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Conserved domains on  [gi|502731563|ref|WP_012966547|]
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nucleotidyltransferase domain-containing protein [Ferroglobus placidus]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 16068202)

nucleotidyltransferase domain-containing protein similar to Methanocaldococcus jannaschii MJ1547, a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and a cognate MNT (minimal nucleotidyltransferase) domain-containing toxin-antitoxin system

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 9-94 4.25e-22

Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in polymorphic toxins (NTox45) and polyvalent proteins.


:

Pssm-ID: 465859  Cd Length: 93  Bit Score: 82.96  E-value: 4.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563    9 KIIETIKSHPNVIAIYLFGSHAKGETTPLSDIDIAVIL-ENPTPESEADIGS-----LSSPEIDVVLFHRLPLHIKYEVF 82
Cdd:pfam18765   2 KIKEILKKNPEIEAAYLFGSRAKGDAREDSDIDLAVLYdEKLDFEELLELASelediLLLRKVDLVDLNKAPPVLAHQIL 81

                          90
                  ....*....|..
gi 502731563   83 KYGKEIFVRDEE 94
Cdd:pfam18765  82 KEGKLLYSRDEE 93
 
Name Accession Description Interval E-value
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 9-94 4.25e-22

Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in polymorphic toxins (NTox45) and polyvalent proteins.


Pssm-ID: 465859  Cd Length: 93  Bit Score: 82.96  E-value: 4.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563    9 KIIETIKSHPNVIAIYLFGSHAKGETTPLSDIDIAVIL-ENPTPESEADIGS-----LSSPEIDVVLFHRLPLHIKYEVF 82
Cdd:pfam18765   2 KIKEILKKNPEIEAAYLFGSRAKGDAREDSDIDLAVLYdEKLDFEELLELASelediLLLRKVDLVDLNKAPPVLAHQIL 81

                          90
                  ....*....|..
gi 502731563   83 KYGKEIFVRDEE 94
Cdd:pfam18765  82 KEGKLLYSRDEE 93
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
2-85 3.40e-17

Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];


Pssm-ID: 441314  Cd Length: 95  Bit Score: 70.83  E-value: 3.40e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563   2 EPNPKISKIIETIKSHPNVIAIYLFGSHAKGETTPLSDIDIAVILENPTPESE-----ADIGSLSSPEIDVVLFHRLPL- 75
Cdd:COG1708    4 LLRELLEEIVEALRRGPEVAAVYLFGSYARGDARPDSDIDLLVVVDDPPLPDErlellADLLRELGLPVDLVVLTPAELe 83

                         90
                 ....*....|..
gi 502731563  76 --HIKYEVFKYG 85
Cdd:COG1708   84 lrLFLREILREG 95
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 4-90 2.40e-15

Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is related to the substrate-binding domain of S. aureus KNTase. The genes encoding HI0073 and HI0074 form an operon. Little is known about the substrate specificity or function of two-component NTs. The characterized members of this subgroup may not be representive of the function of this subgroup. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, co-ordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.


Pssm-ID: 143393  Cd Length: 93  Bit Score: 65.90  E-value: 2.40e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563   4 NPKISKIIETIKSHP-NVIAIYLFGSHAKGETTPLSDIDIAVILENPTPESEADIG-----SLSSPEIDVVLFHRLPLHI 77
Cdd:cd05403    1 EEILEEILEILRELLgGVEKVYLFGSYARGDARPDSDIDLLVIFDDPLDPLELARLleeleLLLGRPVDLVVLNALELEL 80

                         90
                 ....*....|...
gi 502731563  78 KYEVFKYGKEIFV 90
Cdd:cd05403   81 LLRILIEGEGIYL 93
PRK13746 PRK13746
aminoglycoside resistance protein; Provisional
 2-53 1.74e-03

aminoglycoside resistance protein; Provisional


Pssm-ID: 184296 [Multi-domain]  Cd Length: 262  Bit Score: 36.54  E-value: 1.74e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 502731563   2 EPNPKISKIIETIKSH--PNVIAIYLFGSHAKGETTPLSDIDIAVILENPTPES 53
Cdd:PRK13746   8 EISTQLSEACAVIERHlePTLLAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDET 61
CBASS_cyclase_b NF041117
CBASS oligonucleotide cyclase;
6-48 6.53e-03

CBASS oligonucleotide cyclase;


Pssm-ID: 469040  Cd Length: 273  Bit Score: 34.88  E-value: 6.53e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 502731563   6 KISKIIETIKSHPN-VIAIY---LFGSHAKG-ETTPLSDIDIAVILEN 48
Cdd:NF041117  17 LASERLDEIRDALEeEIEIEddfLFGSYRRHtKTKGLSDVDILVVLND 64
 
Name Accession Description Interval E-value
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 9-94 4.25e-22

Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in polymorphic toxins (NTox45) and polyvalent proteins.


Pssm-ID: 465859  Cd Length: 93  Bit Score: 82.96  E-value: 4.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563    9 KIIETIKSHPNVIAIYLFGSHAKGETTPLSDIDIAVIL-ENPTPESEADIGS-----LSSPEIDVVLFHRLPLHIKYEVF 82
Cdd:pfam18765   2 KIKEILKKNPEIEAAYLFGSRAKGDAREDSDIDLAVLYdEKLDFEELLELASelediLLLRKVDLVDLNKAPPVLAHQIL 81

                          90
                  ....*....|..
gi 502731563   83 KYGKEIFVRDEE 94
Cdd:pfam18765  82 KEGKLLYSRDEE 93
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
2-85 3.40e-17

Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];


Pssm-ID: 441314  Cd Length: 95  Bit Score: 70.83  E-value: 3.40e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563   2 EPNPKISKIIETIKSHPNVIAIYLFGSHAKGETTPLSDIDIAVILENPTPESE-----ADIGSLSSPEIDVVLFHRLPL- 75
Cdd:COG1708    4 LLRELLEEIVEALRRGPEVAAVYLFGSYARGDARPDSDIDLLVVVDDPPLPDErlellADLLRELGLPVDLVVLTPAELe 83

                         90
                 ....*....|..
gi 502731563  76 --HIKYEVFKYG 85
Cdd:COG1708   84 lrLFLREILREG 95
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
6-88 3.48e-16

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 68.02  E-value: 3.48e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563   6 KISKIIETIKSHPNVIAIYLFGSHAKGETTPLSDIDIAVILENPTPESE-----ADIGSLSSPEIDVVLFHRLPLHIKYE 80
Cdd:COG1669    9 ILREVIEELAERYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTSLFDlfeleEELEELLGRKVDLVTLDGLSPRLRER 88


                 ....*...
gi 502731563  81 VFKYGKEI 88
Cdd:COG1669   89 ILKEGVLL 96
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 4-90 2.40e-15

Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is related to the substrate-binding domain of S. aureus KNTase. The genes encoding HI0073 and HI0074 form an operon. Little is known about the substrate specificity or function of two-component NTs. The characterized members of this subgroup may not be representive of the function of this subgroup. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, co-ordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.


Pssm-ID: 143393  Cd Length: 93  Bit Score: 65.90  E-value: 2.40e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502731563   4 NPKISKIIETIKSHP-NVIAIYLFGSHAKGETTPLSDIDIAVILENPTPESEADIG-----SLSSPEIDVVLFHRLPLHI 77
Cdd:cd05403    1 EEILEEILEILRELLgGVEKVYLFGSYARGDARPDSDIDLLVIFDDPLDPLELARLleeleLLLGRPVDLVVLNALELEL 80

                         90
                 ....*....|...
gi 502731563  78 KYEVFKYGKEIFV 90
Cdd:cd05403   81 LLRILIEGEGIYL 93
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 7-70 1.16e-09

Nucleotidyltransferase domain; Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.


Pssm-ID: 396474  Cd Length: 91  Bit Score: 51.26  E-value: 1.16e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 502731563    7 ISKIIETIKSHPNVIAIYLFGSHAKGETTPLSDIDIAVILENPTPESEAD--------IGSLSSPEIDVVLF 70
Cdd:pfam01909   1 LRKLREILKELFPVAEVVLFGSYARGTALPGSDIDLLVVFPEPVEEERLLklakiikeLEELLGLEVDLVTR 72
PRK13746 PRK13746
aminoglycoside resistance protein; Provisional
 2-53 1.74e-03

aminoglycoside resistance protein; Provisional


Pssm-ID: 184296 [Multi-domain]  Cd Length: 262  Bit Score: 36.54  E-value: 1.74e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 502731563   2 EPNPKISKIIETIKSH--PNVIAIYLFGSHAKGETTPLSDIDIAVILENPTPES 53
Cdd:PRK13746   8 EISTQLSEACAVIERHlePTLLAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDET 61
PRK05007 PRK05007
bifunctional uridylyltransferase/uridylyl-removing protein GlnD;
21-60 5.84e-03

bifunctional uridylyltransferase/uridylyl-removing protein GlnD;


Pssm-ID: 235329 [Multi-domain]  Cd Length: 884  Bit Score: 35.34  E-value: 5.84e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 502731563  21 IAIYLFGSHAKGETTPLSDIDIAVILENP-TPESEADIGSL 60
Cdd:PRK05007  81 LALVAVGGYGRGELHPLSDIDLLILSRKKlPDEQAQKVGEL 121
CBASS_cyclase_b NF041117
CBASS oligonucleotide cyclase;
6-48 6.53e-03

CBASS oligonucleotide cyclase;


Pssm-ID: 469040  Cd Length: 273  Bit Score: 34.88  E-value: 6.53e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 502731563   6 KISKIIETIKSHPN-VIAIY---LFGSHAKG-ETTPLSDIDIAVILEN 48
Cdd:NF041117  17 LASERLDEIRDALEeEIEIEddfLFGSYRRHtKTKGLSDVDILVVLND 64
 
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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