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Conserved domains on  [gi|354681993|ref|NP_001238936|]
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poly(A) polymerase alpha isoform 3 [Homo sapiens]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 34097)

nucleotidyltransferase domain-containing protein, similar to African swine fever virus repair DNA polymerase X

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PAP_central super family cl47902
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
21-205 4.39e-99

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.


The actual alignment was detected with superfamily member pfam04928:

Pssm-ID: 461486 [Multi-domain]  Cd Length: 344  Bit Score: 292.11  E-value: 4.39e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993   21 GITSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTF 100
Cdd:pfam04928   1 GVTPPISTAGPTEADLKLTDELIEELKAQGLFESEEETQKREEVLGKLNKLVKEFVKRVSKEKGLPESVAKEAGGKIFTF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  101 GSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPE 180
Cdd:pfam04928  81 GSYRLGVHGPGSDIDTLCVVPKHVTREDFFTSFLEMLRERPEVTELTAVPDAFVPVIKFKFSGISIDLLFARLALPSVPD 160
                         170       180
                  ....*....|....*....|....*
gi 354681993  181 DLDLRDDSLLKNLDIRCIRSLNGMR 205
Cdd:pfam04928 161 DLDLSDDNLLRNLDEKCVRSLNGCR 185
 
Name Accession Description Interval E-value
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
21-205 4.39e-99

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: 292.11  E-value: 4.39e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993   21 GITSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTF 100
Cdd:pfam04928   1 GVTPPISTAGPTEADLKLTDELIEELKAQGLFESEEETQKREEVLGKLNKLVKEFVKRVSKEKGLPESVAKEAGGKIFTF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  101 GSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPE 180
Cdd:pfam04928  81 GSYRLGVHGPGSDIDTLCVVPKHVTREDFFTSFLEMLRERPEVTELTAVPDAFVPVIKFKFSGISIDLLFARLALPSVPD 160
                         170       180
                  ....*....|....*....|....*
gi 354681993  181 DLDLRDDSLLKNLDIRCIRSLNGMR 205
Cdd:pfam04928 161 DLDLSDDNLLRNLDEKCVRSLNGCR 185
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
9-205 6.76e-73

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 232.38  E-value: 6.76e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993   9 GSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQS 88
Cdd:PTZ00418  41 YLSYSIECALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEE 120
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  89 VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDI 168
Cdd:PTZ00418 121 EASQISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDL 200
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 354681993 169 LFARLALQTIPEDLDLRD-DSLLKNLDIRCIRSLNGMR 205
Cdd:PTZ00418 201 LFANLPLPTIPDCLNSLDdDYILRNVDEKTVRSLNGCR 238
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
60-173 1.38e-27

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: 101.87  E-value: 1.38e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  60 RRILILGKLNNLVKEWireisesknlpqsvieNVGGKIFTFGSYRLGVHTKGADIDALCVAPRH-VDRSDFFTSFYDKLK 138
Cdd:cd05402    1 KREEVLDRLQELIKEW----------------FPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHrVDREDFLRKLAKLLK 64
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 354681993 139 LQEEVKDLRAVEEAFVPVIKLCFD--GIEIDILFARL 173
Cdd:cd05402   65 KSGEVVEVEPIINARVPIIKFVDKptGIEVDISFNNL 101
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
56-172 1.60e-04

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 42.07  E-value: 1.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  56 EELQRRILILGKLNNLVKewiREISESknlpqsvienvggKIFTFGSYRLGVHTKGADIDaLCV-APRHVDRSDF-FTSF 133
Cdd:COG5260   73 EELKRRKALLEKLRTLLK---KEFPDA-------------DLKVFGSTETGLALPKSDID-LCIiSDPRGYKETRnAGSL 135
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 354681993 134 YDKLKLQEEVKDLRAVEEAFVPVIKLCFD--GIEIDILFAR 172
Cdd:COG5260  136 ASHLFKKNLAKEVVVVSTARVPIIKLVDPqsGLHCDISFNN 176
 
Name Accession Description Interval E-value
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
21-205 4.39e-99

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: 292.11  E-value: 4.39e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993   21 GITSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTF 100
Cdd:pfam04928   1 GVTPPISTAGPTEADLKLTDELIEELKAQGLFESEEETQKREEVLGKLNKLVKEFVKRVSKEKGLPESVAKEAGGKIFTF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  101 GSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPE 180
Cdd:pfam04928  81 GSYRLGVHGPGSDIDTLCVVPKHVTREDFFTSFLEMLRERPEVTELTAVPDAFVPVIKFKFSGISIDLLFARLALPSVPD 160
                         170       180
                  ....*....|....*....|....*
gi 354681993  181 DLDLRDDSLLKNLDIRCIRSLNGMR 205
Cdd:pfam04928 161 DLDLSDDNLLRNLDEKCVRSLNGCR 185
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
9-205 6.76e-73

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 232.38  E-value: 6.76e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993   9 GSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQS 88
Cdd:PTZ00418  41 YLSYSIECALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEE 120
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  89 VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDI 168
Cdd:PTZ00418 121 EASQISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDL 200
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 354681993 169 LFARLALQTIPEDLDLRD-DSLLKNLDIRCIRSLNGMR 205
Cdd:PTZ00418 201 LFANLPLPTIPDCLNSLDdDYILRNVDEKTVRSLNGCR 238
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
60-173 1.38e-27

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: 101.87  E-value: 1.38e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  60 RRILILGKLNNLVKEWireisesknlpqsvieNVGGKIFTFGSYRLGVHTKGADIDALCVAPRH-VDRSDFFTSFYDKLK 138
Cdd:cd05402    1 KREEVLDRLQELIKEW----------------FPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHrVDREDFLRKLAKLLK 64
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 354681993 139 LQEEVKDLRAVEEAFVPVIKLCFD--GIEIDILFARL 173
Cdd:cd05402   65 KSGEVVEVEPIINARVPIIKFVDKptGIEVDISFNNL 101
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
94-175 5.72e-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: 62.82  E-value: 5.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993   94 GGKIFTFGSYRLGVHTKGADIDALCVAPRHVDrsdfFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARL 173
Cdd:pfam01909  14 VAEVVLFGSYARGTALPGSDIDLLVVFPEPVE----EERLLKLAKIIKELEELLGLEVDLVTREKIEFPLVKIDILEERI 89

                  ..
gi 354681993  174 AL 175
Cdd:pfam01909  90 LL 91
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
56-172 1.60e-04

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 42.07  E-value: 1.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 354681993  56 EELQRRILILGKLNNLVKewiREISESknlpqsvienvggKIFTFGSYRLGVHTKGADIDaLCV-APRHVDRSDF-FTSF 133
Cdd:COG5260   73 EELKRRKALLEKLRTLLK---KEFPDA-------------DLKVFGSTETGLALPKSDID-LCIiSDPRGYKETRnAGSL 135
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 354681993 134 YDKLKLQEEVKDLRAVEEAFVPVIKLCFD--GIEIDILFAR 172
Cdd:COG5260  136 ASHLFKKNLAKEVVVVSTARVPIIKLVDPqsGLHCDISFNN 176
 
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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