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Conserved domains on  [gi|17554128|ref|NP_498099|]
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4Fe-4S ferredoxin-type domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

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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; ...
 1029-1151 2.23e-30

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: 116.50  E-value: 2.23e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1029 MLDHKIDELQSFLRKNYrEDVTLTTFGSVMTGLSVNCSDIDICLrfgdgDVPPKDLTAKEVIQKTESVLRKCHLVKRVQA 1108
Cdd:cd05402    1 KREEVLDRLQELIKEWF-PGAKLYPFGSYVTGLGLPGSDIDLCL-----LGPNHRVDREDFLRKLAKLLKKSGEVVEVEP 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 17554128 1109 IVTAKVPIVKFQVKLSNgaiIDVDISYYNILAIYNTALLKEYS 1151
Cdd:cd05402   75 IINARVPIIKFVDKPTG---IEVDISFNNLNGIRNTKLLRAYV 114
TRF4 super family cl34961
DNA polymerase sigma [Replication, recombination and repair];
1034-1317 2.39e-23

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: 105.62  E-value: 2.39e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1034 IDELQSFLRKNYrEDVTLTTFGSVMTGLSVNCSDIDICLRFGDgdVPPKDLTAKEVIQKTesvLRKCHLVKRVQAIVTAK 1113
Cdd:COG5260   82 LEKLRTLLKKEF-PDADLKVFGSTETGLALPKSDIDLCIISDP--RGYKETRNAGSLASH---LFKKNLAKEVVVVSTAR 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1114 VPIVKFQVKLSNgaiIDVDISYYNILAIYNTALLKEYSLWTPdkRFAKLALFVKTWAKNCEIGDASRGSLSSYCHVIMLI 1193
Cdd:COG5260  156 VPIIKLVDPQSG---LHCDISFNNTNGIVNAKLIRSYLKEDP--RLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVL 230

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1194 SYLQNCDPPVlprlqedfrsdnrerrLVDNWDTSFAQVEtsllqrwpKNKESCAQLLIGYFDYYSR-FDFRNFVVQCRR- 1271
Cdd:COG5260  231 SFLQMHPPFL----------------FFDNGLLSPLKYN--------KNIDNLGVLFDDFFELYGKsFNYSLVVLSINSg 286

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17554128 1272 EMILSKMEKEW-----PRPLCVEDPF-DLSHNLSSG-VNKKMfvfIMKVFINS 1317
Cdd:COG5260  287 DFYLPKYEKGWlkpskPNSLSIQDPGtDRNNDISAVsFNIKD---IKAAFIRA 336
TUTase super family cl41074
TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase ...
 257-395 3.89e-09

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.


The actual alignment was detected with superfamily member pfam19088:

Pssm-ID: 465974  Cd Length: 218  Bit Score: 58.60  E-value: 3.89e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128    257 IKKLVDRLEAFPEAIYYCEKCDYHINTIGHAKAHLESSTHFDDVKrQEQREHLLKIIPPPTEAHLESVEKVLEGTlksyq 336
Cdd:pfam19088   36 IHRLKKRSPEYPNFQYLCKLCSVHIENIQGAHKHIKEKRHKKNIM-EKQEENELRALPPPSPAQLKALGAAVLEV----- 109

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17554128    337 qVRQNGI-----EIGETIIYYLSTTVFPSigLQDVILRPFGSVTYDVTLPDSDYN--VAY--TMSIPE 395
Cdd:pfam19088  110 -AQEHGIsdedfEVRQEIVTRMEKIIQQH--LPDCSLRLYGSCLTRFAFKTSDINidVQFpsTMTQPD 174
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 574-625 7.48e-05

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: 41.79  E-value: 7.48e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128    574 NLAELFIGFFRYYVERH--RDVVIQITQLIPMSRDVSRW------NKKILHVVDPFRGDN 625
Cdd:pfam03828    1 SLGELLIGFFEYYGREFdyENVVISIRTGGILSKKEKGWlrnegrRPFLLCIEDPFDLDN 60
 
Name Accession Description Interval E-value
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 1029-1151 2.23e-30

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: 116.50  E-value: 2.23e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1029 MLDHKIDELQSFLRKNYrEDVTLTTFGSVMTGLSVNCSDIDICLrfgdgDVPPKDLTAKEVIQKTESVLRKCHLVKRVQA 1108
Cdd:cd05402    1 KREEVLDRLQELIKEWF-PGAKLYPFGSYVTGLGLPGSDIDLCL-----LGPNHRVDREDFLRKLAKLLKKSGEVVEVEP 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 17554128 1109 IVTAKVPIVKFQVKLSNgaiIDVDISYYNILAIYNTALLKEYS 1151
Cdd:cd05402   75 IINARVPIIKFVDKPTG---IEVDISFNNLNGIRNTKLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
1034-1317 2.39e-23

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 105.62  E-value: 2.39e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1034 IDELQSFLRKNYrEDVTLTTFGSVMTGLSVNCSDIDICLRFGDgdVPPKDLTAKEVIQKTesvLRKCHLVKRVQAIVTAK 1113
Cdd:COG5260   82 LEKLRTLLKKEF-PDADLKVFGSTETGLALPKSDIDLCIISDP--RGYKETRNAGSLASH---LFKKNLAKEVVVVSTAR 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1114 VPIVKFQVKLSNgaiIDVDISYYNILAIYNTALLKEYSLWTPdkRFAKLALFVKTWAKNCEIGDASRGSLSSYCHVIMLI 1193
Cdd:COG5260  156 VPIIKLVDPQSG---LHCDISFNNTNGIVNAKLIRSYLKEDP--RLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVL 230

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1194 SYLQNCDPPVlprlqedfrsdnrerrLVDNWDTSFAQVEtsllqrwpKNKESCAQLLIGYFDYYSR-FDFRNFVVQCRR- 1271
Cdd:COG5260  231 SFLQMHPPFL----------------FFDNGLLSPLKYN--------KNIDNLGVLFDDFFELYGKsFNYSLVVLSINSg 286

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17554128 1272 EMILSKMEKEW-----PRPLCVEDPF-DLSHNLSSG-VNKKMfvfIMKVFINS 1317
Cdd:COG5260  287 DFYLPKYEKGWlkpskPNSLSIQDPGtDRNNDISAVsFNIKD---IKAAFIRA 336
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 1247-1296 2.66e-14

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: 68.75  E-value: 2.66e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17554128   1247 AQLLIGYFDYYSR-FDFRNFVVQCRREMILSKMEKEW-------PRPLCVEDPFDLSH 1296
Cdd:pfam03828    3 GELLIGFFEYYGReFDYENVVISIRTGGILSKKEKGWlrnegrrPFLLCIEDPFDLDN 60
TUTase pfam19088
TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase ...
 257-395 3.89e-09

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: 58.60  E-value: 3.89e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128    257 IKKLVDRLEAFPEAIYYCEKCDYHINTIGHAKAHLESSTHFDDVKrQEQREHLLKIIPPPTEAHLESVEKVLEGTlksyq 336
Cdd:pfam19088   36 IHRLKKRSPEYPNFQYLCKLCSVHIENIQGAHKHIKEKRHKKNIM-EKQEENELRALPPPSPAQLKALGAAVLEV----- 109

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17554128    337 qVRQNGI-----EIGETIIYYLSTTVFPSigLQDVILRPFGSVTYDVTLPDSDYN--VAY--TMSIPE 395
Cdd:pfam19088  110 -AQEHGIsdedfEVRQEIVTRMEKIIQQH--LPDCSLRLYGSCLTRFAFKTSDINidVQFpsTMTQPD 174
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 574-625 7.48e-05

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: 41.79  E-value: 7.48e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128    574 NLAELFIGFFRYYVERH--RDVVIQITQLIPMSRDVSRW------NKKILHVVDPFRGDN 625
Cdd:pfam03828    1 SLGELLIGFFEYYGREFdyENVVISIRTGGILSKKEKGWlrnegrRPFLLCIEDPFDLDN 60
 
Name Accession Description Interval E-value
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 1029-1151 2.23e-30

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: 116.50  E-value: 2.23e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1029 MLDHKIDELQSFLRKNYrEDVTLTTFGSVMTGLSVNCSDIDICLrfgdgDVPPKDLTAKEVIQKTESVLRKCHLVKRVQA 1108
Cdd:cd05402    1 KREEVLDRLQELIKEWF-PGAKLYPFGSYVTGLGLPGSDIDLCL-----LGPNHRVDREDFLRKLAKLLKKSGEVVEVEP 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 17554128 1109 IVTAKVPIVKFQVKLSNgaiIDVDISYYNILAIYNTALLKEYS 1151
Cdd:cd05402   75 IINARVPIIKFVDKPTG---IEVDISFNNLNGIRNTKLLRAYV 114
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
1034-1317 2.39e-23

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 105.62  E-value: 2.39e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1034 IDELQSFLRKNYrEDVTLTTFGSVMTGLSVNCSDIDICLRFGDgdVPPKDLTAKEVIQKTesvLRKCHLVKRVQAIVTAK 1113
Cdd:COG5260   82 LEKLRTLLKKEF-PDADLKVFGSTETGLALPKSDIDLCIISDP--RGYKETRNAGSLASH---LFKKNLAKEVVVVSTAR 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1114 VPIVKFQVKLSNgaiIDVDISYYNILAIYNTALLKEYSLWTPdkRFAKLALFVKTWAKNCEIGDASRGSLSSYCHVIMLI 1193
Cdd:COG5260  156 VPIIKLVDPQSG---LHCDISFNNTNGIVNAKLIRSYLKEDP--RLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVL 230

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128 1194 SYLQNCDPPVlprlqedfrsdnrerrLVDNWDTSFAQVEtsllqrwpKNKESCAQLLIGYFDYYSR-FDFRNFVVQCRR- 1271
Cdd:COG5260  231 SFLQMHPPFL----------------FFDNGLLSPLKYN--------KNIDNLGVLFDDFFELYGKsFNYSLVVLSINSg 286

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17554128 1272 EMILSKMEKEW-----PRPLCVEDPF-DLSHNLSSG-VNKKMfvfIMKVFINS 1317
Cdd:COG5260  287 DFYLPKYEKGWlkpskPNSLSIQDPGtDRNNDISAVsFNIKD---IKAAFIRA 336
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 1247-1296 2.66e-14

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: 68.75  E-value: 2.66e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17554128   1247 AQLLIGYFDYYSR-FDFRNFVVQCRREMILSKMEKEW-------PRPLCVEDPFDLSH 1296
Cdd:pfam03828    3 GELLIGFFEYYGReFDYENVVISIRTGGILSKKEKGWlrnegrrPFLLCIEDPFDLDN 60
TUTase pfam19088
TUTase nucleotidyltransferase domain; This nucleotidyltransferase domain is found in TUTase ...
 257-395 3.89e-09

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: 58.60  E-value: 3.89e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128    257 IKKLVDRLEAFPEAIYYCEKCDYHINTIGHAKAHLESSTHFDDVKrQEQREHLLKIIPPPTEAHLESVEKVLEGTlksyq 336
Cdd:pfam19088   36 IHRLKKRSPEYPNFQYLCKLCSVHIENIQGAHKHIKEKRHKKNIM-EKQEENELRALPPPSPAQLKALGAAVLEV----- 109

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17554128    337 qVRQNGI-----EIGETIIYYLSTTVFPSigLQDVILRPFGSVTYDVTLPDSDYN--VAY--TMSIPE 395
Cdd:pfam19088  110 -AQEHGIsdedfEVRQEIVTRMEKIIQQH--LPDCSLRLYGSCLTRFAFKTSDINidVQFpsTMTQPD 174
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
 574-625 7.48e-05

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: 41.79  E-value: 7.48e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554128    574 NLAELFIGFFRYYVERH--RDVVIQITQLIPMSRDVSRW------NKKILHVVDPFRGDN 625
Cdd:pfam03828    1 SLGELLIGFFEYYGREFdyENVVISIRTGGILSKKEKGWlrnegrRPFLLCIEDPFDLDN 60
 
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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