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Conserved domains on  [gi|857869626|emb|CDT22412|]
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Translation initiation inhibitor, yjgF family [Vibrio coralliirubri]

Protein Classification

RidA family protein( domain architecture ID 10150280)

RidA (reactive intermediate/imine deaminase A) family protein similar to 2-iminobutanoate/2-iminopropanoate deaminase, which catalyzes the deamination of enamine/imine intermediates to yield 2-ketobutyrate and ammonia

CATH:  3.30.1330.40
PubMed:  14624641

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
9-113 2.26e-57

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


:

Pssm-ID: 100007  Cd Length: 105  Bit Score: 172.34  E-value: 2.26e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626   9 QRMSRIVKHNGTIYLCGQVCADATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVPEGH 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFAAMNAVWDAWVPPGH 80
                         90       100
                 ....*....|....*....|....*
gi 857869626  89 APARACVTGDMAREALLVEISVIAA 113
Cdd:cd06150   81 APARACVEAKLADPGYLVEIVVTAA 105
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
9-113 2.26e-57

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100007  Cd Length: 105  Bit Score: 172.34  E-value: 2.26e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626   9 QRMSRIVKHNGTIYLCGQVCADATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVPEGH 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFAAMNAVWDAWVPPGH 80
                         90       100
                 ....*....|....*....|....*
gi 857869626  89 APARACVTGDMAREALLVEISVIAA 113
Cdd:cd06150   81 APARACVEAKLADPGYLVEIVVTAA 105
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
11-113 3.85e-34

Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family [Defense mechanisms]; Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family is part of the Pathway/BioSystem: Pyrimidine degradation


Pssm-ID: 440021  Cd Length: 125  Bit Score: 114.50  E-value: 3.85e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  11 MSRIVKHNGTIYLCGQVCADA-----TQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVP 85
Cdd:COG0251   17 YSQAVRVGNLVFVSGQVPLDPdtgelGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTDMADFAAVNEVYAEYFG 96
                         90       100
                 ....*....|....*....|....*....
gi 857869626  86 EgHAPARACV-TGDMAREAlLVEISVIAA 113
Cdd:COG0251   97 E-GRPARTAVgVAALPKGA-LVEIEAIAA 123
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
10-113 9.43e-28

Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA. Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella.


Pssm-ID: 426010  Cd Length: 117  Bit Score: 98.14  E-value: 9.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626   10 RMSRIVKHNGTIYLCGQVCAD------ATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAW 83
Cdd:pfam01042   8 PYSQAVKAGNLVYVSGQIPLDpdtgklVEGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEVNEVYAEY 87
                          90       100       110
                  ....*....|....*....|....*....|.
gi 857869626   84 VPEGHAPARACV-TGDMAREAlLVEISVIAA 113
Cdd:pfam01042  88 FDADKAPARSAVgVAALPLGA-LVEIEAIAV 117
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
12-114 2.04e-19

reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of protein synthesis intiation, then as an endoribonuclease active on single-stranded mRNA, endoribonuclease L-PSP. Members of this family, conserved in all domains of life and often with several members per bacterial genome, appear to catalyze a reaction that minimizes toxic by-products from reactions catalyzed by pyridoxal phosphate-dependent enzymes. [Cellular processes, Other]


Pssm-ID: 129116  Cd Length: 124  Bit Score: 76.95  E-value: 2.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626   12 SRIVKHNGTIYLCGQVCAD------ATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVP 85
Cdd:TIGR00004  17 SQAVKVGNTVYVSGQIPLDpstgelVGGDIAEQAEQVLENLKAILEAAGLSLDDVVKTTVFLTDLNDFAEVNEVYGQYFD 96
                          90       100       110
                  ....*....|....*....|....*....|.
gi 857869626   86 EgHAPARACVtgDMAR--EALLVEISVIAAE 114
Cdd:TIGR00004  97 E-HYPARSAV--QVAAlpKGVLVEIEAIAVK 124
PRK11401 PRK11401
enamine/imine deaminase;
11-112 1.25e-07

enamine/imine deaminase;


Pssm-ID: 105214  Cd Length: 129  Bit Score: 46.60  E-value: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  11 MSRIVKHNGTIYLCGQVcADATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVPEGHA- 89
Cdd:PRK11401  23 LGSMVFTSGQIPVCPQT-GEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQAt 101
                         90       100
                 ....*....|....*....|....
gi 857869626  90 -PARACVTGDMAREALLVEISVIA 112
Cdd:PRK11401 102 yPTRSCVQVARLPKDVKLEIEAIA 125
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
9-113 2.26e-57

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100007  Cd Length: 105  Bit Score: 172.34  E-value: 2.26e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626   9 QRMSRIVKHNGTIYLCGQVCADATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVPEGH 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFAAMNAVWDAWVPPGH 80
                         90       100
                 ....*....|....*....|....*
gi 857869626  89 APARACVTGDMAREALLVEISVIAA 113
Cdd:cd06150   81 APARACVEAKLADPGYLVEIVVTAA 105
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
11-112 2.08e-35

YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100004 [Multi-domain]  Cd Length: 107  Bit Score: 116.89  E-value: 2.08e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  11 MSRIVKHNGTIYLCGQVCADA-----TQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVP 85
Cdd:cd00448    1 YSQAVRVGNLVFVSGQIPLDPdgelvPGDIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFAAVNEVYDEFFG 80
                         90       100
                 ....*....|....*....|....*..
gi 857869626  86 EGHAPARACVTGDMAREALLVEISVIA 112
Cdd:cd00448   81 EGPPPARTAVGVAALPPGALVEIEAIA 107
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
11-113 3.85e-34

Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family [Defense mechanisms]; Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family is part of the Pathway/BioSystem: Pyrimidine degradation


Pssm-ID: 440021  Cd Length: 125  Bit Score: 114.50  E-value: 3.85e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  11 MSRIVKHNGTIYLCGQVCADA-----TQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVP 85
Cdd:COG0251   17 YSQAVRVGNLVFVSGQVPLDPdtgelGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTDMADFAAVNEVYAEYFG 96
                         90       100
                 ....*....|....*....|....*....
gi 857869626  86 EgHAPARACV-TGDMAREAlLVEISVIAA 113
Cdd:COG0251   97 E-GRPARTAVgVAALPKGA-LVEIEAIAA 123
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
10-113 9.43e-28

Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA. Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella.


Pssm-ID: 426010  Cd Length: 117  Bit Score: 98.14  E-value: 9.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626   10 RMSRIVKHNGTIYLCGQVCAD------ATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAW 83
Cdd:pfam01042   8 PYSQAVKAGNLVYVSGQIPLDpdtgklVEGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEVNEVYAEY 87
                          90       100       110
                  ....*....|....*....|....*....|.
gi 857869626   84 VPEGHAPARACV-TGDMAREAlLVEISVIAA 113
Cdd:pfam01042  88 FDADKAPARSAVgVAALPLGA-LVEIEAIAV 117
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
12-114 2.04e-19

reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of protein synthesis intiation, then as an endoribonuclease active on single-stranded mRNA, endoribonuclease L-PSP. Members of this family, conserved in all domains of life and often with several members per bacterial genome, appear to catalyze a reaction that minimizes toxic by-products from reactions catalyzed by pyridoxal phosphate-dependent enzymes. [Cellular processes, Other]


Pssm-ID: 129116  Cd Length: 124  Bit Score: 76.95  E-value: 2.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626   12 SRIVKHNGTIYLCGQVCAD------ATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVP 85
Cdd:TIGR00004  17 SQAVKVGNTVYVSGQIPLDpstgelVGGDIAEQAEQVLENLKAILEAAGLSLDDVVKTTVFLTDLNDFAEVNEVYGQYFD 96
                          90       100       110
                  ....*....|....*....|....*....|.
gi 857869626   86 EgHAPARACVtgDMAR--EALLVEISVIAAE 114
Cdd:TIGR00004  97 E-HYPARSAV--QVAAlpKGVLVEIEAIAVK 124
eu_AANH_C_1 cd06155
A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine ...
18-113 1.48e-12

A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100012  Cd Length: 101  Bit Score: 58.81  E-value: 1.48e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  18 NGTIYLCGQVCADATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVPEGHAPARACV-T 96
Cdd:cd06155    7 GGLLWISNVTASESDETVEEQMESIFSKLREILQSNGLSLSDILYVTLYLRDMSDFAEVNSVYGTFFDKPNPPSRVCVeC 86
                         90
                 ....*....|....*..
gi 857869626  97 GDmaREALLVEISVIAA 113
Cdd:cd06155   87 GL--PEGCDVQLSCVAA 101
YjgH_like cd02198
YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, ...
10-113 8.77e-11

YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100005  Cd Length: 111  Bit Score: 54.58  E-value: 8.77e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  10 RMSRIVKHNGTIYLCGQVCADAT----QDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDM-KDFQEMNAVWDAWV 84
Cdd:cd02198    2 GYSPAVRVGDTLFVSGQVGSDADgsvaEDFEAQFRLAFQNLGAVLEAAGCSFDDVVELTTFHVDMaAHLPAFAAVKDEYF 81
                         90       100       110
                 ....*....|....*....|....*....|
gi 857869626  85 PEGHaPARACV-TGDMAREALLVEISVIAA 113
Cdd:cd02198   82 KEPY-PAWTAVgVAWLARPGLLVEIKVVAV 110
YjgF_YER057c_UK114_like_6 cd06154
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
12-112 1.36e-08

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100011  Cd Length: 119  Bit Score: 48.70  E-value: 1.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  12 SRIVKHNGTIYLCGQVCADATQ-----DITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQemnAVWDA--WV 84
Cdd:cd06154   14 SRAVRVGNWVFVSGTTGYDYDGmvmpgDAYEQTRQCLEIIEAALAEAGASLEDVVRTRMYVTDIADFE---AVGRAhgEV 90
                         90       100
                 ....*....|....*....|....*....
gi 857869626  85 PEGHAPARACV-TGDMAREALLVEISVIA 112
Cdd:cd06154   91 FGDIRPAATMVvVSLLVDPEMLVEIEVTA 119
PRK11401 PRK11401
enamine/imine deaminase;
11-112 1.25e-07

enamine/imine deaminase;


Pssm-ID: 105214  Cd Length: 129  Bit Score: 46.60  E-value: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  11 MSRIVKHNGTIYLCGQVcADATQDITEQTQTMLDKVEALLEQAGSDKEHMLSATIYLKDMKDFQEMNAVWDAWVPEGHA- 89
Cdd:PRK11401  23 LGSMVFTSGQIPVCPQT-GEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQAt 101
                         90       100
                 ....*....|....*....|....
gi 857869626  90 -PARACVTGDMAREALLVEISVIA 112
Cdd:PRK11401 102 yPTRSCVQVARLPKDVKLEIEAIA 125
YjgF_YER057c_UK114_like_5 cd06153
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
34-112 3.59e-07

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100010  Cd Length: 114  Bit Score: 44.94  E-value: 3.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857869626  34 DITEQTQTMLDKVEALLEQAG-----SDKEHMLSATIYLKDMKDFQEMNAVWDAWVPEGHApaRACVTGDMAREALLVEI 108
Cdd:cd06153   33 DVEAQTRETLENIEALLEAAGrgggaQFLADLLRLKVYLRDREDLPAVRAILAARLGPAVP--AVFLQADVCRPDLLVEI 110

                 ....
gi 857869626 109 SVIA 112
Cdd:cd06153  111 EAVA 114
 
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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