NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|32565538|ref|NP_495546|]
View 

PAP-associated domain-containing protein [Caenorhabditis elegans]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 10143992)

nucleotidyltransferase domain-containing protein similar to Trypanosoma brucei terminal uridylyltransferase 7 (TUTase 7) which, during post-transcriptional editing of mitochondrial RNA, catalyzes the addition of uridine (U) to ssRNA with a preference for a 3'-terminal U and adds the number of Us specified by a guide RNA to precleaved dsRNA editing substrates, and to Drosophila melanogaster Monkey king protein (Mkg)

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; ...
 51-186 7.84e-12

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: 61.80  E-value: 7.84e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538  51 RKLYVALVRKYLKSEgvtkqlaSQGIKLRglsVFGSFPTHCASKDSDLDLCVCATATGNKKQLPVIILQAIFRDMmyske 130
Cdd:cd05402   2 REEVLDRLQELIKEW-------FPGAKLY---PFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKS----- 66

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 32565538 131 gqnifgeNVVSGISFVQTAKVPIIRFKIN--DVPVDLSATFDDNPRTSlaaKYINAYC 186
Cdd:cd05402  67 -------GEVVEVEPIINARVPIIKFVDKptGIEVDISFNNLNGIRNT---KLLRAYV 114
 
Name Accession Description Interval E-value
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 51-186 7.84e-12

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: 61.80  E-value: 7.84e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538  51 RKLYVALVRKYLKSEgvtkqlaSQGIKLRglsVFGSFPTHCASKDSDLDLCVCATATGNKKQLPVIILQAIFRDMmyske 130
Cdd:cd05402   2 REEVLDRLQELIKEW-------FPGAKLY---PFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKS----- 66

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 32565538 131 gqnifgeNVVSGISFVQTAKVPIIRFKIN--DVPVDLSATFDDNPRTSlaaKYINAYC 186
Cdd:cd05402  67 -------GEVVEVEPIINARVPIIKFVDKptGIEVDISFNNLNGIRNT---KLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
30-268 1.34e-11

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 66.33  E-value: 1.34e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538  30 LEQDINIFYMNQRQSQSMLEERKLYVALVRKYLKSEgvtkqlasqgIKLRGLSVFGSFPTHCASKDSDLDLCVCATATGN 109
Cdd:COG5260  57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKE----------FPDADLKVFGSTETGLALPKSDIDLCIISDPRGY 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538 110 KKQLPVIILQAIfrdmmyskegqnIFGENVVSGISFVQTAKVPIIRF--KINDVPVDLSAtfdDNPRTSLAAKYINAYCQ 187
Cdd:COG5260 127 KETRNAGSLASH------------LFKKNLAKEVVVVSTARVPIIKLvdPQSGLHCDISF---NNTNGIVNAKLIRSYLK 191

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538 188 LDDRFKILVMFLKKWMKSEGRAEDHLRIYpNSYSIILLLIHVLQWYDILPnLHQTHSDLFHRGNFKLSDLAELRHEFkFP 267
Cdd:COG5260 192 EDPRLRPLVLIIKHWLKRRALNDVATGTL-SSYTISCMVLSFLQMHPPFL-FFDNGLLSPLKYNKNIDNLGVLFDDF-FE 268


                .
gi 32565538 268 L 268
Cdd:COG5260 269 L 269
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
 42-165 2.30e-03

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 40.55  E-value: 2.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538   42 RQSQSMLEE-RKLYVALVRKYLKSEGVTKQLASQGIKlrGLSVFGSFPTHCASKDSDLD-LCVCatatgnkkqlPVIILQ 119
Cdd:PTZ00418  91 KKRERVLGSlNKLVREFVVEASIEQGINEEEASQISG--KLFTFGSYRLGVVAPGSDIDtLCLA----------PRHITR 158

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 32565538  120 AIFRDMMYSKEGQNIFgenvVSGISFVQTAKVPIIRFKINDVPVDL 165
Cdd:PTZ00418 159 ESFFSDFYAKLQQDPN----ITKLQPVPDAYTPVIKFVYDGIDIDL 200
 
Name Accession Description Interval E-value
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 51-186 7.84e-12

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: 61.80  E-value: 7.84e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538  51 RKLYVALVRKYLKSEgvtkqlaSQGIKLRglsVFGSFPTHCASKDSDLDLCVCATATGNKKQLPVIILQAIFRDMmyske 130
Cdd:cd05402   2 REEVLDRLQELIKEW-------FPGAKLY---PFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKS----- 66

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 32565538 131 gqnifgeNVVSGISFVQTAKVPIIRFKIN--DVPVDLSATFDDNPRTSlaaKYINAYC 186
Cdd:cd05402  67 -------GEVVEVEPIINARVPIIKFVDKptGIEVDISFNNLNGIRNT---KLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
30-268 1.34e-11

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 66.33  E-value: 1.34e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538  30 LEQDINIFYMNQRQSQSMLEERKLYVALVRKYLKSEgvtkqlasqgIKLRGLSVFGSFPTHCASKDSDLDLCVCATATGN 109
Cdd:COG5260  57 LTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKE----------FPDADLKVFGSTETGLALPKSDIDLCIISDPRGY 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538 110 KKQLPVIILQAIfrdmmyskegqnIFGENVVSGISFVQTAKVPIIRF--KINDVPVDLSAtfdDNPRTSLAAKYINAYCQ 187
Cdd:COG5260 127 KETRNAGSLASH------------LFKKNLAKEVVVVSTARVPIIKLvdPQSGLHCDISF---NNTNGIVNAKLIRSYLK 191

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538 188 LDDRFKILVMFLKKWMKSEGRAEDHLRIYpNSYSIILLLIHVLQWYDILPnLHQTHSDLFHRGNFKLSDLAELRHEFkFP 267
Cdd:COG5260 192 EDPRLRPLVLIIKHWLKRRALNDVATGTL-SSYTISCMVLSFLQMHPPFL-FFDNGLLSPLKYNKNIDNLGVLFDDF-FE 268


                .
gi 32565538 268 L 268
Cdd:COG5260 269 L 269
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
 42-165 2.30e-03

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 40.55  E-value: 2.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32565538   42 RQSQSMLEE-RKLYVALVRKYLKSEGVTKQLASQGIKlrGLSVFGSFPTHCASKDSDLD-LCVCatatgnkkqlPVIILQ 119
Cdd:PTZ00418  91 KKRERVLGSlNKLVREFVVEASIEQGINEEEASQISG--KLFTFGSYRLGVVAPGSDIDtLCLA----------PRHITR 158

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 32565538  120 AIFRDMMYSKEGQNIFgenvVSGISFVQTAKVPIIRFKINDVPVDL 165
Cdd:PTZ00418 159 ESFFSDFYAKLQQDPN----ITKLQPVPDAYTPVIKFVYDGIDIDL 200
 
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