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Conserved domains on  [gi|665400997|ref|NP_001286428|]
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Pcf11 cleavage and polyadenylation factor subunit, isoform F [Drosophila melanogaster]

Protein Classification

CTD-interacting domain-containing protein( domain architecture ID 13015791)

CTD-interacting domain (CID)-containing protein similar to Caenorhabditis elegans polyadenylation and cleavage factor homolog 11 (Pcf11)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 17-149 6.32e-53

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 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: 340779  Cd Length: 127  Bit Score: 181.61  E-value: 6.32e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   17 EEYLSSLQDLNCNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSSYVQLFGQCIVNI 96
Cdd:cd16982     2 EEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVDL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 665400997   97 FLHAFEsvqhsqsQVLEKVRERMYALRQTWNEVFPPSKMYALDVKVKRLDNNW 149
Cdd:cd16982    82 FLDAYR-------LVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
DUF5401 super family cl38662
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 650-763 2.91e-04

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


The actual alignment was detected with superfamily member pfam17380:

Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 45.88  E-value: 2.91e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   650 LEELRAKLANSARI--QNKQGKSDKSRDQAVSQRLKQLAELKVNDDSQEAHDEKvRTILSQAQEMYENNGMNQEQYKDLV 727
Cdd:pfam17380  440 LEEERAREMERVRLeeQERQQQVERLRQQEEERKRKKLELEKEKRDRKRAEEQR-RKILEKELEERKQAMIEEERKRKLL 518

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 665400997   728 QKVVAINENSKIKESRRRDNDLERNAARDAVLRKRI 763
Cdd:pfam17380  519 EKEMEERQKAIYEEERRREAEEERRKQQEMEERRRI 554
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 17-149 6.32e-53

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 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: 340779  Cd Length: 127  Bit Score: 181.61  E-value: 6.32e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   17 EEYLSSLQDLNCNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSSYVQLFGQCIVNI 96
Cdd:cd16982     2 EEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVDL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 665400997   97 FLHAFEsvqhsqsQVLEKVRERMYALRQTWNEVFPPSKMYALDVKVKRLDNNW 149
Cdd:cd16982    82 FLDAYR-------LVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
18-143 2.03e-22

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 94.27  E-value: 2.03e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997     18 EYLSSLQDLNcNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVK----SSYVQLFGQCI 93
Cdd:smart00582    1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKrkygSEFGDELGPVF 79

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|..
gi 665400997     94 VNIFLHAFESVQhsqsqvlEKVRERMYALRQTW--NEVFPPSKMYALDVKVK 143
Cdd:smart00582   80 QDALRRVLGAAP-------EELKKKIRRLLNIWeeRGIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 23-135 5.65e-15

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: 73.01  E-value: 5.65e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997    23 LQDLNcNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVK----SSYVQLFGQCIVNIFL 98
Cdd:pfam04818    7 LSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRkkgkSEFADAFEPVLPEAFA 85

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 665400997    99 HAFEsvqhsqsQVLEKVRERMYALRQTWNE--VFPPSKM 135
Cdd:pfam04818   86 SAYK-------KCDEKLKKKLERLLNIWEErnVFSPEVI 117
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 650-763 2.91e-04

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 45.88  E-value: 2.91e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   650 LEELRAKLANSARI--QNKQGKSDKSRDQAVSQRLKQLAELKVNDDSQEAHDEKvRTILSQAQEMYENNGMNQEQYKDLV 727
Cdd:pfam17380  440 LEEERAREMERVRLeeQERQQQVERLRQQEEERKRKKLELEKEKRDRKRAEEQR-RKILEKELEERKQAMIEEERKRKLL 518

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 665400997   728 QKVVAINENSKIKESRRRDNDLERNAARDAVLRKRI 763
Cdd:pfam17380  519 EKEMEERQKAIYEEERRREAEEERRKQQEMEERRRI 554
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 17-149 6.32e-53

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 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: 340779  Cd Length: 127  Bit Score: 181.61  E-value: 6.32e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   17 EEYLSSLQDLNCNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSSYVQLFGQCIVNI 96
Cdd:cd16982     2 EEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVDL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 665400997   97 FLHAFEsvqhsqsQVLEKVRERMYALRQTWNEVFPPSKMYALDVKVKRLDNNW 149
Cdd:cd16982    82 FLDAYR-------LVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
18-143 2.03e-22

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 94.27  E-value: 2.03e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997     18 EYLSSLQDLNcNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVK----SSYVQLFGQCI 93
Cdd:smart00582    1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKrkygSEFGDELGPVF 79

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|..
gi 665400997     94 VNIFLHAFESVQhsqsqvlEKVRERMYALRQTW--NEVFPPSKMYALDVKVK 143
Cdd:smart00582   80 QDALRRVLGAAP-------EELKKKIRRLLNIWeeRGIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 23-135 5.65e-15

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: 73.01  E-value: 5.65e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997    23 LQDLNcNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVK----SSYVQLFGQCIVNIFL 98
Cdd:pfam04818    7 LSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRkkgkSEFADAFEPVLPEAFA 85

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 665400997    99 HAFEsvqhsqsQVLEKVRERMYALRQTWNE--VFPPSKM 135
Cdd:pfam04818   86 SAYK-------KCDEKLKKKLERLLNIWEErnVFSPEVI 117
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 21-101 8.91e-15

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: 72.55  E-value: 8.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   21 SSLQDLNCNSKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSS---YVQLFGQCIVNIF 97
Cdd:cd03562     5 SKLEELSDLSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKgpeFTKDFSPVIVELF 84


                  ....
gi 665400997   98 LHAF 101
Cdd:cd03562    85 KHVY 88
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 30-138 2.00e-08

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: 54.54  E-value: 2.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   30 SKPLINMLTMLAEENI-NYAHIiVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSS-------YVQLFGQCIVNIFLHAF 101
Cdd:cd16983    18 SKSKINAITKLAIKAIkFYKHV-VQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQygkekdvYAPRFAKNLSKTFLNLL 96

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 665400997  102 esvqhsqsQVLEKVRERMYALRQTW--NEVFPPSKMYAL 138
Cdd:cd16983    97 --------KCPEKDKPKVKRVLNLWqkNGVFPKEIIQPL 127
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 30-112 9.95e-06

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and CTD-associated factor 8 (SCAF8) is also called CDC5L complex-associated protein 7 (CCAP7) or RNA-binding motif protein 16 (RBM16). It may play a role in mRNA processing. 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: 340801  Cd Length: 131  Bit Score: 46.95  E-value: 9.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   30 SKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSSYVQ-------LFGQCIVNIFLHAFE 102
Cdd:cd17004    18 SKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQekdvfapRFSNNIISTFQNLYR 97

                          90
                  ....*....|
gi 665400997  103 SVQHSQSQVL 112
Cdd:cd17004    98 CPGDDKSKIV 107
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 20-130 1.07e-04

CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor arginine serine rich 15 (SFRS15) is also called CTD-binding SR-like protein RA4 or SR-related and CTD-associated factor 4 (SCAF4). It may act to physically and functionally link transcription and pre-mRNA processing. SFRS15/SCAF4 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: 340802  Cd Length: 131  Bit Score: 43.80  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   20 LSSLQDLncnsKPLIN-----MLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSSY---VQLFG- 90
Cdd:cd17005     7 LFSLMDM----KPPISrakmiLITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKVPGLYVIDSIVRQSRHQFgadKDVFGp 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 665400997   91 ---QCIVNIFLHAFESVQHSQSQVLekvreRMYALRQTwNEVF 130
Cdd:cd17005    83 rfsKNITATFQYLYLCPSEDKSKIV-----RVLNLWQK-NGVF 119
VHS_ENTH_ANTH cd00197
VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a ...
 30-126 1.30e-04

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.


Pssm-ID: 340764  Cd Length: 115  Bit Score: 43.18  E-value: 1.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   30 SKPLINMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVKNVKSSYVQLFGQCIVNIFLHAFESVQHSQS 109
Cdd:cd00197    17 DWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASNDFAVELLKFDKSGLLGD 96

                          90
                  ....*....|....*..
gi 665400997  110 QVLEKVRERMYALRQTW 126
Cdd:cd00197    97 DVSTNVREKAIELVQLW 113
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 650-763 2.91e-04

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 45.88  E-value: 2.91e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   650 LEELRAKLANSARI--QNKQGKSDKSRDQAVSQRLKQLAELKVNDDSQEAHDEKvRTILSQAQEMYENNGMNQEQYKDLV 727
Cdd:pfam17380  440 LEEERAREMERVRLeeQERQQQVERLRQQEEERKRKKLELEKEKRDRKRAEEQR-RKILEKELEERKQAMIEEERKRKLL 518

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 665400997   728 QKVVAINENSKIKESRRRDNDLERNAARDAVLRKRI 763
Cdd:pfam17380  519 EKEMEERQKAIYEEERRREAEEERRKQQEMEERRRI 554
Stathmin pfam00836
Stathmin family; The Stathmin family of proteins play an important role in the regulation of ...
 633-736 1.43e-03

Stathmin family; The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton. They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerization of tubulin heterodimers.


Pssm-ID: 459956 [Multi-domain]  Cd Length: 136  Bit Score: 40.79  E-value: 1.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665400997   633 DVDKPTKKSGSPPKK-ATLEELRAKLAnsariqnkqgKSDKSRDQAVSQRLKQLAELKvnddsqeahdEKVRTILSQAQE 711
Cdd:pfam00836   26 VNAAPPKLSLSPKKKdSSLEEIQKKLE----------AAEERRKSLEAQKLKQLAEKR----------EKEEEALQKADE 85

                           90       100
                   ....*....|....*....|....*
gi 665400997   712 myENNGMNQEQYKDLVQKVVAINEN 736
Cdd:pfam00836   86 --ENNNFSKMAEEKLKQKMEAYKEN 108
CID_Nrd1_like cd16984
CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes ...
 17-79 5.86e-03

CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein Seb1, and similar proteins. Nrd1 cooperates with Nab3 and Sen1, also called the Nrd1-Nab3-Sen1 (NNS) complex, to terminate the transcription by RNA polymerase (Pol) II (RNAPII) of many noncoding RNAs (ncRNAs), including small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), and cryptic unstable transcripts (CUTs). Schizosaccharomyces pombe Seb1 does not function in an NNS-like termination pathway but promotes polyadenylation site selection of coding and noncoding genes. It cotranscriptionally controls alternative polyadenylation. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Nrd1 CID preferentially interacts with CTD phosphorylated at Ser5. 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: 340781  Cd Length: 145  Bit Score: 39.12  E-value: 5.86e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 665400997   17 EEYLSSLQDLNcNSKPL------INMLTMLAEENINYAHIIVKVVEYYISQVAPEFKLPILYLIDSIVK 79
Cdd:cd16984     1 EEFEATLKSLQ-ALKPPgvsgskIKKLTDIAVDNVQSESQIVSKLYRYFKKAPPTHKLGVLYVVDSVVR 68
 
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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