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Conserved domains on  [gi|442615527|ref|NP_001259340|]
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topoisomerase related function 4-1, isoform J [Drosophila melanogaster]

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];
271-583 6.93e-67

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: 232.74  E-value: 6.93e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  271 LHEEIEHFYQYVLPTPCEHAIRNEVVKRIEAVVHSIWPQAVVEIFGSFRTGLFLPTSDIDLVVL----GLWEKLPLRTLE 346
Cdd:COG5260    57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIIsdprGYKETRNAGSLA 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  347 FELVSRgiAEACTVRVLDKASVPIIKLTDRETQVKVDISFNMQSGVQSAELIKKFKRDYPVLEKLVLVLKQFLLLRDLNE 426
Cdd:COG5260   137 SHLFKK--NLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALND 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  427 VFTGGISSYSLILMCISFLQMHPRGIYHDTA------------NLGVLLLEFFELYGRRFNYMKIGISIKNGGRYMPKde 494
Cdd:COG5260   215 VATGTLSSYTISCMVLSFLQMHPPFLFFDNGllsplkynknidNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPK-- 292

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  495 LQRDMVDGHRPSLLCIEDPLT-PGNDIGRSSYGVFQVQQAFKCAYRVLALAVSPLNLLGI-DPRVNSILGRIIHITDDVI 572
Cdd:COG5260   293 YEKGWLKPSKPNSLSIQDPGTdRNNDISAVSFNIKDIKAAFIRAFELLSNKLFTLTSAIKhDAYGLLIEFNEASYSNTSR 372

                         330
                  ....*....|.
gi 442615527  573 DYREWIRENFE 583
Cdd:COG5260   373 SLKEEYDSIYE 383
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
271-583 6.93e-67

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 232.74  E-value: 6.93e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  271 LHEEIEHFYQYVLPTPCEHAIRNEVVKRIEAVVHSIWPQAVVEIFGSFRTGLFLPTSDIDLVVL----GLWEKLPLRTLE 346
Cdd:COG5260    57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIIsdprGYKETRNAGSLA 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  347 FELVSRgiAEACTVRVLDKASVPIIKLTDRETQVKVDISFNMQSGVQSAELIKKFKRDYPVLEKLVLVLKQFLLLRDLNE 426
Cdd:COG5260   137 SHLFKK--NLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALND 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  427 VFTGGISSYSLILMCISFLQMHPRGIYHDTA------------NLGVLLLEFFELYGRRFNYMKIGISIKNGGRYMPKde 494
Cdd:COG5260   215 VATGTLSSYTISCMVLSFLQMHPPFLFFDNGllsplkynknidNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPK-- 292

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  495 LQRDMVDGHRPSLLCIEDPLT-PGNDIGRSSYGVFQVQQAFKCAYRVLALAVSPLNLLGI-DPRVNSILGRIIHITDDVI 572
Cdd:COG5260   293 YEKGWLKPSKPNSLSIQDPGTdRNNDISAVSFNIKDIKAAFIRAFELLSNKLFTLTSAIKhDAYGLLIEFNEASYSNTSR 372

                         330
                  ....*....|.
gi 442615527  573 DYREWIRENFE 583
Cdd:COG5260   373 SLKEEYDSIYE 383
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 291-401 3.89e-33

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: 123.82  E-value: 3.89e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  291 IRNEVVKRIEAVVHSIWPQAVVEIFGSFRTGLFLPTSDIDLVVLG----LWEKLPLRTLEFELVSRGiaEACTVRVLDKA 366
Cdd:cd05402     1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGpnhrVDREDFLRKLAKLLKKSG--EVVEVEPIINA 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 442615527  367 SVPIIKLTDRETQVKVDISFNMQSGVQSAELIKKF 401
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 ...
 458-518 4.49e-20

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: 84.55  E-value: 4.49e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 442615527   458 NLGVLLLEFFELYGRRFNYMKIGISIKNGGrYMPKDELQRDMVDGHRPSLLCIEDPLTPGN 518
Cdd:pfam03828    1 SLGELLIGFFEYYGREFDYENVVISIRTGG-ILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
PRK13300 PRK13300
CCA tRNA nucleotidyltransferase;
293-435 1.31e-03

CCA tRNA nucleotidyltransferase;


Pssm-ID: 237340 [Multi-domain]  Cd Length: 447  Bit Score: 42.57  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  293 NEVVKRIEAVVHSIWPQAVVEIFGSFRTGLFLP-TSDIDLVVLglwekLPLRTLEFELVSRG--IAEACTVRVLDK---- 365
Cdd:PRK13300   25 EELIERLEEAIKELGLDAEVELVGSTARGTWLSgDRDIDIFVL-----FPKDTSREELEEKGleIGKEVAKELLGDyeer 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  366 -ASVPIIKLTDREtqVKVDI--SFNMQSG--VQSA------------ELIKKFKRDypvlEklVLVLKQFllLRDLN--- 425
Cdd:PRK13300  100 yAEHPYVTGEIDG--FEVDIvpCYKVESGeeIISAvdrtpfhtkyvkERLKGKLED----E--VRLLKQF--LKGIGvyg 169

                         170
                  ....*....|.
gi 442615527  426 -EVFTGGISSY 435
Cdd:PRK13300  170 sELKTRGFSGY 180
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
271-583 6.93e-67

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 232.74  E-value: 6.93e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  271 LHEEIEHFYQYVLPTPCEHAIRNEVVKRIEAVVHSIWPQAVVEIFGSFRTGLFLPTSDIDLVVL----GLWEKLPLRTLE 346
Cdd:COG5260    57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIIsdprGYKETRNAGSLA 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  347 FELVSRgiAEACTVRVLDKASVPIIKLTDRETQVKVDISFNMQSGVQSAELIKKFKRDYPVLEKLVLVLKQFLLLRDLNE 426
Cdd:COG5260   137 SHLFKK--NLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALND 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  427 VFTGGISSYSLILMCISFLQMHPRGIYHDTA------------NLGVLLLEFFELYGRRFNYMKIGISIKNGGRYMPKde 494
Cdd:COG5260   215 VATGTLSSYTISCMVLSFLQMHPPFLFFDNGllsplkynknidNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPK-- 292

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  495 LQRDMVDGHRPSLLCIEDPLT-PGNDIGRSSYGVFQVQQAFKCAYRVLALAVSPLNLLGI-DPRVNSILGRIIHITDDVI 572
Cdd:COG5260   293 YEKGWLKPSKPNSLSIQDPGTdRNNDISAVSFNIKDIKAAFIRAFELLSNKLFTLTSAIKhDAYGLLIEFNEASYSNTSR 372

                         330
                  ....*....|.
gi 442615527  573 DYREWIRENFE 583
Cdd:COG5260   373 SLKEEYDSIYE 383
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 291-401 3.89e-33

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: 123.82  E-value: 3.89e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  291 IRNEVVKRIEAVVHSIWPQAVVEIFGSFRTGLFLPTSDIDLVVLG----LWEKLPLRTLEFELVSRGiaEACTVRVLDKA 366
Cdd:cd05402     1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGpnhrVDREDFLRKLAKLLKKSG--EVVEVEPIINA 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 442615527  367 SVPIIKLTDRETQVKVDISFNMQSGVQSAELIKKF 401
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 ...
 458-518 4.49e-20

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: 84.55  E-value: 4.49e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 442615527   458 NLGVLLLEFFELYGRRFNYMKIGISIKNGGrYMPKDELQRDMVDGHRPSLLCIEDPLTPGN 518
Cdd:pfam03828    1 SLGELLIGFFEYYGREFDYENVVISIRTGG-ILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 296-403 1.36e-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: 55.88  E-value: 1.36e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527   296 VKRIEAVVHSIWPQAVVEIFGSFRTGLFLPTSDIDLVVLGLWEKLPLRTLEFelvsrgiaeactvrvldkasVPIIKLTD 375
Cdd:pfam01909    1 LRKLREILKELFPVAEVVLFGSYARGTALPGSDIDLLVVFPEPVEEERLLKL--------------------AKIIKELE 60

                           90       100
                   ....*....|....*....|....*...
gi 442615527   376 RETQVKVDISFNMQSGVQSAELIKKFKR 403
Cdd:pfam01909   61 ELLGLEVDLVTREKIEFPLVKIDILEER 88
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 294-384 2.78e-04

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. 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, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 44.11  E-value: 2.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  294 EVVKRIEAVVHSIWPQAVVEIFGSFRTGlfLPTS-DIDLVV-------LGLWEKLPLRTLEFELVSRGIAEACTvrvldK 365
Cdd:cd00141   145 AIAEIIKEALREVDPVLQVEIAGSYRRG--KETVgDIDILVthpdatsRGLLEKVVDALVELGFVTEVLSKGDT-----K 217

                          90
                  ....*....|....*....
gi 442615527  366 ASVpIIKLTDRETQVKVDI 384
Cdd:cd00141   218 ASG-ILKLPGGWKGRRVDL 235
PRK13300 PRK13300
CCA tRNA nucleotidyltransferase;
293-435 1.31e-03

CCA tRNA nucleotidyltransferase;


Pssm-ID: 237340 [Multi-domain]  Cd Length: 447  Bit Score: 42.57  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  293 NEVVKRIEAVVHSIWPQAVVEIFGSFRTGLFLP-TSDIDLVVLglwekLPLRTLEFELVSRG--IAEACTVRVLDK---- 365
Cdd:PRK13300   25 EELIERLEEAIKELGLDAEVELVGSTARGTWLSgDRDIDIFVL-----FPKDTSREELEEKGleIGKEVAKELLGDyeer 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  366 -ASVPIIKLTDREtqVKVDI--SFNMQSG--VQSA------------ELIKKFKRDypvlEklVLVLKQFllLRDLN--- 425
Cdd:PRK13300  100 yAEHPYVTGEIDG--FEVDIvpCYKVESGeeIISAvdrtpfhtkyvkERLKGKLED----E--VRLLKQF--LKGIGvyg 169

                         170
                  ....*....|.
gi 442615527  426 -EVFTGGISSY 435
Cdd:PRK13300  170 sELKTRGFSGY 180
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 294-383 3.07e-03

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: 37.78  E-value: 3.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442615527  294 EVVKRIEAVVHSIWpqavveIFGSFRTGLFLPTSDIDLVVLG-----LWEKLPLRTLEFELVSRGIaeacTVRVLDKASV 368
Cdd:cd05403     9 EILRELLGGVEKVY------LFGSYARGDARPDSDIDLLVIFddpldPLELARLLEELELLLGRPV----DLVVLNALEL 78

                          90
                  ....*....|....*
gi 442615527  369 PIIKLTDRETQVKVD 383
Cdd:cd05403    79 ELLLRILIEGEGIYL 93
 
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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