NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1348901646|ref|NP_001347937|]
View 

poly(A) RNA polymerase, mitochondrial isoform 2 [Mus musculus]

Protein Classification

NT_PAP_TUTase domain-containing protein( domain architecture ID 12942010)

NT_PAP_TUTase domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 28-99 3.34e-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: 70.66  E-value: 3.34e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1348901646  28 NVPSERIATQKILSVIGECLDNFGPgCVGVQKILNARCPLVRFSHQGSGFQCDLTANNSIALKSSELLYIYG 99
Cdd:cd05402    44 LGPNHRVDREDFLRKLAKLLKKSGE-VVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
TRF4 super family cl34961
DNA polymerase sigma [Replication, recombination and repair];
57-248 6.38e-12

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: 66.33  E-value: 6.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1348901646  57 VQKILNARCPLVRFSHQGSGFQCDLTANNSIALKSSELLYIYGSLDSRVRALVFSVRCWARAHSLTSSIPGAwITNFSLT 136
Cdd:COG5260   148 VVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGT-LSSYTIS 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1348901646 137 VMVIFFLQRRSPPILptldsLKSIadaedrcilegnnctfvqDVNKIQPSGNTETLELLIKEFFEYFG------NFAFNK 210
Cdd:COG5260   227 CMVLSFLQMHPPFLF-----FDNG------------------LLSPLKYNKNIDNLGVLFDDFFELYGksfnysLVVLSI 283

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1348901646 211 NS----INIRQGREQNKPDSSPLYIQNPFETSLNISKNVSQS 248
Cdd:COG5260   284 NSgdfyLPKYEKGWLKPSKPNSLSIQDPGTDRNNDISAVSFN 325
 
Name Accession Description Interval E-value
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 28-99 3.34e-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: 70.66  E-value: 3.34e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1348901646  28 NVPSERIATQKILSVIGECLDNFGPgCVGVQKILNARCPLVRFSHQGSGFQCDLTANNSIALKSSELLYIYG 99
Cdd:cd05402    44 LGPNHRVDREDFLRKLAKLLKKSGE-VVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
57-248 6.38e-12

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 66.33  E-value: 6.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1348901646  57 VQKILNARCPLVRFSHQGSGFQCDLTANNSIALKSSELLYIYGSLDSRVRALVFSVRCWARAHSLTSSIPGAwITNFSLT 136
Cdd:COG5260   148 VVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGT-LSSYTIS 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1348901646 137 VMVIFFLQRRSPPILptldsLKSIadaedrcilegnnctfvqDVNKIQPSGNTETLELLIKEFFEYFG------NFAFNK 210
Cdd:COG5260   227 CMVLSFLQMHPPFLF-----FDNG------------------LLSPLKYNKNIDNLGVLFDDFFELYGksfnysLVVLSI 283

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1348901646 211 NS----INIRQGREQNKPDSSPLYIQNPFETSLNISKNVSQS 248
Cdd:COG5260   284 NSgdfyLPKYEKGWLKPSKPNSLSIQDPGTDRNNDISAVSFN 325
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 193-238 7.94e-06

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: 42.95  E-value: 7.94e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1348901646 193 ELLIkEFFEYFG-NFAFNKNSINIRQGR----------EQNKPDSSPLYIQNPFETS 238
Cdd:pfam03828   4 ELLI-GFFEYYGrEFDYENVVISIRTGGilskkekgwlRNEGRRPFLLCIEDPFDLD 59
 
Name Accession Description Interval E-value
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 28-99 3.34e-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: 70.66  E-value: 3.34e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1348901646  28 NVPSERIATQKILSVIGECLDNFGPgCVGVQKILNARCPLVRFSHQGSGFQCDLTANNSIALKSSELLYIYG 99
Cdd:cd05402    44 LGPNHRVDREDFLRKLAKLLKKSGE-VVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
57-248 6.38e-12

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 66.33  E-value: 6.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1348901646  57 VQKILNARCPLVRFSHQGSGFQCDLTANNSIALKSSELLYIYGSLDSRVRALVFSVRCWARAHSLTSSIPGAwITNFSLT 136
Cdd:COG5260   148 VVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGT-LSSYTIS 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1348901646 137 VMVIFFLQRRSPPILptldsLKSIadaedrcilegnnctfvqDVNKIQPSGNTETLELLIKEFFEYFG------NFAFNK 210
Cdd:COG5260   227 CMVLSFLQMHPPFLF-----FDNG------------------LLSPLKYNKNIDNLGVLFDDFFELYGksfnysLVVLSI 283

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1348901646 211 NS----INIRQGREQNKPDSSPLYIQNPFETSLNISKNVSQS 248
Cdd:COG5260   284 NSgdfyLPKYEKGWLKPSKPNSLSIQDPGTDRNNDISAVSFN 325
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 193-238 7.94e-06

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: 42.95  E-value: 7.94e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1348901646 193 ELLIkEFFEYFG-NFAFNKNSINIRQGR----------EQNKPDSSPLYIQNPFETS 238
Cdd:pfam03828   4 ELLI-GFFEYYGrEFDYENVVISIRTGGilskkekgwlRNEGRRPFLLCIEDPFDLD 59
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH