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Conserved domains on  [gi|488642079|ref|WP_002578722|]
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MULTISPECIES: aminoglycoside nucleotidyltransferase ANT(9) [Bacteria]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13746 super family cl32927
aminoglycoside resistance protein; Provisional
 9-256 3.62e-73

aminoglycoside resistance protein; Provisional


The actual alignment was detected with superfamily member PRK13746:

Pssm-ID: 184296 [Multi-domain]  Cd Length: 262  Bit Score: 224.13  E-value: 3.62e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   9 QVNQVISIAETILQGQILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGSVGCIE-KRPLEVTII 87
Cdd:PRK13746  12 QLSEACAVIERHLEPTLLAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDETTRRALMNDLLEVSAPPGESEiLRALEVTVV 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079  88 NQSDIVPLQFPPKCQYMYGEWLRGEMEAGEYPQACNDPDIMILLWQARKNSITLKGAESKELIPAIPFHEIKKAIRFSLP 167
Cdd:PRK13746  92 VHDDVVPWRYPAKRELQFGEWLRNDILAGIFEPAMIDHDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALRDTLA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079 168 GLISS--FKGDERNVLLTLSRMWFTLVTEEITTKDVAAKWVILKLPERFPPLLTTAKEAYLGNLSDEWETVEKEAMALVE 245
Cdd:PRK13746 172 LWNSPpdWAGDERNVVLTLARIWYSASTGKIAPKDVAADWALERLPAEYQPVLLEARQAYLGQEEDDLASRADALEAFVR 251

                        250
                 ....*....|.
gi 488642079 246 YMKKQIEELLR 256
Cdd:PRK13746 252 YAKGEIEKVVG 262
 
Name Accession Description Interval E-value
PRK13746 PRK13746
aminoglycoside resistance protein; Provisional
 9-256 3.62e-73

aminoglycoside resistance protein; Provisional


Pssm-ID: 184296 [Multi-domain]  Cd Length: 262  Bit Score: 224.13  E-value: 3.62e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   9 QVNQVISIAETILQGQILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGSVGCIE-KRPLEVTII 87
Cdd:PRK13746  12 QLSEACAVIERHLEPTLLAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDETTRRALMNDLLEVSAPPGESEiLRALEVTVV 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079  88 NQSDIVPLQFPPKCQYMYGEWLRGEMEAGEYPQACNDPDIMILLWQARKNSITLKGAESKELIPAIPFHEIKKAIRFSLP 167
Cdd:PRK13746  92 VHDDVVPWRYPAKRELQFGEWLRNDILAGIFEPAMIDHDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALRDTLA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079 168 GLISS--FKGDERNVLLTLSRMWFTLVTEEITTKDVAAKWVILKLPERFPPLLTTAKEAYLGNLSDEWETVEKEAMALVE 245
Cdd:PRK13746 172 LWNSPpdWAGDERNVVLTLARIWYSASTGKIAPKDVAADWALERLPAEYQPVLLEARQAYLGQEEDDLASRADALEAFVR 251

                        250
                 ....*....|.
gi 488642079 246 YMKKQIEELLR 256
Cdd:PRK13746 252 YAKGEIEKVVG 262
DUF4111 pfam13427
Domain of unknown function (DUF4111); Although the exact function of this domain is not known ...
 148-249 7.98e-31

Domain of unknown function (DUF4111); Although the exact function of this domain is not known it frequently appears downstream of the family Nucleotidyltransferase, pfam01909. It is also found in species associated with methicillin-resistant bacteria.


Pssm-ID: 433197  Cd Length: 102  Bit Score: 110.37  E-value: 7.98e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079  148 ELIPAIPFHEIKKAIRFSLPGLISSFKGDERNVLLTLSRMWFTLVTEEITTKDVAAKWVILKLPERFPPLLTTAKEAYLG 227
Cdd:pfam13427   1 EVFPPVPRADYRDAILADVPELLEEIEEDPRYVVLTLARVWATLETGEILSKDEAAEWALPRLPKEYRPLLAQARDAYLG 80

                          90       100
                  ....*....|....*....|..
gi 488642079  228 NLSDEWETVEKEAMALVEYMKK 249
Cdd:pfam13427  81 GAEEDWDGDREELEEFADYMLA 102
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
7-97 1.23e-12

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


Pssm-ID: 441314  Cd Length: 95  Bit Score: 62.35  E-value: 1.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   7 PQQVNQVISIAETILQ--GQILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGsvgciekRPLEV 84
Cdd:COG1708    2 STLLRELLEEIVEALRrgPEVAAVYLFGSYARGDARPDSDIDLLVVVDDPPLPDERLELLADLLRELG-------LPVDL 74

                         90
                 ....*....|...
gi 488642079  85 TIINQSDIVPLQF 97
Cdd:COG1708   75 VVLTPAELELRLF 87
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 8-97 2.66e-10

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: 55.89  E-value: 2.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   8 QQVNQVISIAETILQGqILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGsvgciekRPLEVTII 87
Cdd:cd05403    2 EILEEILEILRELLGG-VEKVYLFGSYARGDARPDSDIDLLVIFDDPLDPLELARLLEELELLLG-------RPVDLVVL 73

                         90
                 ....*....|
gi 488642079  88 NQSDIVPLQF 97
Cdd:cd05403   74 NALELELLLR 83
 
Name Accession Description Interval E-value
PRK13746 PRK13746
aminoglycoside resistance protein; Provisional
 9-256 3.62e-73

aminoglycoside resistance protein; Provisional


Pssm-ID: 184296 [Multi-domain]  Cd Length: 262  Bit Score: 224.13  E-value: 3.62e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   9 QVNQVISIAETILQGQILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGSVGCIE-KRPLEVTII 87
Cdd:PRK13746  12 QLSEACAVIERHLEPTLLAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDETTRRALMNDLLEVSAPPGESEiLRALEVTVV 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079  88 NQSDIVPLQFPPKCQYMYGEWLRGEMEAGEYPQACNDPDIMILLWQARKNSITLKGAESKELIPAIPFHEIKKAIRFSLP 167
Cdd:PRK13746  92 VHDDVVPWRYPAKRELQFGEWLRNDILAGIFEPAMIDHDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALRDTLA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079 168 GLISS--FKGDERNVLLTLSRMWFTLVTEEITTKDVAAKWVILKLPERFPPLLTTAKEAYLGNLSDEWETVEKEAMALVE 245
Cdd:PRK13746 172 LWNSPpdWAGDERNVVLTLARIWYSASTGKIAPKDVAADWALERLPAEYQPVLLEARQAYLGQEEDDLASRADALEAFVR 251

                        250
                 ....*....|.
gi 488642079 246 YMKKQIEELLR 256
Cdd:PRK13746 252 YAKGEIEKVVG 262
DUF4111 pfam13427
Domain of unknown function (DUF4111); Although the exact function of this domain is not known ...
 148-249 7.98e-31

Domain of unknown function (DUF4111); Although the exact function of this domain is not known it frequently appears downstream of the family Nucleotidyltransferase, pfam01909. It is also found in species associated with methicillin-resistant bacteria.


Pssm-ID: 433197  Cd Length: 102  Bit Score: 110.37  E-value: 7.98e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079  148 ELIPAIPFHEIKKAIRFSLPGLISSFKGDERNVLLTLSRMWFTLVTEEITTKDVAAKWVILKLPERFPPLLTTAKEAYLG 227
Cdd:pfam13427   1 EVFPPVPRADYRDAILADVPELLEEIEEDPRYVVLTLARVWATLETGEILSKDEAAEWALPRLPKEYRPLLAQARDAYLG 80

                          90       100
                  ....*....|....*....|..
gi 488642079  228 NLSDEWETVEKEAMALVEYMKK 249
Cdd:pfam13427  81 GAEEDWDGDREELEEFADYMLA 102
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
7-97 1.23e-12

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


Pssm-ID: 441314  Cd Length: 95  Bit Score: 62.35  E-value: 1.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   7 PQQVNQVISIAETILQ--GQILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGsvgciekRPLEV 84
Cdd:COG1708    2 STLLRELLEEIVEALRrgPEVAAVYLFGSYARGDARPDSDIDLLVVVDDPPLPDERLELLADLLRELG-------LPVDL 74

                         90
                 ....*....|...
gi 488642079  85 TIINQSDIVPLQF 97
Cdd:COG1708   75 VVLTPAELELRLF 87
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 8-97 2.66e-10

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: 55.89  E-value: 2.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   8 QQVNQVISIAETILQGqILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGsvgciekRPLEVTII 87
Cdd:cd05403    2 EILEEILEILRELLGG-VEKVYLFGSYARGDARPDSDIDLLVIFDDPLDPLELARLLEELELLLG-------RPVDLVVL 73

                         90
                 ....*....|
gi 488642079  88 NQSDIVPLQF 97
Cdd:cd05403   74 NALELELLLR 83
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 11-93 7.89e-09

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: 51.76  E-value: 7.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488642079   11 NQVISIAETilQGQILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISGsvgcieKRPLEVTIINQS 90
Cdd:pfam18765   1 EKIKEILKK--NPEIEAAYLFGSRAKGDAREDSDIDLAVLYDEKLDFEELLELASELEDILL------LRKVDLVDLNKA 72


                  ...
gi 488642079   91 DIV 93
Cdd:pfam18765  73 PPV 75
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
1-72 1.80e-04

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 39.51  E-value: 1.80e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488642079   1 MNINEFPQQVNQVISIAETILQgqILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISG 72
Cdd:COG1669    1 MNREEILEILREVIEELAERYG--VSRLGLFGSVARGEAREDSDIDLLVEFDEPTSLFDLFELEEELEELLG 70
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 23-93 1.70e-03

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: 36.62  E-value: 1.70e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488642079   23 GQILGIYLYGSATMNGLRPDSDIDILIITKQELSNSIRADLTKQLLKISgsvgciEKRPLEVTIINQSDIV 93
Cdd:pfam01909  12 FPVAEVVLFGSYARGTALPGSDIDLLVVFPEPVEEERLLKLAKIIKELE------ELLGLEVDLVTREKIE 76
 
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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