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Conserved domains on  [gi|18406841|ref|NP_566048|]
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Nucleotidyltransferase family protein [Arabidopsis thaliana]

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];
401-740 1.09e-52

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: 190.37  E-value: 1.09e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 401 EKESRVDNRGQRLLGQKARMVK------MYMACRNDIHRYDATFIAIYKSLIPAEEELEKQRQLMAHLENLVAKEWPHAK 474
Cdd:COG5260  18 EFETIMEQKERRPLDAKKVSIQellelsIDSVFNEESDELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDAD 97

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 475 LYLYGSCANSFGFPKSDIDVCL----AIEGDDINKSE---MLLKLAEILEsdnlqnVQALTRARVPIVKLMDPVTGISCD 547
Cdd:COG5260  98 LKVFGSTETGLALPKSDIDLCIisdpRGYKETRNAGSlasHLFKKNLAKE------VVVVSTARVPIIKLVDPQSGLHCD 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 548 ICINNVLAVVNTKLLRDYAQIDVRLRQLAFIVKHWAKSRRVNETYQGTLSSYAYVLMCIHFLQQRRPPILpclqemepty 627
Cdd:COG5260 172 ISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLF---------- 241

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 628 svrvdnirctyFDNVDRLRNFGSNNRETIAELVWGFFNYWAYAHDYAYNVVSVRTG-SILGKREKDWTrrVGNDRHLICI 706
Cdd:COG5260 242 -----------FDNGLLSPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGdFYLPKYEKGWL--KPSKPNSLSI 308

                       330       340       350
                ....*....|....*....|....*....|....
gi 18406841 707 EDPFeTSHDLGRVVDKFSIRVLREEFERAARIMH 740
Cdd:COG5260 309 QDPG-TDRNNDISAVSFNIKDIKAAFIRAFELLS 341
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 5-107 4.97e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 4.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841     5 GAEPPAPPSSINAGEFLLSILHGS----PSPSSQGPQH--H----QSFALD-----------PAIAAIGPTVNNP-FPPS 62
Cdd:pfam03154 251 PMTQPPPPSQVSPQPLPQPSLHGQmppmPHSLQTGPSHmqHpvppQPFPLTpqssqsqvppgPSPAAPGQSQQRIhTPPS 330

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 18406841    63 NWQSNGHRPSNHNP-PSWPLAFspPHNLSPNFLGFPQFP-------------PSPFTTN 107
Cdd:pfam03154 331 QSQLQSQQPPREQPlPPAPLSM--PHIKPPPTTPIPQLPnpqshkhpphlsgPSPFQMN 387
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
401-740 1.09e-52

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 190.37  E-value: 1.09e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 401 EKESRVDNRGQRLLGQKARMVK------MYMACRNDIHRYDATFIAIYKSLIPAEEELEKQRQLMAHLENLVAKEWPHAK 474
Cdd:COG5260  18 EFETIMEQKERRPLDAKKVSIQellelsIDSVFNEESDELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDAD 97

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 475 LYLYGSCANSFGFPKSDIDVCL----AIEGDDINKSE---MLLKLAEILEsdnlqnVQALTRARVPIVKLMDPVTGISCD 547
Cdd:COG5260  98 LKVFGSTETGLALPKSDIDLCIisdpRGYKETRNAGSlasHLFKKNLAKE------VVVVSTARVPIIKLVDPQSGLHCD 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 548 ICINNVLAVVNTKLLRDYAQIDVRLRQLAFIVKHWAKSRRVNETYQGTLSSYAYVLMCIHFLQQRRPPILpclqemepty 627
Cdd:COG5260 172 ISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLF---------- 241

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 628 svrvdnirctyFDNVDRLRNFGSNNRETIAELVWGFFNYWAYAHDYAYNVVSVRTG-SILGKREKDWTrrVGNDRHLICI 706
Cdd:COG5260 242 -----------FDNGLLSPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGdFYLPKYEKGWL--KPSKPNSLSI 308

                       330       340       350
                ....*....|....*....|....*....|....
gi 18406841 707 EDPFeTSHDLGRVVDKFSIRVLREEFERAARIMH 740
Cdd:COG5260 309 QDPG-TDRNNDISAVSFNIKDIKAAFIRAFELLS 341
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 456-566 1.82e-39

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: 141.16  E-value: 1.82e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 456 RQLMAHLENLVAKEWPHAKLYLYGSCANSFGFPKSDIDVCLAIEGDDINKSEMLLKLAEILE-SDNLQNVQALTRARVPI 534
Cdd:cd05402   3 EEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKkSGEVVEVEPIINARVPI 82

                        90       100       110
                ....*....|....*....|....*....|..
gi 18406841 535 VKLMDPVTGISCDICINNVLAVVNTKLLRDYA 566
Cdd:cd05402  83 IKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 655-714 2.43e-20

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: 84.93  E-value: 2.43e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841   655 TIAELVWGFFNYWAYAHDYAYNVVSVRTGSILGKREKDWTRRVGNDRHLICIEDPFETSH 714
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGGILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 5-107 4.97e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 4.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841     5 GAEPPAPPSSINAGEFLLSILHGS----PSPSSQGPQH--H----QSFALD-----------PAIAAIGPTVNNP-FPPS 62
Cdd:pfam03154 251 PMTQPPPPSQVSPQPLPQPSLHGQmppmPHSLQTGPSHmqHpvppQPFPLTpqssqsqvppgPSPAAPGQSQQRIhTPPS 330

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 18406841    63 NWQSNGHRPSNHNP-PSWPLAFspPHNLSPNFLGFPQFP-------------PSPFTTN 107
Cdd:pfam03154 331 QSQLQSQQPPREQPlPPAPLSM--PHIKPPPTTPIPQLPnpqshkhpphlsgPSPFQMN 387
 
Name Accession Description Interval E-value
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
401-740 1.09e-52

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 190.37  E-value: 1.09e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 401 EKESRVDNRGQRLLGQKARMVK------MYMACRNDIHRYDATFIAIYKSLIPAEEELEKQRQLMAHLENLVAKEWPHAK 474
Cdd:COG5260  18 EFETIMEQKERRPLDAKKVSIQellelsIDSVFNEESDELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDAD 97

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 475 LYLYGSCANSFGFPKSDIDVCL----AIEGDDINKSE---MLLKLAEILEsdnlqnVQALTRARVPIVKLMDPVTGISCD 547
Cdd:COG5260  98 LKVFGSTETGLALPKSDIDLCIisdpRGYKETRNAGSlasHLFKKNLAKE------VVVVSTARVPIIKLVDPQSGLHCD 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 548 ICINNVLAVVNTKLLRDYAQIDVRLRQLAFIVKHWAKSRRVNETYQGTLSSYAYVLMCIHFLQQRRPPILpclqemepty 627
Cdd:COG5260 172 ISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLF---------- 241

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 628 svrvdnirctyFDNVDRLRNFGSNNRETIAELVWGFFNYWAYAHDYAYNVVSVRTG-SILGKREKDWTrrVGNDRHLICI 706
Cdd:COG5260 242 -----------FDNGLLSPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGdFYLPKYEKGWL--KPSKPNSLSI 308

                       330       340       350
                ....*....|....*....|....*....|....
gi 18406841 707 EDPFeTSHDLGRVVDKFSIRVLREEFERAARIMH 740
Cdd:COG5260 309 QDPG-TDRNNDISAVSFNIKDIKAAFIRAFELLS 341
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 456-566 1.82e-39

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: 141.16  E-value: 1.82e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 456 RQLMAHLENLVAKEWPHAKLYLYGSCANSFGFPKSDIDVCLAIEGDDINKSEMLLKLAEILE-SDNLQNVQALTRARVPI 534
Cdd:cd05402   3 EEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKkSGEVVEVEPIINARVPI 82

                        90       100       110
                ....*....|....*....|....*....|..
gi 18406841 535 VKLMDPVTGISCDICINNVLAVVNTKLLRDYA 566
Cdd:cd05402  83 IKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 655-714 2.43e-20

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: 84.93  E-value: 2.43e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841   655 TIAELVWGFFNYWAYAHDYAYNVVSVRTGSILGKREKDWTRRVGNDRHLICIEDPFETSH 714
Cdd:pfam03828   1 SLGELLIGFFEYYGREFDYENVVISIRTGGILSKKEKGWLRNEGRRPFLLCIEDPFDLDN 60
TUTase pfam19088
TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase ...
 449-546 2.78e-07

TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase enzymes. Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species.


Pssm-ID: 465974  Cd Length: 218  Bit Score: 52.06  E-value: 2.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841   449 EEELEKQRQLMAHLENLVAKEWPHAKLYLYGSCANSFGFPKSDIDVclaiegdDI------NKSEMLLKLAEILE-SDNL 521
Cdd:pfam19088 117 DEDFEVRQEIVTRMEKIIQQHLPDCSLRLYGSCLTRFAFKTSDINI-------DVqfpstmTQPDVLIQVLEILKnSESY 189

                          90       100
                  ....*....|....*....|....*
gi 18406841   522 QNVQALTRARVPIVKLMDPVTGISC 546
Cdd:pfam19088 190 SDVESDFHAKVPVVFCRDKQSGLMC 214
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 5-107 4.97e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 4.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841     5 GAEPPAPPSSINAGEFLLSILHGS----PSPSSQGPQH--H----QSFALD-----------PAIAAIGPTVNNP-FPPS 62
Cdd:pfam03154 251 PMTQPPPPSQVSPQPLPQPSLHGQmppmPHSLQTGPSHmqHpvppQPFPLTpqssqsqvppgPSPAAPGQSQQRIhTPPS 330

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 18406841    63 NWQSNGHRPSNHNP-PSWPLAFspPHNLSPNFLGFPQFP-------------PSPFTTN 107
Cdd:pfam03154 331 QSQLQSQQPPREQPlPPAPLSM--PHIKPPPTTPIPQLPnpqshkhpphlsgPSPFQMN 387
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 462-517 5.05e-04

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: 39.71  E-value: 5.05e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 18406841   462 LENLVAKEWPHAKLYLYGSCANSFGFPKSDIDVClaIEGDDINKSEMLLKLAEILE 517
Cdd:pfam01909   4 LREILKELFPVAEVVLFGSYARGTALPGSDIDLL--VVFPEPVEEERLLKLAKIIK 57
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 456-524 5.72e-04

Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is related to the substrate-binding domain of S. aureus KNTase. The genes encoding HI0073 and HI0074 form an operon. Little is known about the substrate specificity or function of two-component NTs. The characterized members of this subgroup may not be representive of the function of this subgroup. This subgroup 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, co-ordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.


Pssm-ID: 143393  Cd Length: 93  Bit Score: 39.71  E-value: 5.72e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 456 RQLMAHLENLVAKEWPH-AKLYLYGSCANSFGFPKSDIDvcLAIEGDDINKSEMLLKLAEILESDNLQNV 524
Cdd:cd05403   1 EEILEEILEILRELLGGvEKVYLFGSYARGDARPDSDID--LLVIFDDPLDPLELARLLEELELLLGRPV 68
SOBP pfam15279
Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual ...
 7-108 5.75e-04

Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein.


Pssm-ID: 464609 [Multi-domain]  Cd Length: 325  Bit Score: 42.88  E-value: 5.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841     7 EPPAPPSSINAGEFLLSILHGSPSPSSQGPQhhqSFALDPAIAAIGPtvnNPFPPSNWQ--SNG---------HRPSNHN 75
Cdd:pfam15279 180 HPPPSPLPAFMEPSSMPPPFLRPPPSIPQPN---SPLSNPMLPGIGP---PPKPPRNLGppSNPmhrppfsphHPPPPPT 253

                          90       100       110
                  ....*....|....*....|....*....|...
gi 18406841    76 PPSWPLAFSPPHNLSPNFLGFPQFPPSPFTTNQ 108
Cdd:pfam15279 254 PPGPPPGLPPPPPRGFTPPFGPPFPPVNMMPNP 286
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
 449-588 1.05e-03

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: 42.12  E-value: 1.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841   449 EEELEKQRQLMAHLENLVaKEW----------PHAKLYLYGSCANSFGF-------PKSDIDVCLAIEGDDINK---SEM 508
Cdd:pfam04928  35 EEETQKREEVLGKLNKLV-KEFvkrvskekglPESVAKEAGGKIFTFGSyrlgvhgPGSDIDTLCVVPKHVTREdffTSF 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841   509 LLKLAEILESDNLQNVQAltrARVPIVKLMdpVTGISCD-ICINNVLAVV-------NTKLLRDYAQIDVR--------- 571
Cdd:pfam04928 114 LEMLRERPEVTELTAVPD---AFVPVIKFK--FSGISIDlLFARLALPSVpddldlsDDNLLRNLDEKCVRslngcrvtd 188

                         170       180
                  ....*....|....*....|....*....
gi 18406841   572 --LRQ----------LAFIvKHWAKSRRV 588
Cdd:pfam04928 189 eiLRLvpnvetfrtaLRAI-KLWAKRRGI 216
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
449-517 3.06e-03

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 37.59  E-value: 3.06e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18406841 449 EEELEKQRQLMAHLenlvAKEWPHAKLYLYGSCA-NSFGfPKSDIDVClaIEGDDINKSEMLLKLAEILE 517
Cdd:COG1669   4 EEILEILREVIEEL----AERYGVSRLGLFGSVArGEAR-EDSDIDLL--VEFDEPTSLFDLFELEEELE 66
 
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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