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Conserved domains on  [gi|1034643406|ref|XP_016864477|]
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terminal nucleotidyltransferase 4A isoform X2 [Homo sapiens]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 1001423)

nucleotidyltransferase domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TRF4 super family cl34961
DNA polymerase sigma [Replication, recombination and repair];
2-286 8.17e-63

DNA polymerase sigma [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG5260:

Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 213.09  E-value: 8.17e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   2 RREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVV-----FGKWERPPLQLLEQALRKHNVAEpcsIKVLDKA 76
Cdd:COG5260    78 RKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIisdprGYKETRNAGSLASHLFKKNLAKE---VVVVSTA 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406  77 TVPIIKLTDQETEVKVDISFNMETGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQ 156
Cdd:COG5260   155 RVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQ 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406 157 LHP---RID--------ARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSgyRPSMLCIEDPL 225
Cdd:COG5260   235 MHPpflFFDngllsplkYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWLKPS--KPNSLSIQDPG 312

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034643406 226 L-PGNDVGRSSYGAMQVKQVFDYAYIVLsHAVSPLARSYPNRDA--ESTLGRIIKVTQEVIDYR 286
Cdd:COG5260   313 TdRNNDISAVSFNIKDIKAAFIRAFELL-SNKLFTLTSAIKHDAygLLIEFNEASYSNTSRSLK 375
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
2-286 8.17e-63

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 213.09  E-value: 8.17e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   2 RREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVV-----FGKWERPPLQLLEQALRKHNVAEpcsIKVLDKA 76
Cdd:COG5260    78 RKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIisdprGYKETRNAGSLASHLFKKNLAKE---VVVVSTA 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406  77 TVPIIKLTDQETEVKVDISFNMETGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQ 156
Cdd:COG5260   155 RVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQ 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406 157 LHP---RID--------ARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSgyRPSMLCIEDPL 225
Cdd:COG5260   235 MHPpflFFDngllsplkYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWLKPS--KPNSLSIQDPG 312

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034643406 226 L-PGNDVGRSSYGAMQVKQVFDYAYIVLsHAVSPLARSYPNRDA--ESTLGRIIKVTQEVIDYR 286
Cdd:COG5260   313 TdRNNDISAVSFNIKDIKAAFIRAFELL-SNKLFTLTSAIKHDAygLLIEFNEASYSNTSRSLK 375
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 1-112 6.54e-39

Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family 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, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved.


Pssm-ID: 143392 [Multi-domain]  Cd Length: 114  Bit Score: 137.69  E-value: 6.54e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   1 MRREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVVFG----KWERPPLQLLEQALRKHNvaEPCSIKVLDKA 76
Cdd:cd05402     1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGpnhrVDREDFLRKLAKLLKKSG--EVVEVEPIINA 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1034643406  77 TVPIIKLTDQETEVKVDISFNMETGVRAAEFIKNYM 112
Cdd:cd05402    79 RVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 169-229 5.73e-19

Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.


Pssm-ID: 427532  Cd Length: 60  Bit Score: 80.69  E-value: 5.73e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034643406 169 NLGMLLVEFFELYGRNFNYLKTGIRIKEGGaYIAKEEIMKAMTSGYRPSMLCIEDPLLPGN 229
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGG-ILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
2-286 8.17e-63

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 213.09  E-value: 8.17e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   2 RREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVV-----FGKWERPPLQLLEQALRKHNVAEpcsIKVLDKA 76
Cdd:COG5260    78 RKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIisdprGYKETRNAGSLASHLFKKNLAKE---VVVVSTA 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406  77 TVPIIKLTDQETEVKVDISFNMETGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQ 156
Cdd:COG5260   155 RVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQ 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406 157 LHP---RID--------ARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSgyRPSMLCIEDPL 225
Cdd:COG5260   235 MHPpflFFDngllsplkYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWLKPS--KPNSLSIQDPG 312

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034643406 226 L-PGNDVGRSSYGAMQVKQVFDYAYIVLsHAVSPLARSYPNRDA--ESTLGRIIKVTQEVIDYR 286
Cdd:COG5260   313 TdRNNDISAVSFNIKDIKAAFIRAFELL-SNKLFTLTSAIKHDAygLLIEFNEASYSNTSRSLK 375
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 1-112 6.54e-39

Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family 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, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved.


Pssm-ID: 143392 [Multi-domain]  Cd Length: 114  Bit Score: 137.69  E-value: 6.54e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   1 MRREVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVVFG----KWERPPLQLLEQALRKHNvaEPCSIKVLDKA 76
Cdd:cd05402     1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGpnhrVDREDFLRKLAKLLKKSG--EVVEVEPIINA 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1034643406  77 TVPIIKLTDQETEVKVDISFNMETGVRAAEFIKNYM 112
Cdd:cd05402    79 RVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 169-229 5.73e-19

Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.


Pssm-ID: 427532  Cd Length: 60  Bit Score: 80.69  E-value: 5.73e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034643406 169 NLGMLLVEFFELYGRNFNYLKTGIRIKEGGaYIAKEEIMKAMTSGYRPSMLCIEDPLLPGN 229
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGG-ILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 6-115 8.36e-14

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: 67.06  E-value: 8.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   6 VKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLEqalrkhnvaepcsikvldkaTVPIIKLTD 85
Cdd:pfam01909   1 LRKLREILKELFPVAEVVLFGSYARGTALPGSDIDLLVVFPEPVEEERLLK--------------------LAKIIKELE 60

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1034643406  86 QETEVKVDISFNMETGV-RAAEFIKNYMKKY 115
Cdd:pfam01909  61 ELLGLEVDLVTREKIEFpLVKIDILEERILL 91
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
3-78 4.65e-05

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


Pssm-ID: 441314  Cd Length: 95  Bit Score: 42.32  E-value: 4.65e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034643406   3 REVVKRIETVVKDLWPTADVQIFGSFSTGLYLPTSDIDL-VVFGKWERPP--LQLLEQALRKhnVAEPCSIKVLDKATV 78
Cdd:COG1708     6 RELLEEIVEALRRGPEVAAVYLFGSYARGDARPDSDIDLlVVVDDPPLPDerLELLADLLRE--LGLPVDLVVLTPAEL 82
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 3-93 1.76e-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: 40.48  E-value: 1.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   3 REVVKRIETVVKDLWptadvqIFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLE-QALRKHNVAEPCSIKVLDKATVPII 81
Cdd:cd05403     8 LEILRELLGGVEKVY------LFGSYARGDARPDSDIDLLVIFDDPLDPLELARlLEELELLLGRPVDLVVLNALELELL 81

                          90
                  ....*....|..
gi 1034643406  82 KLTDQETEVKVD 93
Cdd:cd05403    82 LRILIEGEGIYL 93
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
1-56 5.62e-04

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 39.13  E-value: 5.62e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   1 MRRE-VVKRIETVVKDL---WPTADVQIFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLE 56
Cdd:COG1669     1 MNREeILEILREVIEELaerYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTSLFDLFE 60
NT_2-5OAS_ClassI-CCAase cd05400
Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class ...
 2-94 2.64e-03

Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It 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, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this family.


Pssm-ID: 143390 [Multi-domain]  Cd Length: 143  Bit Score: 38.53  E-value: 2.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034643406   2 RREVVKRIETVVKDL--------WPTADVQIFGSFSTGLYL-PTSDIDLVVF---GKWERPP-----LQLLEQALRKHnv 64
Cdd:cd05400     2 LEEAKERYREIREALkeslselaGRVAEVFLQGSYARGTALrGDSDIDLVVVlpdDTSFAEYgpaelLDELGEALKEY-- 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1034643406  65 aEPCSIKVldKATVPIIKLTDQETEVKVDI 94
Cdd:cd05400    80 -YGANEEV--KAQHRSVTVKFKGQGFHVDV 106
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 24-82 6.38e-03

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: 35.97  E-value: 6.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034643406  24 IFGSFSTGLYLPTSDIDLVVFGKWERPPLQLLE--QALRKHNVAEPCSIKVLDKATVPIIK 82
Cdd:pfam18765  18 LFGSRAKGDAREDSDIDLAVLYDEKLDFEELLElaSELEDILLLRKVDLVDLNKAPPVLAH 78
 
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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