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Conserved domains on  [gi|1160927438|ref|NP_001336477|]
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poly(A) RNA polymerase GLD2 isoform 4 [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];
4-245 5.28e-30

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: 116.80  E-value: 5.28e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438   4 RRVNQKTEARHILTlvhkHFCTRLSGYIERPQLIRAKVPIVKFRDKVSCVEFDLNVNNIVGIRNTFLLRTYAYLENRVRP 83
Cdd:COG5260   123 PRGYKETRNAGSLA----SHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRP 198
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438  84 LVLVIKKWASHHQINDASRGTLSSYSLVLMVLHYLQTLPEPilpslqkiypesfspaiqlhLVHQAPCNVPPYLSKNESN 163
Cdd:COG5260   199 LVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPF--------------------LFFDNGLLSPLKYNKNIDN 258
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438 164 LGDLLLGFLKYYATEFDWNSQMISVREAKAIPRPDGIEW----RNKYICVEEPF-DGTNTARAVHEKQKfdMIKDQFLKS 238
Cdd:COG5260   259 LGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWlkpsKPNSLSIQDPGtDRNNDISAVSFNIK--DIKAAFIRA 336

                  ....*..
gi 1160927438 239 WHRLKNK 245
Cdd:COG5260   337 FELLSNK 343
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
4-245 5.28e-30

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 116.80  E-value: 5.28e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438   4 RRVNQKTEARHILTlvhkHFCTRLSGYIERPQLIRAKVPIVKFRDKVSCVEFDLNVNNIVGIRNTFLLRTYAYLENRVRP 83
Cdd:COG5260   123 PRGYKETRNAGSLA----SHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRP 198
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438  84 LVLVIKKWASHHQINDASRGTLSSYSLVLMVLHYLQTLPEPilpslqkiypesfspaiqlhLVHQAPCNVPPYLSKNESN 163
Cdd:COG5260   199 LVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPF--------------------LFFDNGLLSPLKYNKNIDN 258
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438 164 LGDLLLGFLKYYATEFDWNSQMISVREAKAIPRPDGIEW----RNKYICVEEPF-DGTNTARAVHEKQKfdMIKDQFLKS 238
Cdd:COG5260   259 LGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWlkpsKPNSLSIQDPGtDRNNDISAVSFNIK--DIKAAFIRA 336

                  ....*..
gi 1160927438 239 WHRLKNK 245
Cdd:COG5260   337 FELLSNK 343
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
7-75 1.03e-15

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: 71.05  E-value: 1.03e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1160927438   7 NQKTEARHILTLVHKHFCtRLSGYIERPQLIRAKVPIVKFRDKVSCVEFDLNVNNIVGIRNTFLLRTYA 75
Cdd:cd05402    47 NHRVDREDFLRKLAKLLK-KSGEVVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
163-217 1.21e-14

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: 66.44  E-value: 1.21e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438 163 NLGDLLLGFLKYYATEFDWNSQMISVREAKAIPRPD-----GIEWRNKYICVEEPFDGTN 217
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGGILSKKEkgwlrNEGRRPFLLCIEDPFDLDN 60
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
4-245 5.28e-30

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 116.80  E-value: 5.28e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438   4 RRVNQKTEARHILTlvhkHFCTRLSGYIERPQLIRAKVPIVKFRDKVSCVEFDLNVNNIVGIRNTFLLRTYAYLENRVRP 83
Cdd:COG5260   123 PRGYKETRNAGSLA----SHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRP 198
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438  84 LVLVIKKWASHHQINDASRGTLSSYSLVLMVLHYLQTLPEPilpslqkiypesfspaiqlhLVHQAPCNVPPYLSKNESN 163
Cdd:COG5260   199 LVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPF--------------------LFFDNGLLSPLKYNKNIDN 258
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438 164 LGDLLLGFLKYYATEFDWNSQMISVREAKAIPRPDGIEW----RNKYICVEEPF-DGTNTARAVHEKQKfdMIKDQFLKS 238
Cdd:COG5260   259 LGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWlkpsKPNSLSIQDPGtDRNNDISAVSFNIK--DIKAAFIRA 336

                  ....*..
gi 1160927438 239 WHRLKNK 245
Cdd:COG5260   337 FELLSNK 343
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
7-75 1.03e-15

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: 71.05  E-value: 1.03e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1160927438   7 NQKTEARHILTLVHKHFCtRLSGYIERPQLIRAKVPIVKFRDKVSCVEFDLNVNNIVGIRNTFLLRTYA 75
Cdd:cd05402    47 NHRVDREDFLRKLAKLLK-KSGEVVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
163-217 1.21e-14

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: 66.44  E-value: 1.21e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160927438 163 NLGDLLLGFLKYYATEFDWNSQMISVREAKAIPRPD-----GIEWRNKYICVEEPFDGTN 217
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGGILSKKEkgwlrNEGRRPFLLCIEDPFDLDN 60
 
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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