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Conserved domains on  [gi|398365589|ref|NP_012676|]
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uncharacterized protein YJR142W [Saccharomyces cerevisiae S288C]

Protein Classification

NUDIX hydrolase( domain architecture ID 13599039)

NUDIX hydrolase family protein may catalyze the hydrolysis of nucleoside diphosphates linked to other moieties (X); it would require a divalent cation, such as Mg2+ or Mn2+ for its activity; contains a DUF4743 domain

CATH:  3.90.79.10
EC:  3.6.1.-
Gene Ontology:  GO:0016817|GO:0009132|GO:0046872
SCOP:  3000098

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
NUDIX_Tnr3_like cd03676
thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a ...
150-314 1.46e-76

thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a bifunctional enzyme composed of a C-terminal thiamine pyrophosphokinase domain, which transfers pyrophosphate from ATP to thiamine and an N-terminal NUDIX hydrolase domain that converts oxidized derivatives of thiamine diphosphate (oxothiamine and oxythiamine) to their respective monophosphates. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


:

Pssm-ID: 467544  Cd Length: 153  Bit Score: 232.00  E-value: 1.46e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 150 VLGIITYGIHINGYVLDPKSKKvqFWVPRRSKTKQTWPLMLDNIIAGGLGYPYGIYETVLKESMEEANLEKSVIEDNIKA 229
Cdd:cd03676    1 LFGIVTYGVHLNGYVRDGDGLR--LWVARRSATKATYPGKLDNLVAGGVPAGESPLETLVREAEEEAGLPEDLARQARPA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 230 TGSVSYLYFTGDisvtkfnkesDFIVGEVQYVYDLKLSEDIIPKPNDGEVESFNLFSLQETINALRKKEFKPNCALVMVD 309
Cdd:cd03676   79 AGRVSYFYRSDE----------GGLQPEVLYVYDLELPEDFVPKPQDGEVESFELMSVDEVLEALRAGEFKPNCALVMLD 148

                 ....*
gi 398365589 310 FLIRH 314
Cdd:cd03676  149 FLIRH 153
DUF4743 super family cl38476
Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. ...
80-153 7.27e-06

Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with pfam00293.


The actual alignment was detected with superfamily member pfam15916:

Pssm-ID: 406365  Cd Length: 119  Bit Score: 44.49  E-value: 7.27e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398365589   80 FEETFQLDESRHELRFKSEDFDHRNNLIDQLARKMYLESSLSGVKGWRNEKYAV---WvNKKPYVLVERAVAGVLGI 153
Cdd:pfam15916  42 FPDVFRVSPDAVSLNPSLRTYEERSAAVAEVLRELREEGSFVTLPGWRDECYEVrasF-GDPPLFKMERAAAPLFGV 117
 
Name Accession Description Interval E-value
NUDIX_Tnr3_like cd03676
thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a ...
150-314 1.46e-76

thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a bifunctional enzyme composed of a C-terminal thiamine pyrophosphokinase domain, which transfers pyrophosphate from ATP to thiamine and an N-terminal NUDIX hydrolase domain that converts oxidized derivatives of thiamine diphosphate (oxothiamine and oxythiamine) to their respective monophosphates. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467544  Cd Length: 153  Bit Score: 232.00  E-value: 1.46e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 150 VLGIITYGIHINGYVLDPKSKKvqFWVPRRSKTKQTWPLMLDNIIAGGLGYPYGIYETVLKESMEEANLEKSVIEDNIKA 229
Cdd:cd03676    1 LFGIVTYGVHLNGYVRDGDGLR--LWVARRSATKATYPGKLDNLVAGGVPAGESPLETLVREAEEEAGLPEDLARQARPA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 230 TGSVSYLYFTGDisvtkfnkesDFIVGEVQYVYDLKLSEDIIPKPNDGEVESFNLFSLQETINALRKKEFKPNCALVMVD 309
Cdd:cd03676   79 AGRVSYFYRSDE----------GGLQPEVLYVYDLELPEDFVPKPQDGEVESFELMSVDEVLEALRAGEFKPNCALVMLD 148

                 ....*
gi 398365589 310 FLIRH 314
Cdd:cd03676  149 FLIRH 153
PLN02839 PLN02839
nudix hydrolase
123-335 1.01e-47

nudix hydrolase


Pssm-ID: 178432 [Multi-domain]  Cd Length: 372  Bit Score: 164.81  E-value: 1.01e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 123 VKGWRNEKYAV--WVNKKPYVLVERAVAGVLGIITYGIHINGYVldPKSKKVQFWVPRRSKTKQTWPLMLDNIIAGGLgy 200
Cdd:PLN02839 169 IPGIRNELYPVkpSFNAPVFFSLERAAAPYFGIKGYGVHMNGYV--ERDGQKFLWIGKRSLSKSTYPGMLDHLVAGGL-- 244
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 201 PYGIY--ETVLKESMEEANLEKsVIEDNIKATGSVSYLyftgDISVTKFNKEsdfivgeVQYVYDLKLSEDIIPKPNDGE 278
Cdd:PLN02839 245 PHGIScgENLVKECEEEAGISK-AIADRAIAVGAVSYM----DIDQYCFKRD-------VLFCYDLELPQDFVPKNQDGE 312
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 398365589 279 VESFNLFSLQETINALRKKE-FKPNCALVMVDFLIRHGYITPENePNYLELVTRMHRR 335
Cdd:PLN02839 313 VESFKLIPVAQVANVIRKTSfFKANCSLVIIDFLFRHGFIRPES-SGYLDLYRRLRNG 369
DUF4743 pfam15916
Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. ...
80-153 7.27e-06

Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with pfam00293.


Pssm-ID: 406365  Cd Length: 119  Bit Score: 44.49  E-value: 7.27e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398365589   80 FEETFQLDESRHELRFKSEDFDHRNNLIDQLARKMYLESSLSGVKGWRNEKYAV---WvNKKPYVLVERAVAGVLGI 153
Cdd:pfam15916  42 FPDVFRVSPDAVSLNPSLRTYEERSAAVAEVLRELREEGSFVTLPGWRDECYEVrasF-GDPPLFKMERAAAPLFGV 117
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
158-289 2.49e-05

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 44.03  E-value: 2.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 158 IHIngYVLDPKSkkvQFWVPRRSKTKQTWPLMLDNIIAGGLGYPYGIYETVLKESMEEANLEksvIEDNIKATGSVSYly 237
Cdd:COG1443   32 FSV--FVFNSDG---RLLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEAAVRELEEELGIT---VDDDLRPLGTFRY-- 101
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 398365589 238 ftgdisvtKFNKESDFIVGEVQYVYDLKLSEDiiPKPNDGEVESFNLFSLQE 289
Cdd:COG1443  102 --------RAVDANGLVENEFCHVFVARLDGP--LTPQPEEVAEVRWVTLEE 143
 
Name Accession Description Interval E-value
NUDIX_Tnr3_like cd03676
thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a ...
150-314 1.46e-76

thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins; Tnr3 is a bifunctional enzyme composed of a C-terminal thiamine pyrophosphokinase domain, which transfers pyrophosphate from ATP to thiamine and an N-terminal NUDIX hydrolase domain that converts oxidized derivatives of thiamine diphosphate (oxothiamine and oxythiamine) to their respective monophosphates. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467544  Cd Length: 153  Bit Score: 232.00  E-value: 1.46e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 150 VLGIITYGIHINGYVLDPKSKKvqFWVPRRSKTKQTWPLMLDNIIAGGLGYPYGIYETVLKESMEEANLEKSVIEDNIKA 229
Cdd:cd03676    1 LFGIVTYGVHLNGYVRDGDGLR--LWVARRSATKATYPGKLDNLVAGGVPAGESPLETLVREAEEEAGLPEDLARQARPA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 230 TGSVSYLYFTGDisvtkfnkesDFIVGEVQYVYDLKLSEDIIPKPNDGEVESFNLFSLQETINALRKKEFKPNCALVMVD 309
Cdd:cd03676   79 AGRVSYFYRSDE----------GGLQPEVLYVYDLELPEDFVPKPQDGEVESFELMSVDEVLEALRAGEFKPNCALVMLD 148

                 ....*
gi 398365589 310 FLIRH 314
Cdd:cd03676  149 FLIRH 153
PLN02839 PLN02839
nudix hydrolase
123-335 1.01e-47

nudix hydrolase


Pssm-ID: 178432 [Multi-domain]  Cd Length: 372  Bit Score: 164.81  E-value: 1.01e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 123 VKGWRNEKYAV--WVNKKPYVLVERAVAGVLGIITYGIHINGYVldPKSKKVQFWVPRRSKTKQTWPLMLDNIIAGGLgy 200
Cdd:PLN02839 169 IPGIRNELYPVkpSFNAPVFFSLERAAAPYFGIKGYGVHMNGYV--ERDGQKFLWIGKRSLSKSTYPGMLDHLVAGGL-- 244
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 201 PYGIY--ETVLKESMEEANLEKsVIEDNIKATGSVSYLyftgDISVTKFNKEsdfivgeVQYVYDLKLSEDIIPKPNDGE 278
Cdd:PLN02839 245 PHGIScgENLVKECEEEAGISK-AIADRAIAVGAVSYM----DIDQYCFKRD-------VLFCYDLELPQDFVPKNQDGE 312
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 398365589 279 VESFNLFSLQETINALRKKE-FKPNCALVMVDFLIRHGYITPENePNYLELVTRMHRR 335
Cdd:PLN02839 313 VESFKLIPVAQVANVIRKTSfFKANCSLVIIDFLFRHGFIRPES-SGYLDLYRRLRNG 369
DUF4743 pfam15916
Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. ...
80-153 7.27e-06

Domain of unknown function (DUF4743); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with pfam00293.


Pssm-ID: 406365  Cd Length: 119  Bit Score: 44.49  E-value: 7.27e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398365589   80 FEETFQLDESRHELRFKSEDFDHRNNLIDQLARKMYLESSLSGVKGWRNEKYAV---WvNKKPYVLVERAVAGVLGI 153
Cdd:pfam15916  42 FPDVFRVSPDAVSLNPSLRTYEERSAAVAEVLRELREEGSFVTLPGWRDECYEVrasF-GDPPLFKMERAAAPLFGV 117
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
158-289 2.49e-05

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 44.03  E-value: 2.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 158 IHIngYVLDPKSkkvQFWVPRRSKTKQTWPLMLDNIIAGGLGYPYGIYETVLKESMEEANLEksvIEDNIKATGSVSYly 237
Cdd:COG1443   32 FSV--FVFNSDG---RLLLQRRALTKDHWPGLWDNTVCGHPRAGETYEEAAVRELEEELGIT---VDDDLRPLGTFRY-- 101
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 398365589 238 ftgdisvtKFNKESDFIVGEVQYVYDLKLSEDiiPKPNDGEVESFNLFSLQE 289
Cdd:COG1443  102 --------RAVDANGLVENEFCHVFVARLDGP--LTPQPEEVAEVRWVTLEE 143
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
160-224 4.72e-04

NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus radiodurans protein DR_0079 is one of 21 NUDIX hydrolases that it encodes, and it has been observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP), and for their corresponding deoxyribose nucleotides, dCDP and dCTP, to a lesser degree. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467602 [Multi-domain]  Cd Length: 121  Bit Score: 39.51  E-value: 4.72e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398365589 160 INGYVLDPKSkkvQFWVPRRSKTKQTWPLMLDNIIAG----GLGYpygiYETVLKESMEEANLEKSVIE 224
Cdd:cd24154    5 VNAFLINSQG---QLWIPRRTADKRIFPLALDMSVGGhvssGETY----EQAFVRELQEELNLDLDQLS 66
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
143-301 1.59e-03

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467578 [Multi-domain]  Cd Length: 157  Bit Score: 38.75  E-value: 1.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 143 VERAVA---GVLGIITYGIhingyVLDPKSKkvqFWVPRRSKTKQTWPLMLDNIIAGGLGYPYGIYETVLKESMEEANLe 219
Cdd:cd04697   14 ATRAEMrrqKLIHRATYIV-----VRNAAGR---LLVQKRTMDKDYCPGYLDPATGGVVGAGESYEENARRELEEELGI- 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365589 220 ksvieDNIKATGSVSYlYFTGDISvtkfnkesdFIVGEVQY-VYDLKLsediipKPNDGEVESFNLFSLQETINALRKKE 298
Cdd:cd04697   85 -----DGVPLRPLFTF-YYEDDRS---------RVWGALFEcVYDGPL------KLQPEEVAEVDWMSEDEILQAARGEE 143

                 ...
gi 398365589 299 FKP 301
Cdd:cd04697  144 FTP 146
 
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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