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Conserved domains on  [gi|86562618|ref|NP_498807|]
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CID domain-containing protein 1 [Caenorhabditis elegans]

Protein Classification

ENTH domain-containing protein( domain architecture ID 581786)

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
VHS_ENTH_ANTH super family cl02544
VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a ...
 4-133 1.59e-58

VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a VHS, CID, ENTH, or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The CTD-Interacting Domain (CID) is present in several RNA-processing factors and binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP II or Pol II). The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-Terminal Homology (ANTH) domain. VHS, ENTH, and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH and ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding.


The actual alignment was detected with superfamily member cd17002:

Pssm-ID: 470608  Cd Length: 128  Bit Score: 184.00  E-value: 1.59e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   4 FTEQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKEThGSKIVNLLYVANDVSQNARKTCPQFKDEFF 83
Cdd:cd17002   1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEK-PSKKLTLLYLANDVIQNSRKKGPEFTKEFA 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 86562618  84 PAIESSFRHAIELkNAKEVEHAIGKLINVWKDRQIFTPSQCKRLHEVHQQ 133
Cdd:cd17002  80 PVLEDAFKHVAKL-TDSEVLKALERILNIWKERQVYEKDFIEQLRAALRK 128
CREPT super family cl24960
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 169-310 2.51e-44

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.


The actual alignment was detected with superfamily member pfam16566:

Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 148.15  E-value: 2.51e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   169 QDVLLSLKRLQNPPSTEREIRTELSKYPDNISCPEKLQSVRSSQEAQSLLVQNEEALPMLEEYVKRLKNETNERETLESN 248
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 86562618   249 LNMLIENVRMSIEHHEKLCREVKRREDRIKADLLEVEKTFESLPDLaAEMPN-----APLPTLEALF 310
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDL-TLLPDvtgglAPLPSAGDLF 146
 
Name Accession Description Interval E-value
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 4-133 1.59e-58

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: 184.00  E-value: 1.59e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   4 FTEQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKEThGSKIVNLLYVANDVSQNARKTCPQFKDEFF 83
Cdd:cd17002   1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEK-PSKKLTLLYLANDVIQNSRKKGPEFTKEFA 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 86562618  84 PAIESSFRHAIELkNAKEVEHAIGKLINVWKDRQIFTPSQCKRLHEVHQQ 133
Cdd:cd17002  80 PVLEDAFKHVAKL-TDSEVLKALERILNIWKERQVYEKDFIEQLRAALRK 128
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 169-310 2.51e-44

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: 148.15  E-value: 2.51e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   169 QDVLLSLKRLQNPPSTEREIRTELSKYPDNISCPEKLQSVRSSQEAQSLLVQNEEALPMLEEYVKRLKNETNERETLESN 248
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 86562618   249 LNMLIENVRMSIEHHEKLCREVKRREDRIKADLLEVEKTFESLPDLaAEMPN-----APLPTLEALF 310
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDL-TLLPDvtgglAPLPSAGDLF 146
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-132 4.20e-37

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 128.93  E-value: 4.20e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618      8 TLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKETHGSKIVnLLYVANDVSQNA-RKTCPQFKDEFFPAI 86
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLP-LLYLLDSIVQNSkRKYGSEFGDELGPVF 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 86562618     87 ESSFRHAIELKNaKEVEHAIGKLINVWKDRQIFTPSQCKRLHEVHQ 132
Cdd:smart00582  80 QDALRRVLGAAP-EELKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 7-124 3.45e-26

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: 99.98  E-value: 3.45e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618     7 QTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKEThGSKIVNLLYVANDVSQNAR-KTCPQFKDEFFPA 85
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAK-PEKKLHLLYLANDVLQNSRkKGKSEFADAFEPV 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 86562618    86 IESSFRHAIElKNAKEVEHAIGKLINVWKDRQIFTPSQC 124
Cdd:pfam04818  80 LPEAFASAYK-KCDEKLKKKLERLLNIWEERNVFSPEVI 117
 
Name Accession Description Interval E-value
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 4-133 1.59e-58

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: 184.00  E-value: 1.59e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   4 FTEQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKEThGSKIVNLLYVANDVSQNARKTCPQFKDEFF 83
Cdd:cd17002   1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEK-PSKKLTLLYLANDVIQNSRKKGPEFTKEFA 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 86562618  84 PAIESSFRHAIELkNAKEVEHAIGKLINVWKDRQIFTPSQCKRLHEVHQQ 133
Cdd:cd17002  80 PVLEDAFKHVAKL-TDSEVLKALERILNIWKERQVYEKDFIEQLRAALRK 128
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 169-310 2.51e-44

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: 148.15  E-value: 2.51e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   169 QDVLLSLKRLQNPPSTEREIRTELSKYPDNISCPEKLQSVRSSQEAQSLLVQNEEALPMLEEYVKRLKNETNERETLESN 248
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 86562618   249 LNMLIENVRMSIEHHEKLCREVKRREDRIKADLLEVEKTFESLPDLaAEMPN-----APLPTLEALF 310
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDL-TLLPDvtgglAPLPSAGDLF 146
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-132 4.20e-37

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 128.93  E-value: 4.20e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618      8 TLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKETHGSKIVnLLYVANDVSQNA-RKTCPQFKDEFFPAI 86
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLP-LLYLLDSIVQNSkRKYGSEFGDELGPVF 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 86562618     87 ESSFRHAIELKNaKEVEHAIGKLINVWKDRQIFTPSQCKRLHEVHQ 132
Cdd:smart00582  80 QDALRRVLGAAP-EELKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 7-124 3.45e-26

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: 99.98  E-value: 3.45e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618     7 QTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKEThGSKIVNLLYVANDVSQNAR-KTCPQFKDEFFPA 85
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAK-PEKKLHLLYLANDVLQNSRkKGKSEFADAFEPV 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 86562618    86 IESSFRHAIElKNAKEVEHAIGKLINVWKDRQIFTPSQC 124
Cdd:pfam04818  80 LPEAFASAYK-KCDEKLKKKLERLLNIWEERNVFSPEVI 117
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 6-130 5.86e-26

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: 99.58  E-value: 5.86e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   6 EQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKETHGSKIVnLLYVANDVSQNARKT-CPQFKDEFFP 84
Cdd:cd16981   1 EEALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLT-LLYLANDVLQNSRRKgAPEFVEAFKK 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 86562618  85 AIESSFRHAIELKNAKeVEHAIGKLINVWKDRQIFTPSQCKRLHEV 130
Cdd:cd16981  80 VLPEALALVRSEGDES-VRKKVLRVLNIWEERNVFGSEFLAELRAI 124
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 4-130 2.51e-21

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: 87.79  E-value: 2.51e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   4 FTEQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKETHGSKIvNLLYVANDVSQNARKTCPQFKDEFF 83
Cdd:cd17011   1 FSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKL-TFLYLANDVIQNSKRKGPEFTKDFA 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 86562618  84 PAIESSFRHaIELKNAKEVEHAIGKLINVWKDRQIFTPSQCKRLHEV 130
Cdd:cd17011  80 PVIVEAFKH-VSSETDESCKKHLGRVLSIWEERSVYENDVLEQLKQA 125
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 4-137 2.43e-18

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: 79.66  E-value: 2.43e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   4 FTEQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKeTHGSKIVNLLYVANDVSQNARKTCPQFKDEFF 83
Cdd:cd17012   2 FSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRK-AKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 86562618  84 PAIESSFRHAielknAKEVEHAIGK----LINVWKDRQIFTPsqckrlhEVHQQVKLS 137
Cdd:cd17012  81 SVLVDAFSHV-----AREADEGCKKplerLLNIWQERSVYGG-------DFIQQLKLS 126
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 6-129 9.38e-18

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: 78.03  E-value: 9.38e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   6 EQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKETHGS-KIVNLLYVANDVSQNAR-KTCPQFKDEFF 83
Cdd:cd17003   1 EEQFISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSSVNSrRKLLLIYLANDVVQQAKaKKKTEFIDAFS 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 86562618  84 P----AIESSFRHAI-ELKNakevehAIGKLINVWKDRQIFTPSQCKRLHE 129
Cdd:cd17003  81 KvlpeVLEKIYPSLPsDIKK------KIKRVVNVWKQRQIFSKDVIDDIEE 125
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 6-119 1.60e-11

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: 60.70  E-value: 1.60e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   6 EQTLRQKLTNLSNHPSSIQTTSAWLLQNHSNRELIIRVWLKTVKKETHGSKIvNLLYVANDVSQNA-RKTCPQFKDEFFP 84
Cdd:cd17001   3 ESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRL-NLFYLANDVIQNCkRKNAIVFRESFAE 81

                        90       100       110
                ....*....|....*....|....*....|....*
gi 86562618  85 AIESSfrhAIELKNAKeVEHAIGKLINVWKDRQIF 119
Cdd:cd17001  82 VLPEA---AALVKDAS-VSKSVERIFKIWEERNVY 112
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 7-119 1.31e-09

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: 55.22  E-value: 1.31e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86562618   7 QTLRQKLTNLSNHP-SSIQTTSAWLLQNHSNRELIIRVWLKTVKKETHGSKiVNLLYVANDVSQNARKTCPQFKDEFFPA 85
Cdd:cd03562   1 KAFNSKLEELSDLSqQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRK-LTFLYLIDSIIRNSKRKGPEFTKDFSPV 79

                        90       100       110
                ....*....|....*....|....*....|....
gi 86562618  86 IESSFRHAIELKNAKEVEHaIGKLINVWKDRQIF 119
Cdd:cd03562  80 IVELFKHVYSETDEDCKKK-LGRVLSIWEERNVF 112
 
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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