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Conserved domains on  [gi|190194365|ref|NP_060579|]
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poly(A) RNA polymerase, mitochondrial precursor [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RL pfam17797
RL domain; The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase ...
63-132 1.76e-38

RL domain; The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase PAPD1. It contributes to PAPD1 dimerization and has a fold similar to RNP-type RBDs.


:

Pssm-ID: 436051  Cd Length: 71  Bit Score: 135.51  E-value: 1.76e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365   63 FSEMQNERREQAQRTVLIHCPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNGTH 132
Cdd:pfam17797   2 FSEVQAERREQAERSVLISCPSKISEKKFLKYLSQHGKINNHFFYESYGVYAVVEFSSKESIASLQDSTH 71
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
206-344 1.03e-25

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: 1.03e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 206 LRYLTCSLIEDMAAAYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLdetrnlsahkisgnflmefqvknvPSERIATQKIL 285
Cdd:cd05402    1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLG------------------------PNHRVDREDFL 56
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 190194365 286 SVLGECLDHFGPgCVGVQKILNARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYG 344
Cdd:cd05402   57 RKLAKLLKKSGE-VVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
TRF4 super family cl34961
DNA polymerase sigma [Replication, recombination and repair];
140-493 2.37e-14

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: 75.58  E-value: 2.37e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 140 TAIPFRSRFFNLKLKNQTSERSRVRSSNQLPRSNKQLFELLcyaeSIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDMAA 219
Cdd:COG5260   15 SEEEFETIMEQKERRPLDAKKVSIQELLELSIDSVFNEESD----ELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLK 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 220 AYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLDETRNLSAHKISGNFLMEFQvknvpseriatqKILSVLGECLDHfgpgc 299
Cdd:COG5260   91 KEFPDADLKVFGSTETGLALPKSDIDLCIISDPRGYKETRNAGSLASHLFK------------KNLAKEVVVVST----- 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 300 vgvqkilnARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWARAHSLTSSIPGAwITNFS 379
Cdd:COG5260  154 --------ARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGT-LSSYT 224
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 380 LTMMVIFFLQRRSPPILptldslktladaedkcVIEGnnctfvrDLSRIKPSQNTETLELLLKEFFEYFG-NFAFDKNSI 458
Cdd:COG5260  225 ISCMVLSFLQMHPPFLF----------------FDNG-------LLSPLKYNKNIDNLGVLFDDFFELYGkSFNYSLVVL 281
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*.
gi 190194365 459 NIRQGR-----------EQNKPDSspLYIQNPFETSLNISKNVSQS 493
Cdd:COG5260  282 SINSGDfylpkyekgwlKPSKPNS--LSIQDPGTDRNNDISAVSFN 325
 
Name Accession Description Interval E-value
RL pfam17797
RL domain; The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase ...
63-132 1.76e-38

RL domain; The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase PAPD1. It contributes to PAPD1 dimerization and has a fold similar to RNP-type RBDs.


Pssm-ID: 436051  Cd Length: 71  Bit Score: 135.51  E-value: 1.76e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365   63 FSEMQNERREQAQRTVLIHCPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNGTH 132
Cdd:pfam17797   2 FSEVQAERREQAERSVLISCPSKISEKKFLKYLSQHGKINNHFFYESYGVYAVVEFSSKESIASLQDSTH 71
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
206-344 1.03e-25

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: 1.03e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 206 LRYLTCSLIEDMAAAYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLdetrnlsahkisgnflmefqvknvPSERIATQKIL 285
Cdd:cd05402    1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLG------------------------PNHRVDREDFL 56
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 190194365 286 SVLGECLDHFGPgCVGVQKILNARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYG 344
Cdd:cd05402   57 RKLAKLLKKSGE-VVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
140-493 2.37e-14

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 75.58  E-value: 2.37e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 140 TAIPFRSRFFNLKLKNQTSERSRVRSSNQLPRSNKQLFELLcyaeSIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDMAA 219
Cdd:COG5260   15 SEEEFETIMEQKERRPLDAKKVSIQELLELSIDSVFNEESD----ELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLK 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 220 AYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLDETRNLSAHKISGNFLMEFQvknvpseriatqKILSVLGECLDHfgpgc 299
Cdd:COG5260   91 KEFPDADLKVFGSTETGLALPKSDIDLCIISDPRGYKETRNAGSLASHLFK------------KNLAKEVVVVST----- 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 300 vgvqkilnARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWARAHSLTSSIPGAwITNFS 379
Cdd:COG5260  154 --------ARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGT-LSSYT 224
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 380 LTMMVIFFLQRRSPPILptldslktladaedkcVIEGnnctfvrDLSRIKPSQNTETLELLLKEFFEYFG-NFAFDKNSI 458
Cdd:COG5260  225 ISCMVLSFLQMHPPFLF----------------FDNG-------LLSPLKYNKNIDNLGVLFDDFFELYGkSFNYSLVVL 281
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*.
gi 190194365 459 NIRQGR-----------EQNKPDSspLYIQNPFETSLNISKNVSQS 493
Cdd:COG5260  282 SINSGDfylpkyekgwlKPSKPNS--LSIQDPGTDRNNDISAVSFN 325
TUTase pfam19088
TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase ...
195-397 1.53e-12

TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase enzymes.


Pssm-ID: 436954 [Multi-domain]  Cd Length: 333  Bit Score: 69.01  E-value: 1.53e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365  195 KEFQLTEENTKLRYLTCSLIEDMAAAYFPDCIVRPFGSSVNTFGKLGCDLDmfLDLDETRNLSAhkisgnflmefqvknv 274
Cdd:pfam19088 100 QEHGISDEDFEVRQEIVTRMEKIIQQHLPDCSLRLYGSCLTRFAFKTSDIN--IDVQFPSTMTQ---------------- 161
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365  275 PSERIATQKILSVLGECLDhfgpgcvgVQKILNARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYGALDSRVRALV 354
Cdd:pfam19088 162 PDVLIQVLEILKNSESYSD--------VESDFHAKVPVVFCRDKSSGLMCKVSAGNDVACLTTNHLAALAKLEPRLVPLV 233
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 190194365  355 FSVRCWARAHSLTSSIPGAwITNFSLTMMVIFFLQRRSPPILP 397
Cdd:pfam19088 234 LAFRYWAKLCHIDCQAEGG-IPSYSFALMVIFFLQQRKEPILP 275
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
440-483 6.81e-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: 43.72  E-value: 6.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 190194365  440 LLKEFFEYFG-NFAFDKNSINIRQGR----------EQNKPDSSPLYIQNPFETS 483
Cdd:pfam03828   5 LLIGFFEYYGrEFDYENVVISIRTGGilskkekgwlRNEGRRPFLLCIEDPFDLD 59
 
Name Accession Description Interval E-value
RL pfam17797
RL domain; The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase ...
63-132 1.76e-38

RL domain; The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase PAPD1. It contributes to PAPD1 dimerization and has a fold similar to RNP-type RBDs.


Pssm-ID: 436051  Cd Length: 71  Bit Score: 135.51  E-value: 1.76e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365   63 FSEMQNERREQAQRTVLIHCPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNGTH 132
Cdd:pfam17797   2 FSEVQAERREQAERSVLISCPSKISEKKFLKYLSQHGKINNHFFYESYGVYAVVEFSSKESIASLQDSTH 71
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
206-344 1.03e-25

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: 1.03e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 206 LRYLTCSLIEDMAAAYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLdetrnlsahkisgnflmefqvknvPSERIATQKIL 285
Cdd:cd05402    1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLG------------------------PNHRVDREDFL 56
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 190194365 286 SVLGECLDHFGPgCVGVQKILNARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYG 344
Cdd:cd05402   57 RKLAKLLKKSGE-VVEVEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
140-493 2.37e-14

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 75.58  E-value: 2.37e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 140 TAIPFRSRFFNLKLKNQTSERSRVRSSNQLPRSNKQLFELLcyaeSIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDMAA 219
Cdd:COG5260   15 SEEEFETIMEQKERRPLDAKKVSIQELLELSIDSVFNEESD----ELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLK 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 220 AYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLDETRNLSAHKISGNFLMEFQvknvpseriatqKILSVLGECLDHfgpgc 299
Cdd:COG5260   91 KEFPDADLKVFGSTETGLALPKSDIDLCIISDPRGYKETRNAGSLASHLFK------------KNLAKEVVVVST----- 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 300 vgvqkilnARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWARAHSLTSSIPGAwITNFS 379
Cdd:COG5260  154 --------ARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGT-LSSYT 224
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365 380 LTMMVIFFLQRRSPPILptldslktladaedkcVIEGnnctfvrDLSRIKPSQNTETLELLLKEFFEYFG-NFAFDKNSI 458
Cdd:COG5260  225 ISCMVLSFLQMHPPFLF----------------FDNG-------LLSPLKYNKNIDNLGVLFDDFFELYGkSFNYSLVVL 281
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*.
gi 190194365 459 NIRQGR-----------EQNKPDSspLYIQNPFETSLNISKNVSQS 493
Cdd:COG5260  282 SINSGDfylpkyekgwlKPSKPNS--LSIQDPGTDRNNDISAVSFN 325
TUTase pfam19088
TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase ...
195-397 1.53e-12

TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase enzymes.


Pssm-ID: 436954 [Multi-domain]  Cd Length: 333  Bit Score: 69.01  E-value: 1.53e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365  195 KEFQLTEENTKLRYLTCSLIEDMAAAYFPDCIVRPFGSSVNTFGKLGCDLDmfLDLDETRNLSAhkisgnflmefqvknv 274
Cdd:pfam19088 100 QEHGISDEDFEVRQEIVTRMEKIIQQHLPDCSLRLYGSCLTRFAFKTSDIN--IDVQFPSTMTQ---------------- 161
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194365  275 PSERIATQKILSVLGECLDhfgpgcvgVQKILNARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYGALDSRVRALV 354
Cdd:pfam19088 162 PDVLIQVLEILKNSESYSD--------VESDFHAKVPVVFCRDKSSGLMCKVSAGNDVACLTTNHLAALAKLEPRLVPLV 233
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 190194365  355 FSVRCWARAHSLTSSIPGAwITNFSLTMMVIFFLQRRSPPILP 397
Cdd:pfam19088 234 LAFRYWAKLCHIDCQAEGG-IPSYSFALMVIFFLQQRKEPILP 275
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
440-483 6.81e-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: 43.72  E-value: 6.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 190194365  440 LLKEFFEYFG-NFAFDKNSINIRQGR----------EQNKPDSSPLYIQNPFETS 483
Cdd:pfam03828   5 LLIGFFEYYGrEFDYENVVISIRTGGilskkekgwlRNEGRRPFLLCIEDPFDLD 59
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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