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Conserved domains on  [gi|167876243|gb|EDS39626|]
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conserved hypothetical protein [Culex quinquefasciatus]

Protein Classification

ENTH domain-containing protein( domain architecture ID 13017379)

ENTH (Epsin N-Terminal Homology) domain-containing protein may be involved in clathrin-mediated endocytosis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 234-380 8.09e-80

Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours.


:

Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 241.37  E-value: 8.09e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243  234 EELIRVIQELENSASSDAAVRERIANLPPEVSELSALAKLEDKEAAMRLAVKVNDAIKILNDYNARLASEMDDRKKLTTM 313
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167876243  314 LKDFQREQQELLAQAEQRLEEYTSKLSKIKEVQREVRNHMNNLPDLTALPDVTGGLAPLPSAGDLFN 380
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDLTLLPDVTGGLAPLPSAGDLFS 147
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 4-132 8.42e-66

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and similar proteins; This subfamily contains Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A) and 1B (RPRD1B) from jawed vertebrates, CID domain-containing protein 1 (CIDS1 or cids-1) from Caenorhabditis elegans, and similar proteins. RPRD1A and RPRD1B are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains. Both associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. The function of CIDS1 is not yet known. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


:

Pssm-ID: 340799  Cd Length: 128  Bit Score: 204.80  E-value: 8.42e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   4 FTESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGPEFGKEYEN 83
Cdd:cd17002    1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGPEFTKEFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 167876243  84 VLLKAFKLIAGSGpEEKTIHSLNRILNIWGERGVYDEPKIKEYSAALNQ 132
Cdd:cd17002   81 VLEDAFKHVAKLT-DSEVLKALERILNIWKERQVYEKDFIEQLRAALRK 128
 
Name Accession Description Interval E-value
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 234-380 8.09e-80

Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours.


Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 241.37  E-value: 8.09e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243  234 EELIRVIQELENSASSDAAVRERIANLPPEVSELSALAKLEDKEAAMRLAVKVNDAIKILNDYNARLASEMDDRKKLTTM 313
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167876243  314 LKDFQREQQELLAQAEQRLEEYTSKLSKIKEVQREVRNHMNNLPDLTALPDVTGGLAPLPSAGDLFN 380
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDLTLLPDVTGGLAPLPSAGDLFS 147
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 4-132 8.42e-66

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and similar proteins; This subfamily contains Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A) and 1B (RPRD1B) from jawed vertebrates, CID domain-containing protein 1 (CIDS1 or cids-1) from Caenorhabditis elegans, and similar proteins. RPRD1A and RPRD1B are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains. Both associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. The function of CIDS1 is not yet known. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340799  Cd Length: 128  Bit Score: 204.80  E-value: 8.42e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   4 FTESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGPEFGKEYEN 83
Cdd:cd17002    1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGPEFTKEFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 167876243  84 VLLKAFKLIAGSGpEEKTIHSLNRILNIWGERGVYDEPKIKEYSAALNQ 132
Cdd:cd17002   81 VLEDAFKHVAKLT-DSEVLKALERILNIWKERQVYEKDFIEQLRAALRK 128
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 9-123 1.01e-45

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 152.75  E-value: 1.01e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243    9 LVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKG-PEFGKEYENVLLK 87
Cdd:pfam04818   3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVLPE 82

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 167876243   88 AFKLIAGSGPeEKTIHSLNRILNIWGERGVYDEPKI 123
Cdd:pfam04818  83 AFASAYKKCD-EKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
9-131 1.01e-38

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 134.71  E-value: 1.01e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243     9 LVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSK-KKGPEFGKEYENVLLK 87
Cdd:smart00582   2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKrKYGSEFGDELGPVFQD 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 167876243    88 AFKLIAGSGPEEkTIHSLNRILNIWGERGVYDEPKIKEYSAALN 131
Cdd:smart00582  82 ALRRVLGAAPEE-LKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
 
Name Accession Description Interval E-value
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 234-380 8.09e-80

Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours.


Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 241.37  E-value: 8.09e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243  234 EELIRVIQELENSASSDAAVRERIANLPPEVSELSALAKLEDKEAAMRLAVKVNDAIKILNDYNARLASEMDDRKKLTTM 313
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167876243  314 LKDFQREQQELLAQAEQRLEEYTSKLSKIKEVQREVRNHMNNLPDLTALPDVTGGLAPLPSAGDLFN 380
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDLTLLPDVTGGLAPLPSAGDLFS 147
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 4-132 8.42e-66

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and similar proteins; This subfamily contains Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A) and 1B (RPRD1B) from jawed vertebrates, CID domain-containing protein 1 (CIDS1 or cids-1) from Caenorhabditis elegans, and similar proteins. RPRD1A and RPRD1B are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains. Both associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. The function of CIDS1 is not yet known. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340799  Cd Length: 128  Bit Score: 204.80  E-value: 8.42e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   4 FTESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGPEFGKEYEN 83
Cdd:cd17002    1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGPEFTKEFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 167876243  84 VLLKAFKLIAGSGpEEKTIHSLNRILNIWGERGVYDEPKIKEYSAALNQ 132
Cdd:cd17002   81 VLEDAFKHVAKLT-DSEVLKALERILNIWKERQVYEKDFIEQLRAALRK 128
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 6-130 6.90e-53

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340778  Cd Length: 125  Bit Score: 171.61  E-value: 6.90e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   6 ESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKG-PEFGKEYENV 84
Cdd:cd16981    1 EEALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGaPEFVEAFKKV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 167876243  85 LLKAFKLIAGSGpEEKTIHSLNRILNIWGERGVYDEPKIKEYSAAL 130
Cdd:cd16981   81 LPEALALVRSEG-DESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 3-125 3.68e-48

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; Regulation of nuclear pre-mRNA domain-containing protein 1B (RPRD1B) is also called Cell cycle-related and expression-elevated protein in tumor (CREPT). RPRD1B is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1B form homodimers and heterodimers with RPRD1A through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. RPRD1B is highly expressed during tumorigenesis and in endometrial cancer, has been shown to promote tumor growth by accelerating the cell cycle. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340809  Cd Length: 129  Bit Score: 159.79  E-value: 3.68e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   3 SFTESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGPEFGKEYE 82
Cdd:cd17012    1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 167876243  83 NVLLKAFKLIAGSGpEEKTIHSLNRILNIWGERGVYDEPKIKE 125
Cdd:cd17012   81 SVLVDAFSHVAREA-DEGCKKPLERLLNIWQERSVYGGDFIQQ 122
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 4-130 7.55e-47

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; Regulation of nuclear pre-mRNA domain-containing protein 1A (RPRD1A) is also called Cyclin-dependent kinase inhibitor 2B-related protein or p15INK4B-related protein (P15RS). RPRD1A is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A form homodimers and heterodimers with RPRD1B through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340808  Cd Length: 128  Bit Score: 156.36  E-value: 7.55e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   4 FTESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGPEFGKEYEN 83
Cdd:cd17011    1 FSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGPEFTKDFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 167876243  84 VLLKAFKLIAGSGPEEKTIHsLNRILNIWGERGVYDEPKIKEYSAAL 130
Cdd:cd17011   81 VIVEAFKHVSSETDESCKKH-LGRVLSIWEERSVYENDVLEQLKQAL 126
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 9-123 1.01e-45

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 152.75  E-value: 1.01e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243    9 LVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKG-PEFGKEYENVLLK 87
Cdd:pfam04818   3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVLPE 82

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 167876243   88 AFKLIAGSGPeEKTIHSLNRILNIWGERGVYDEPKI 123
Cdd:pfam04818  83 AFASAYKKCD-EKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
9-131 1.01e-38

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 134.71  E-value: 1.01e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243     9 LVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSK-KKGPEFGKEYENVLLK 87
Cdd:smart00582   2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKrKYGSEFGDELGPVFQD 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 167876243    88 AFKLIAGSGPEEkTIHSLNRILNIWGERGVYDEPKIKEYSAALN 131
Cdd:smart00582  82 ALRRVLGAAPEE-LKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 6-130 7.70e-27

CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar proteins; Yeast transcription termination factor Rtt103 is a CID (CTD-Interacting Domain) containing protein that functions in DNA damage response. It associates with sites of DNA breaks and is essential for recovery from DNA double strand breaks in the chromosome. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). Rtt103 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340800  Cd Length: 127  Bit Score: 103.46  E-value: 7.70e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   6 ESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHR--VSSSKKLTFMYLANDVIQNSK-KKGPEFGKEYE 82
Cdd:cd17003    1 EEQFISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKssVNSRRKLLLIYLANDVVQQAKaKKKTEFIDAFS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 167876243  83 NVLLKAFKLIAGSGPEEktIHS-LNRILNIWGERGVYDEPKIKEYSAAL 130
Cdd:cd17003   81 KVLPEVLEKIYPSLPSD--IKKkIKRVVNVWKQRQIFSKDVIDDIEERL 127
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 9-118 1.73e-23

CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several eukaryotic RNA-processing factors including yeast proteins, Pcf11 and Nrd1, and vertebrate proteins, CTD-associated factors 8 (SCAF8) and Regulation of nuclear pre-mRNA domain-containing proteins (such as RPRD1 and RPRD2). Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340766  Cd Length: 123  Bit Score: 94.51  E-value: 1.73e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   9 LVKKLSEL-NPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGPEFGKEYENVLLK 87
Cdd:cd03562    3 FNSKLEELsDLSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKGPEFTKDFSPVIVE 82

                         90       100       110
                 ....*....|....*....|....*....|.
gi 167876243  88 AFKLIAGSGPEEKTIHsLNRILNIWGERGVY 118
Cdd:cd03562   83 LFKHVYSETDEDCKKK-LGRVLSIWEERNVF 112
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 6-131 2.52e-23

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; Regulation of nuclear pre-mRNA domain-containing protein 2 (RPRD2) is a CID (CTD-Interacting Domain) domain containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340798  Cd Length: 125  Bit Score: 93.83  E-value: 2.52e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   6 ESGLVKKLSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGP-EFGKEYENV 84
Cdd:cd17001    3 ESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAiVFRESFAEV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 167876243  85 LLKAFKLIAgsgpEEKTIHSLNRILNIWGERGVYDEPKIKEYSAALN 131
Cdd:cd17001   83 LPEAAALVK----DASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 19-123 8.51e-06

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340780  Cd Length: 131  Bit Score: 44.91  E-value: 8.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243  19 SQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKK-GPE---FGKEYENVLLKAFKLIAG 94
Cdd:cd16983   18 SKSKINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQyGKEkdvYAPRFAKNLSKTFLNLLK 97

                         90       100
                 ....*....|....*....|....*....
gi 167876243  95 SGPEEKTihSLNRILNIWGERGVYDEPKI 123
Cdd:cd16983   98 CPEKDKP--KVKRVLNLWQKNGVFPKEII 124
CTK3 pfam12243
CTD kinase subunit gamma CTK3; The C-terminal domain kinase (CTDK-1), is a three-subunit ...
 13-119 2.35e-03

CTD kinase subunit gamma CTK3; The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation. The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2.


Pssm-ID: 403455  Cd Length: 123  Bit Score: 37.81  E-value: 2.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167876243   13 LSELNPSQQSIQTLSLWLIHHRKHHSIIVKTWLKELHRVSSSKKLTFMYLANDVIQNSKKKGPEfGKEYENVLLKAF-KL 91
Cdd:pfam12243  13 LRKLNASVQSLQKAAHFALKNRDLEEDLHSCILEQLERGDLNTRANIFYFIDTLCEESLKNGQS-GKPYVRSLKRDIpRL 91

                          90       100       110
                  ....*....|....*....|....*....|..
gi 167876243   92 IAGSGPEEKT----IHSLNRILNIWGERGVYD 119
Cdd:pfam12243  92 VDSVAPDDGSgaanVKSVRKILQSLKLKSLLD 123
 
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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