.


Pssm-ID: 214912  Cd Length: 231  Bit Score: 78.61  E-value: 3.22e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272    2 EQKALAQIGEPsFDSKDLVEVVKniKPDCIIGaVGRAPNCFNKQVIEEMVKvqeakkhpgRPLVFALSNPKSQAECTAED 81
Cdd:smart00919  74 YKKPFARKTNE-RETGTLEEAVK--GADVLIG-VSGPGGAFTEEMVKSMAE---------RPIIFALSNPTPEIEPTAAD 140

                           90
                   ....*....|....*....
gi 1962495272   82 AYKFSDgkVIFGSGTRFSP 100
Cdd:smart00919 141 AYRWTA--AIVATGRSDYP 157
SfcA COG0281
Malic enzyme [Energy production and conversion]; Malic enzyme is part of the Pathway/BioSystem: ...
 2-91 2.73e-14

Malic enzyme [Energy production and conversion]; Malic enzyme is part of the Pathway/BioSystem: Urea cycle


Pssm-ID: 440050 [Multi-domain]  Cd Length: 414  Bit Score: 66.57  E-value: 2.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272   2 EQKALAQIGEPSFDSKDLVEVVKNIkpDCIIGAvgRAPNCFNKQVIEEMvkvqeAKkhpgRPLVFALSNPKSqaECTAED 81
Cdd:COG0281   239 YKREFARDTNPRGLKGTLAEAIKGA--DVFIGV--SAPGAFTEEMVKSM-----AK----RPIIFALANPTP--EITPED 303

                          90
                  ....*....|
gi 1962495272  82 AYKFSDGKVI 91
Cdd:COG0281   304 AKAWGDGAIV 313
 
Name Accession Description Interval E-value
NAD_bind_1_malic_enz cd05312
NAD(P) binding domain of malic enzyme (ME), subgroup 1; Malic enzyme (ME), a member of the ...
 17-104 2.09e-33

NAD(P) binding domain of malic enzyme (ME), subgroup 1; Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.


Pssm-ID: 133454  Cd Length: 279  Bit Score: 116.49  E-value: 2.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272  17 KDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMVKVQEakkhpgRPLVFALSNPKSQAECTAEDAYKFSDGKVIFGSGT 96
Cdd:cd05312    95 KSLLEVVKAVKPTVLIGLSG-VGGAFTEEVVRAMAKSNE------RPIIFALSNPTSKAECTAEDAYKWTDGRALFASGS 167


                  ....*...
gi 1962495272  97 RFSPVKIK 104
Cdd:cd05312   168 PFPPVEYN 175
PLN03129 PLN03129
NADP-dependent malic enzyme; Provisional
 17-103 7.17e-32

NADP-dependent malic enzyme; Provisional


Pssm-ID: 215594 [Multi-domain]  Cd Length: 581  Bit Score: 116.55  E-value: 7.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272  17 KDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMVKVQEakkhpgRPLVFALSNPKSQAECTAEDAYKFSDGKVIFGSGT 96
Cdd:PLN03129  391 ASLLEAVKAIKPTVLIGLSG-VGGTFTKEVLEAMASLNE------RPIIFALSNPTSKAECTAEEAYTWTGGRAIFASGS 463


                  ....*..
gi 1962495272  97 RFSPVKI 103
Cdd:PLN03129  464 PFDPVEY 470
Malic_M pfam03949
Malic enzyme, NAD binding domain;
15-104 5.64e-31

Malic enzyme, NAD binding domain;


Pssm-ID: 427608 [Multi-domain]  Cd Length: 257  Bit Score: 109.59  E-value: 5.64e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272  15 DSKDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMvkvqeaKKHPGRPLVFALSNPKSQAECTAEDAYKFSDGKVIFGS 94
Cdd:pfam03949  97 DGITLLEVVRKVKPTVLIGASG-VPGAFTEEIVRAM------AAHTERPIIFPLSNPTSKAEATPEDAYKWTDGRALFAT 169

                          90
                  ....*....|
gi 1962495272  95 GTRFSPVKIK 104
Cdd:pfam03949 170 GSPFPPVEYN 179
PRK13529 PRK13529
oxaloacetate-decarboxylating malate dehydrogenase;
2-104 3.95e-28

oxaloacetate-decarboxylating malate dehydrogenase;


Pssm-ID: 237414 [Multi-domain]  Cd Length: 563  Bit Score: 105.98  E-value: 3.95e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272   2 EQKALAQIGEP------SFDSKDLVEVVKNIKPDCIIGAVGrAPNCFNKQVIEEMVKVQEakkhpgRPLVFALSNPKSQA 75
Cdd:PRK13529  351 FQKPYARKREEladwdtEGDVISLLEVVRNVKPTVLIGVSG-QPGAFTEEIVKEMAAHCE------RPIIFPLSNPTSRA 423

                          90       100
                  ....*....|....*....|....*....
gi 1962495272  76 ECTAEDAYKFSDGKVIFGSGTRFSPVKIK 104
Cdd:PRK13529  424 EATPEDLIAWTDGRALVATGSPFAPVEYN 452
PTZ00317 PTZ00317
NADP-dependent malic enzyme; Provisional
 9-104 2.38e-26

NADP-dependent malic enzyme; Provisional


Pssm-ID: 240357 [Multi-domain]  Cd Length: 559  Bit Score: 101.24  E-value: 2.38e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272   9 IGEPSFDSKDLVEVVKNIKPDCIIGaVGRAPNCFNKQVIEEMvkvqeaKKHPGRPLVFALSNPKSQAECTAEDAYKFSDG 88
Cdd:PTZ00317  363 ISAEDSSLKTLEDVVRFVKPTALLG-LSGVGGVFTEEVVKTM------ASNVERPIIFPLSNPTSKAECTAEDAYKWTNG 435

                          90
                  ....*....|....*.
gi 1962495272  89 KVIFGSGTRFSPVKIK 104
Cdd:PTZ00317  436 RAIVASGSPFPPVTLN 451
NAD_bind_malic_enz cd00762
NAD(P) binding domain of malic enzyme; Malic enzyme (ME), a member of the amino acid ...
 6-103 5.54e-22

NAD(P) binding domain of malic enzyme; Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.


Pssm-ID: 133442  Cd Length: 254  Bit Score: 86.12  E-value: 5.54e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272   6 LAQIGEPSFDSKDLVEVVKNIKPDCIIGaVGRAPNCFNKQVIEEMVKVQEakkhpgRPLVFALSNPKSQAECTAEDAYKF 85
Cdd:cd00762    85 LARFANPERESGDLEDAVEAAKPDFLIG-VSRVGGAFTPEVIRA*AEINE------RPVIFALSNPTSKAECTAEEAYTA 157

                          90
                  ....*....|....*...
gi 1962495272  86 SDGKVIFGSGTRFSPVKI 103
Cdd:cd00762   158 TEGRAIFASGSPFHPVEL 175
Malic_M smart00919
Malic enzyme, NAD binding domain; Malic enzymes (malate oxidoreductases) catalyse the ...
 2-100 3.22e-19

Malic enzyme, NAD binding domain; Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate.


Pssm-ID: 214912  Cd Length: 231  Bit Score: 78.61  E-value: 3.22e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272    2 EQKALAQIGEPsFDSKDLVEVVKniKPDCIIGaVGRAPNCFNKQVIEEMVKvqeakkhpgRPLVFALSNPKSQAECTAED 81
Cdd:smart00919  74 YKKPFARKTNE-RETGTLEEAVK--GADVLIG-VSGPGGAFTEEMVKSMAE---------RPIIFALSNPTPEIEPTAAD 140

                           90
                   ....*....|....*....
gi 1962495272   82 AYKFSDgkVIFGSGTRFSP 100
Cdd:smart00919 141 AYRWTA--AIVATGRSDYP 157
SfcA COG0281
Malic enzyme [Energy production and conversion]; Malic enzyme is part of the Pathway/BioSystem: ...
 2-91 2.73e-14

Malic enzyme [Energy production and conversion]; Malic enzyme is part of the Pathway/BioSystem: Urea cycle


Pssm-ID: 440050 [Multi-domain]  Cd Length: 414  Bit Score: 66.57  E-value: 2.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1962495272   2 EQKALAQIGEPSFDSKDLVEVVKNIkpDCIIGAvgRAPNCFNKQVIEEMvkvqeAKkhpgRPLVFALSNPKSqaECTAED 81
Cdd:COG0281   239 YKREFARDTNPRGLKGTLAEAIKGA--DVFIGV--SAPGAFTEEMVKSM-----AK----RPIIFALANPTP--EITPED 303

                          90
                  ....*....|
gi 1962495272  82 AYKFSDGKVI 91
Cdd:COG0281   304 AKAWGDGAIV 313
 
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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