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Conserved domains on  [gi|1031985653|ref|NP_001313625|]
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terminal nucleotidyltransferase 4B [Danio rerio]

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];
168-440 1.48e-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: 218.10  E-value: 1.48e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 168 LHEEIKDFYEYISPRPEEEQMRHEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDLVVF----GNWETLPLWTLE 243
Cdd:COG5260    57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIIsdprGYKETRNAGSLA 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 244 EALRKRKVADEnsIKVLDKATVPIIKLMDSHTEVKVDISFNVQSGVKAANLIKDYKQQYPVLPYLVLVLKQFLLQRELNE 323
Cdd:COG5260   137 SHLFKKNLAKE--VVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALND 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 324 VFTGGIGSYSLFLMAVSFLQLHCREDVSSSN-----------PNLGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDE 392
Cdd:COG5260   215 VATGTLSSYTISCMVLSFLQMHPPFLFFDNGllsplkynkniDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYE 294

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1031985653 393 vqKSMLDGYRPSMLYIEDP-LQPGNDVGRSSYGAMQVKEAFDYAYVILS 440
Cdd:COG5260   295 --KGWLKPSKPNSLSIQDPgTDRNNDISAVSFNIKDIKAAFIRAFELLS 341
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
168-440 1.48e-63

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 218.10  E-value: 1.48e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 168 LHEEIKDFYEYISPRPEEEQMRHEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDLVVF----GNWETLPLWTLE 243
Cdd:COG5260    57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIIsdprGYKETRNAGSLA 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 244 EALRKRKVADEnsIKVLDKATVPIIKLMDSHTEVKVDISFNVQSGVKAANLIKDYKQQYPVLPYLVLVLKQFLLQRELNE 323
Cdd:COG5260   137 SHLFKKNLAKE--VVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALND 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 324 VFTGGIGSYSLFLMAVSFLQLHCREDVSSSN-----------PNLGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDE 392
Cdd:COG5260   215 VATGTLSSYTISCMVLSFLQMHPPFLFFDNGllsplkynkniDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYE 294

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1031985653 393 vqKSMLDGYRPSMLYIEDP-LQPGNDVGRSSYGAMQVKEAFDYAYVILS 440
Cdd:COG5260   295 --KGWLKPSKPNSLSIQDPgTDRNNDISAVSFNIKDIKAAFIRAFELLS 341
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 188-298 5.69e-36

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: 130.76  E-value: 5.69e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 188 MRHEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDLVVFGN----WETLPLWTLEEALRKRKVADEnsIKVLDKA 263
Cdd:cd05402     1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPnhrvDREDFLRKLAKLLKKSGEVVE--VEPIINA 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1031985653 264 TVPIIKLMDSHTEVKVDISFNVQSGVKAANLIKDY 298
Cdd:cd05402    79 RVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAY 113
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 356-416 5.05e-18

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: 78.38  E-value: 5.05e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1031985653 356 NLGVLLIEFFELYGRHFNYLKTGIRIKDGGsYVAKDEVQKSMLDGYRPSMLYIEDPLQPGN 416
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGG-ILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
PRK13300 PRK13300
CCA tRNA nucleotidyltransferase;
170-249 2.53e-03

CCA tRNA nucleotidyltransferase;


Pssm-ID: 237340 [Multi-domain]  Cd Length: 447  Bit Score: 40.65  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 170 EEIKDFYEYISPRPEEEQMR----HEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLP-TSDIDLVVFgnwetLPLWTLEE 244
Cdd:PRK13300    1 EVLEEVLERIKPTEEEREKLkkvaEELIERLEEAIKELGLDAEVELVGSTARGTWLSgDRDIDIFVL-----FPKDTSRE 75


                  ....*
gi 1031985653 245 ALRKR 249
Cdd:PRK13300   76 ELEEK 80
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
168-440 1.48e-63

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 218.10  E-value: 1.48e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 168 LHEEIKDFYEYISPRPEEEQMRHEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDLVVF----GNWETLPLWTLE 243
Cdd:COG5260    57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIIsdprGYKETRNAGSLA 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 244 EALRKRKVADEnsIKVLDKATVPIIKLMDSHTEVKVDISFNVQSGVKAANLIKDYKQQYPVLPYLVLVLKQFLLQRELNE 323
Cdd:COG5260   137 SHLFKKNLAKE--VVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALND 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 324 VFTGGIGSYSLFLMAVSFLQLHCREDVSSSN-----------PNLGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDE 392
Cdd:COG5260   215 VATGTLSSYTISCMVLSFLQMHPPFLFFDNGllsplkynkniDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYE 294

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1031985653 393 vqKSMLDGYRPSMLYIEDP-LQPGNDVGRSSYGAMQVKEAFDYAYVILS 440
Cdd:COG5260   295 --KGWLKPSKPNSLSIQDPgTDRNNDISAVSFNIKDIKAAFIRAFELLS 341
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 188-298 5.69e-36

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: 130.76  E-value: 5.69e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 188 MRHEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDLVVFGN----WETLPLWTLEEALRKRKVADEnsIKVLDKA 263
Cdd:cd05402     1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPnhrvDREDFLRKLAKLLKKSGEVVE--VEPIINA 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1031985653 264 TVPIIKLMDSHTEVKVDISFNVQSGVKAANLIKDY 298
Cdd:cd05402    79 RVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAY 113
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 356-416 5.05e-18

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: 78.38  E-value: 5.05e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1031985653 356 NLGVLLIEFFELYGRHFNYLKTGIRIKDGGsYVAKDEVQKSMLDGYRPSMLYIEDPLQPGN 416
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGG-ILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 193-270 7.02e-13

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: 64.74  E-value: 7.02e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1031985653 193 VARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDLVVFGNWETlPLWTLEEALRKRKVadENSIKVLDKATVPIIKL 270
Cdd:pfam01909   1 LRKLREILKELFPVAEVVLFGSYARGTALPGSDIDLLVVFPEPV-EEERLLKLAKIIKE--LEELLGLEVDLVTREKI 75
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 190-280 1.75e-05

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: 43.56  E-value: 1.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 190 HEVVARIQRVIKDLWPNAEVC-VFGSFSTGLYLPTSDIDLVVFGNWETLPlwtLEEALRKRKVADENSIKV----LDKAT 264
Cdd:cd05403     1 EEILEEILEILRELLGGVEKVyLFGSYARGDARPDSDIDLLVIFDDPLDP---LELARLLEELELLLGRPVdlvvLNALE 77

                          90
                  ....*....|....*.
gi 1031985653 265 VPIIKLMDSHTEVKVD 280
Cdd:cd05403    78 LELLLRILIEGEGIYL 93
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
 168-270 1.03e-04

Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.


Pssm-ID: 461486 [Multi-domain]  Cd Length: 344  Bit Score: 44.81  E-value: 1.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 168 LHEEIKDFYEYISPrpEEEQMRHEVVARIQRVIKDL-----------WPNAE-----VCVFGSFSTGLYLPTSDIDL--- 228
Cdd:pfam04928  22 LIEELKAQGLFESE--EETQKREEVLGKLNKLVKEFvkrvskekglpESVAKeaggkIFTFGSYRLGVHGPGSDIDTlcv 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1031985653 229 ----VVFGNWETLplwtLEEALRKRKVADEnsIKVLDKATVPIIKL 270
Cdd:pfam04928 100 vpkhVTREDFFTS----FLEMLRERPEVTE--LTAVPDAFVPVIKF 139
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
189-258 1.54e-04

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 41.05  E-value: 1.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 189 RHEVVARIQRVIKDL---WPNAEVCVFGSFSTGLYLPTSDIDLVVFGNwETLPLWT-------LEEALrKRKV--ADENS 256
Cdd:COG1669     3 REEILEILREVIEELaerYGVSRLGLFGSVARGEAREDSDIDLLVEFD-EPTSLFDlfeleeeLEELL-GRKVdlVTLDG 80


                  ..
gi 1031985653 257 IK 258
Cdd:COG1669    81 LS 82
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
190-233 2.36e-04

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


Pssm-ID: 441314  Cd Length: 95  Bit Score: 40.40  E-value: 2.36e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1031985653 190 HEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDLVVFGN 233
Cdd:COG1708     6 RELLEEIVEALRRGPEVAAVYLFGSYARGDARPDSDIDLLVVVD 49
NT_Pol-beta-like cd05397
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This ...
 191-228 1.46e-03

Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes.


Pssm-ID: 143387 [Multi-domain]  Cd Length: 49  Bit Score: 36.92  E-value: 1.46e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1031985653 191 EVVARIQRVIKDLWPNAEVCVFGSFSTGLYLPTSDIDL 228
Cdd:cd05397     2 ELLDIIKERLKKLVPGYEIVVYGSLVRGLLKKSSDIDL 39
PRK13300 PRK13300
CCA tRNA nucleotidyltransferase;
170-249 2.53e-03

CCA tRNA nucleotidyltransferase;


Pssm-ID: 237340 [Multi-domain]  Cd Length: 447  Bit Score: 40.65  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031985653 170 EEIKDFYEYISPRPEEEQMR----HEVVARIQRVIKDLWPNAEVCVFGSFSTGLYLP-TSDIDLVVFgnwetLPLWTLEE 244
Cdd:PRK13300    1 EVLEEVLERIKPTEEEREKLkkvaEELIERLEEAIKELGLDAEVELVGSTARGTWLSgDRDIDIFVL-----FPKDTSRE 75


                  ....*
gi 1031985653 245 ALRKR 249
Cdd:PRK13300   76 ELEEK 80
 
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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