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Conserved domains on  [gi|493798192|ref|WP_006746165|]
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nucleotidyltransferase domain-containing protein [Thioalkalivibrio paradoxus]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 14395937)

nucleotidyltransferase domain-containing protein similar to Haemophilus influenzae HI0073, which is the the nucleotide-binding component of a two-protein nucleotidyltransferase

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 ...
 8-52 2.34e-06

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: 42.90  E-value: 2.34e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 493798192    8 DVFESEPDLELAILIGSRQRGAATPASDWDFAIQWARHFGFTETL 52
Cdd:pfam18765   5 EILKKNPEIEAAYLFGSRAKGDAREDSDIDLAVLYDEKLDFEELL 49
MJ0435 super family cl41953
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
2-96 2.78e-06

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


The actual alignment was detected with superfamily member COG1669:

Pssm-ID: 441275  Cd Length: 96  Bit Score: 42.59  E-value: 2.78e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493798192   2 ELQLVRDVFESEPDLELAILIGSRQRGAATPASDWDFAIQWARHFGFTETLaateGLRHRLAKVLDVapaRIDLIDLAAA 81
Cdd:COG1669    9 ILREVIEELAERYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTSLFDLF----ELEEELEELLGR---KVDLVTLDGL 81

                         90
                 ....*....|....*
gi 493798192  82 RLAIRAVVAEEGRLL 96
Cdd:COG1669   82 SPRLRERILKEGVLL 96
 
Name Accession Description Interval E-value
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 8-52 2.34e-06

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: 42.90  E-value: 2.34e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 493798192    8 DVFESEPDLELAILIGSRQRGAATPASDWDFAIQWARHFGFTETL 52
Cdd:pfam18765   5 EILKKNPEIEAAYLFGSRAKGDAREDSDIDLAVLYDEKLDFEELL 49
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
2-96 2.78e-06

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 42.59  E-value: 2.78e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493798192   2 ELQLVRDVFESEPDLELAILIGSRQRGAATPASDWDFAIQWARHFGFTETLaateGLRHRLAKVLDVapaRIDLIDLAAA 81
Cdd:COG1669    9 ILREVIEELAERYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTSLFDLF----ELEEELEELLGR---KVDLVTLDGL 81

                         90
                 ....*....|....*
gi 493798192  82 RLAIRAVVAEEGRLL 96
Cdd:COG1669   82 SPRLRERILKEGVLL 96
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
3-76 3.61e-06

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


Pssm-ID: 441314  Cd Length: 95  Bit Score: 42.32  E-value: 3.61e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493798192   3 LQLVRDVFESEPDLELAILIGSRQRGAATPASDWDFAIqwarhfgFTETLAATEGLRHRLAKVLDVAPARIDLI 76
Cdd:COG1708    9 LEEIVEALRRGPEVAAVYLFGSYARGDARPDSDIDLLV-------VVDDPPLPDERLELLADLLRELGLPVDLV 75
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 4-94 7.98e-04

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: 36.24  E-value: 7.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493798192   4 QLVRDVFESEPDLELAILIGSRQRGAATPASDWDFAIqwarhfgFTETLAATEGLRHRLAKVLDVAPARIDLIDLAAARL 83
Cdd:cd05403    6 EILEILRELLGGVEKVYLFGSYARGDARPDSDIDLLV-------IFDDPLDPLELARLLEELELLLGRPVDLVVLNALEL 78

                         90
                 ....*....|.
gi 493798192  84 AIRAVVAEEGR 94
Cdd:cd05403   79 ELLLRILIEGE 89
 
Name Accession Description Interval E-value
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 8-52 2.34e-06

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: 42.90  E-value: 2.34e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 493798192    8 DVFESEPDLELAILIGSRQRGAATPASDWDFAIQWARHFGFTETL 52
Cdd:pfam18765   5 EILKKNPEIEAAYLFGSRAKGDAREDSDIDLAVLYDEKLDFEELL 49
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
2-96 2.78e-06

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 42.59  E-value: 2.78e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493798192   2 ELQLVRDVFESEPDLELAILIGSRQRGAATPASDWDFAIQWARHFGFTETLaateGLRHRLAKVLDVapaRIDLIDLAAA 81
Cdd:COG1669    9 ILREVIEELAERYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTSLFDLF----ELEEELEELLGR---KVDLVTLDGL 81

                         90
                 ....*....|....*
gi 493798192  82 RLAIRAVVAEEGRLL 96
Cdd:COG1669   82 SPRLRERILKEGVLL 96
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
3-76 3.61e-06

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


Pssm-ID: 441314  Cd Length: 95  Bit Score: 42.32  E-value: 3.61e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493798192   3 LQLVRDVFESEPDLELAILIGSRQRGAATPASDWDFAIqwarhfgFTETLAATEGLRHRLAKVLDVAPARIDLI 76
Cdd:COG1708    9 LEEIVEALRRGPEVAAVYLFGSYARGDARPDSDIDLLV-------VVDDPPLPDERLELLADLLRELGLPVDLV 75
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 4-94 7.98e-04

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: 36.24  E-value: 7.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493798192   4 QLVRDVFESEPDLELAILIGSRQRGAATPASDWDFAIqwarhfgFTETLAATEGLRHRLAKVLDVAPARIDLIDLAAARL 83
Cdd:cd05403    6 EILEILRELLGGVEKVYLFGSYARGDARPDSDIDLLV-------IFDDPLDPLELARLLEELELLLGRPVDLVVLNALEL 78

                         90
                 ....*....|.
gi 493798192  84 AIRAVVAEEGR 94
Cdd:cd05403   79 ELLLRILIEGE 89
 
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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