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Conserved domains on  [gi|193202742|ref|NP_001122472|]
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CID domain-containing protein [Caenorhabditis elegans]

Protein Classification

VHS/ENTH/ANTH domain-containing protein; ENTH domain-containing protein( domain architecture ID 10651854)

VHS (Vps27/Hrs/STAM) /ENTH (Epsin N-Terminal Homology) /ANTH (AP180 N-Terminal Homology) domain-containing protein similar to Homo sapiens ADP-ribosylation factor-binding protein GGA3 that plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes| ENTH (Epsin N-Terminal Homology) domain-containing protein may be involved in clathrin-mediated endocytosis; similar to epsin that plays an important role as accessory proteins in clathrin-mediated endocytosis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
20-134 8.40e-31

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


:

Pssm-ID: 214731  Cd Length: 124  Bit Score: 116.99  E-value: 8.40e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742    20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAgTDNKRIALFYVMNDVVQKAKMKHA----DTLIPAFQPAVLTA 95
Cdd:smart00582  10 NNSQESIQTLTKWAIEHASHA--KEIVELWEKYIKKA-PVPRKLPLLYLLDSIVQNSKRKYGsefgDELGPVFQDALRRV 86

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 193202742    96 VGIGrkQDKVKAVMKRCIQIFKSRNVFSPASTTAMENLL 134
Cdd:smart00582  87 LGAA--PEELKKKIRRLLNIWEERGIFPPEVLRPLREKL 123
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 375-559 9.44e-07

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.63  E-value: 9.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  375 PSTFQPPPSKPAVINASKFSMPPPAITS-----APLSDPRIRsdgeGPSQYAIALkqhglpPPTGQQPVQNRMNAPPPAQ 449
Cdd:PHA03247 2824 PAGPLPPPTSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRR----PPSRSPAAK------PAAPARPPVRRLARPAVSR 2893

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  450 PSPYQAIPQKPVEqtvyqgqfggaRDPRLANSVTPQSVAVAQQPPITGYQAQYEQIRDPRILQQAAPQQGYQATFEVQKP 529
Cdd:PHA03247 2894 STESFALPPDQPE-----------RPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQP 2962

                         170       180       190
                  ....*....|....*....|....*....|
gi 193202742  530 QLvSPQIQNNGYQARFEQSQLSPSIPQHQP 559
Cdd:PHA03247 2963 WL-GALVPGRVAVPRFRVPQPAPSREAPAS 2991
 
Name Accession Description Interval E-value
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
20-134 8.40e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 116.99  E-value: 8.40e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742    20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAgTDNKRIALFYVMNDVVQKAKMKHA----DTLIPAFQPAVLTA 95
Cdd:smart00582  10 NNSQESIQTLTKWAIEHASHA--KEIVELWEKYIKKA-PVPRKLPLLYLLDSIVQNSKRKYGsefgDELGPVFQDALRRV 86

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 193202742    96 VGIGrkQDKVKAVMKRCIQIFKSRNVFSPASTTAMENLL 134
Cdd:smart00582  87 LGAA--PEELKKKIRRLLNIWEERGIFPPEVLRPLREKL 123
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 20-134 1.76e-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: 104.59  E-value: 1.76e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAGTDnKRIALFYVMNDVVQKAKMKHADTLIPAFQPAVLTAVGIG 99
Cdd:cd16981   12 NNTQQSIQTLSLWCLFHKKHA--KQIVKIWLKELKKAKPE-RKLTLLYLANDVLQNSRRKGAPEFVEAFKKVLPEALALV 88

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 193202742 100 RKQ--DKVKAVMKRCIQIFKSRNVFSPASTTAMENLL 134
Cdd:cd16981   89 RSEgdESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 20-125 1.10e-22

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: 93.43  E-value: 1.10e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742   20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAGTDnKRIALFYVMNDVVQKAKMKHADTLIPAFQPAVLTAVG-I 98
Cdd:pfam04818  11 NNSQESIQTLSKWILFHRKHA--KAIVEVWEKYLKKAKPE-KKLHLLYLANDVLQNSRKKGKSEFADAFEPVLPEAFAsA 87

                          90       100
                  ....*....|....*....|....*...
gi 193202742   99 GRKQD-KVKAVMKRCIQIFKSRNVFSPA 125
Cdd:pfam04818  88 YKKCDeKLKKKLERLLNIWEERNVFSPE 115
PHA03247 PHA03247
large tegument protein UL36; Provisional
 375-559 9.44e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.63  E-value: 9.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  375 PSTFQPPPSKPAVINASKFSMPPPAITS-----APLSDPRIRsdgeGPSQYAIALkqhglpPPTGQQPVQNRMNAPPPAQ 449
Cdd:PHA03247 2824 PAGPLPPPTSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRR----PPSRSPAAK------PAAPARPPVRRLARPAVSR 2893

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  450 PSPYQAIPQKPVEqtvyqgqfggaRDPRLANSVTPQSVAVAQQPPITGYQAQYEQIRDPRILQQAAPQQGYQATFEVQKP 529
Cdd:PHA03247 2894 STESFALPPDQPE-----------RPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQP 2962

                         170       180       190
                  ....*....|....*....|....*....|
gi 193202742  530 QLvSPQIQNNGYQARFEQSQLSPSIPQHQP 559
Cdd:PHA03247 2963 WL-GALVPGRVAVPRFRVPQPAPSREAPAS 2991
Androgen_recep pfam02166
Androgen receptor;
469-561 3.82e-05

Androgen receptor;


Pssm-ID: 426632 [Multi-domain]  Cd Length: 501  Bit Score: 46.84  E-value: 3.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  469 QFGGARDPRLANSVTPQSVAVAQQppitgyQAQYEQIRDPRILQQAAPQQGYQATFEVQKPQLVSPQIQNN---GYQARF 545
Cdd:pfam02166  30 QNPGPRHPEAAGGAAPPGARLQHQ------QQQQQQVPQQPQQQESSPRQPQASVQPQQAGDDGSPPAHNRgpaGYLALE 103

                          90
                  ....*....|....*.
gi 193202742  546 EQSQLSPSIPQHQPVG 561
Cdd:pfam02166 104 DDEQPQPSQAQPAAEC 119
KLF1_2_4_N-like cd22056
N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of ...
 439-570 4.45e-04

N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of Kruppel-like factor (KLF)1, KLF2, and KLF4; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domains of an unknown subfamily of KLFs, predominantly found in fish, related to the N-terminal domains of KLF1, KLF2, and KLF4.


Pssm-ID: 409231 [Multi-domain]  Cd Length: 339  Bit Score: 43.11  E-value: 4.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742 439 QNRMNAPPPAQPSPYQAIP------QKPVEQT-----VYQGQFGGARDPRLANSVTPQSVAVAQQPPITGYQAQYEQIRD 507
Cdd:cd22056  162 LRALPTAPPAHQPATSPPPlgykikTEPVEQScmmaaGGGGFMGQQKPKHQMHSVHPQAFTHHQAAGPGALQGRGGRGGP 241

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 193202742 508 PRILQQAAPQQgyqatfevQKPQLVSPQIQNNGYQARFeqsqlspsipQHQPVGQYHQQKNTY 570
Cdd:cd22056  242 DCHLLHSSHHH--------HHHHHLQYQYMNAPYPPHY----------AHQGAPQFHGQYSVF 286
 
Name Accession Description Interval E-value
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
20-134 8.40e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 116.99  E-value: 8.40e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742    20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAgTDNKRIALFYVMNDVVQKAKMKHA----DTLIPAFQPAVLTA 95
Cdd:smart00582  10 NNSQESIQTLTKWAIEHASHA--KEIVELWEKYIKKA-PVPRKLPLLYLLDSIVQNSKRKYGsefgDELGPVFQDALRRV 86

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 193202742    96 VGIGrkQDKVKAVMKRCIQIFKSRNVFSPASTTAMENLL 134
Cdd:smart00582  87 LGAA--PEELKKKIRRLLNIWEERGIFPPEVLRPLREKL 123
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 20-134 1.76e-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: 104.59  E-value: 1.76e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAGTDnKRIALFYVMNDVVQKAKMKHADTLIPAFQPAVLTAVGIG 99
Cdd:cd16981   12 NNTQQSIQTLSLWCLFHKKHA--KQIVKIWLKELKKAKPE-RKLTLLYLANDVLQNSRRKGAPEFVEAFKKVLPEALALV 88

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 193202742 100 RKQ--DKVKAVMKRCIQIFKSRNVFSPASTTAMENLL 134
Cdd:cd16981   89 RSEgdESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 20-125 1.10e-22

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: 93.43  E-value: 1.10e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742   20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAGTDnKRIALFYVMNDVVQKAKMKHADTLIPAFQPAVLTAVG-I 98
Cdd:pfam04818  11 NNSQESIQTLSKWILFHRKHA--KAIVEVWEKYLKKAKPE-KKLHLLYLANDVLQNSRKKGKSEFADAFEPVLPEAFAsA 87

                          90       100
                  ....*....|....*....|....*...
gi 193202742   99 GRKQD-KVKAVMKRCIQIFKSRNVFSPA 125
Cdd:pfam04818  88 YKKCDeKLKKKLERLLNIWEERNVFSPE 115
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 20-124 2.63e-19

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: 84.23  E-value: 2.63e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  20 NPTQEAIETMSMWIMHYKDNAsiDLIVDGWLNCFKTAgTDNKRIALFYVMNDVVQKAKMKHAD-------TLIPAFQPAV 92
Cdd:cd17002   14 SNSQQSIQTLSLWLIHHRKHA--KTIVRVWLKELRKE-KPSKKLTLLYLANDVIQNSRKKGPEftkefapVLEDAFKHVA 90

                         90       100       110
                 ....*....|....*....|....*....|..
gi 193202742  93 ltavgiGRKQDKVKAVMKRCIQIFKSRNVFSP 124
Cdd:cd17002   91 ------KLTDSEVLKALERILNIWKERQVYEK 116
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 20-132 7.95e-15

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: 71.49  E-value: 7.95e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  20 NPTQEAIETMSMWIM-HYKDnasIDLIVDGWLNCFKTAGT-DNKRIALFYVMNDVVQKAKMKHADTLIPAFQPAVLTAVG 97
Cdd:cd17003   12 NETQESIVSISQWVLfHYRH---ADEIAEIWSDYLLKSSVnSRRKLLLIYLANDVVQQAKAKKKTEFIDAFSKVLPEVLE 88

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 193202742  98 -IGRKQD-KVKAVMKRCIQIFKSRNVFSPASTTAMEN 132
Cdd:cd17003   89 kIYPSLPsDIKKKIKRVVNVWKQRQIFSKDVIDDIEE 125
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 16-122 4.59e-10

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: 57.62  E-value: 4.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  16 FQVKNPTQEAIETMSMWIMHYKDNASidLIVDGWLNCFKTAGTdNKRIALFYVMNDVVQKAKMKHADTLIPAFqPAVLTA 95
Cdd:cd17001   10 FQSVTNTMESIQGLSSWCIENKKHHS--TIVYHWMKWLRRSAY-PHRLNLFYLANDVIQNCKRKNAIVFRESF-AEVLPE 85

                         90       100
                 ....*....|....*....|....*..
gi 193202742  96 VGIGRKQDKVKAVMKRCIQIFKSRNVF 122
Cdd:cd17001   86 AAALVKDASVSKSVERIFKIWEERNVY 112
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 22-124 9.51e-10

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: 56.94  E-value: 9.51e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  22 TQEAIETMSMWIMHYKDNASidLIVDGWLNCFKTAGTdNKRIALFYVMNDVVQKAKMKHADtLIPAFQPAVLTAVG--IG 99
Cdd:cd17012   17 SQQSVQTLSLWLIHHRKHAG--PIVSVWHRELRKAKS-SRKLTFLYLANDVIQNSKRKGPE-FTREFESVLVDAFShvAR 92

                         90       100
                 ....*....|....*....|....*
gi 193202742 100 RKQDKVKAVMKRCIQIFKSRNVFSP 124
Cdd:cd17012   93 EADEGCKKPLERLLNIWQERSVYGG 117
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 22-122 1.04e-08

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: 53.89  E-value: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  22 TQEAIETMSMWIMHYKDNASidLIVDGWLNCFKTAGTdNKRIALFYVMNDVVQKAKMKHADtLIPAFQPAVLTAVG-IGR 100
Cdd:cd17011   16 SQQSVQTLSLWLIHHRKHSR--PIVTVWERELRKAKP-NRKLTFLYLANDVIQNSKRKGPE-FTKDFAPVIVEAFKhVSS 91

                         90       100
                 ....*....|....*....|...
gi 193202742 101 KQDK-VKAVMKRCIQIFKSRNVF 122
Cdd:cd17011   92 ETDEsCKKHLGRVLSIWEERSVY 114
PHA03247 PHA03247
large tegument protein UL36; Provisional
 375-559 9.44e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.63  E-value: 9.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  375 PSTFQPPPSKPAVINASKFSMPPPAITS-----APLSDPRIRsdgeGPSQYAIALkqhglpPPTGQQPVQNRMNAPPPAQ 449
Cdd:PHA03247 2824 PAGPLPPPTSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRR----PPSRSPAAK------PAAPARPPVRRLARPAVSR 2893

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  450 PSPYQAIPQKPVEqtvyqgqfggaRDPRLANSVTPQSVAVAQQPPITGYQAQYEQIRDPRILQQAAPQQGYQATFEVQKP 529
Cdd:PHA03247 2894 STESFALPPDQPE-----------RPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQP 2962

                         170       180       190
                  ....*....|....*....|....*....|
gi 193202742  530 QLvSPQIQNNGYQARFEQSQLSPSIPQHQP 559
Cdd:PHA03247 2963 WL-GALVPGRVAVPRFRVPQPAPSREAPAS 2991
Androgen_recep pfam02166
Androgen receptor;
469-561 3.82e-05

Androgen receptor;


Pssm-ID: 426632 [Multi-domain]  Cd Length: 501  Bit Score: 46.84  E-value: 3.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  469 QFGGARDPRLANSVTPQSVAVAQQppitgyQAQYEQIRDPRILQQAAPQQGYQATFEVQKPQLVSPQIQNN---GYQARF 545
Cdd:pfam02166  30 QNPGPRHPEAAGGAAPPGARLQHQ------QQQQQQVPQQPQQQESSPRQPQASVQPQQAGDDGSPPAHNRgpaGYLALE 103

                          90
                  ....*....|....*.
gi 193202742  546 EQSQLSPSIPQHQPVG 561
Cdd:pfam02166 104 DDEQPQPSQAQPAAEC 119
PHA03247 PHA03247
large tegument protein UL36; Provisional
 370-562 5.37e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.86  E-value: 5.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  370 ADTPLPSTFQPPPSKPAVINASKFSMPPPAITSAPLSDPrirsdgeGPSQYAIALKQHGLPPPTGQQPvqnrmnAPPPAQ 449
Cdd:PHA03247 2776 AAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAP-------AAALPPAASPAGPLPPPTSAQP------TAPPPP 2842

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  450 PSPYQaiPQKPVEQTVYQGQFGGARDPRLANSVTP--------QSVAVAQQPPITGYQAQyEQIRDPRILQQAAPQQGyQ 521
Cdd:PHA03247 2843 PGPPP--PSLPLGGSVAPGGDVRRRPPSRSPAAKPaaparppvRRLARPAVSRSTESFAL-PPDQPERPPQPQAPPPP-Q 2918

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 193202742  522 ATFEVQKPQLVSPQIQNNGYqarfEQSQLSPSiPQHQPVGQ 562
Cdd:PHA03247 2919 PQPQPPPPPQPQPPPPPPPR----PQPPLAPT-TDPAGAGE 2954
PHA03247 PHA03247
large tegument protein UL36; Provisional
 375-562 7.67e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 7.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  375 PSTFQPPPSKPAVINASkfsmPPPAITSAPLSDPRIRSDGEGPSQYAIALKQHGLPPPTGQQPVQNRMNAPPPAQPSPYQ 454
Cdd:PHA03247 2761 PTTAGPPAPAPPAAPAA----GPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQP 2836

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  455 AIPQKPVEQTVYQGQFGGARDP------RLANSVTPQSVAVAQQPPITGYqAQYEQIRDPRILQQAAPQQGYQATFEVQK 528
Cdd:PHA03247 2837 TAPPPPPGPPPPSLPLGGSVAPggdvrrRPPSRSPAAKPAAPARPPVRRL-ARPAVSRSTESFALPPDQPERPPQPQAPP 2915

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 193202742  529 PQLVSPQIQNNGYQARFEQSQ---LSPSIPQHQPVGQ 562
Cdd:PHA03247 2916 PPQPQPQPPPPPQPQPPPPPPprpQPPLAPTTDPAGA 2952
KLF1_2_4_N-like cd22056
N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of ...
 439-570 4.45e-04

N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of Kruppel-like factor (KLF)1, KLF2, and KLF4; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domains of an unknown subfamily of KLFs, predominantly found in fish, related to the N-terminal domains of KLF1, KLF2, and KLF4.


Pssm-ID: 409231 [Multi-domain]  Cd Length: 339  Bit Score: 43.11  E-value: 4.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742 439 QNRMNAPPPAQPSPYQAIP------QKPVEQT-----VYQGQFGGARDPRLANSVTPQSVAVAQQPPITGYQAQYEQIRD 507
Cdd:cd22056  162 LRALPTAPPAHQPATSPPPlgykikTEPVEQScmmaaGGGGFMGQQKPKHQMHSVHPQAFTHHQAAGPGALQGRGGRGGP 241

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 193202742 508 PRILQQAAPQQgyqatfevQKPQLVSPQIQNNGYQARFeqsqlspsipQHQPVGQYHQQKNTY 570
Cdd:cd22056  242 DCHLLHSSHHH--------HHHHHLQYQYMNAPYPPHY----------AHQGAPQFHGQYSVF 286
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 282-559 1.45e-03

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


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 42.06  E-value: 1.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  282 SPRNEDDRQTYGRSNNRSLSQQWGDnrnqidmeMDEDERPQAPMMkPSLQALVGiASQPSLQSRIMQLGLKKIANGDEEM 361
Cdd:pfam03154 112 SPSEGEGESSDGRSVNDEGSSDPKD--------IDQDNRSTSPSI-PSPQDNES-DSDSSAQQQILQTQPPVLQAQSGAA 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  362 FQPTTTTTADTPLPSTfQPPPSKPAVinaskfsmppPAITSAPLSDPrirsdgegPSQYAIALKQHGLPPPTGQQPVQNR 441
Cdd:pfam03154 182 SPPSPPPPGTTQAATA-GPTPSAPSV----------PPQGSPATSQP--------PNQTQSTAAPHTLIQQTPTLHPQRL 242

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  442 MNAPPPAQPSPYQAIPQKPVEQTvyqgqfggardprlansvTPQSVAVAQQPPItGYQAQyeqiRDPRILQQAAPQQGYQ 521
Cdd:pfam03154 243 PSPHPPLQPMTQPPPPSQVSPQP------------------LPQPSLHGQMPPM-PHSLQ----TGPSHMQHPVPPQPFP 299

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 193202742  522 ATFEVQKPQL-VSPQIQNNGY-QARFEQSQLSPSIPQHQP 559
Cdd:pfam03154 300 LTPQSSQSQVpPGPSPAAPGQsQQRIHTPPSQSQLQSQQP 339
PHA03377 PHA03377
EBNA-3C; Provisional
 311-555 1.64e-03

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 41.58  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  311 IDMEMDEDERPQAPMMKPSLQALVGIASQPSLQSRIMQLGLKKIANGDEEMFQPTTTTTADTP----LPSTFQPPPSKPA 386
Cdd:PHA03377  515 IDVETTEEEESVTQPAKPHRKVQDGFQRSGRRQKRATPPKVSPSDRGPPKASPPVMAPPSTGPrvmaTPSTGPRDMAPPS 594

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  387 VI--NASKFSMPPPAITSAPLSDPRIRSDGEGPSQYAIALKQHGLPPPTGQQPVQ----------NRMNAPPPAQPSP-Y 453
Cdd:PHA03377  595 TGprQQAKCKDGPPASGPHEKQPPSSAPRDMAPSVVRMFLRERLLEQSTGPKPKSfwemragrdgSGIQQEPSSRRQPaT 674

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  454 QAIPQKPVE-QTVYQGQFGGARDPRLANSVTPQSVAvAQQPPITGYQAQYEQIRDPRILQ-------QAAPQQGYQATFE 525
Cdd:PHA03377  675 QSTPPRPSWlPSVFVLPSVDAGRAQPSEESHLSSMS-PTQPISHEEQPRYEDPDDPLDLSlhpdqapPPSHQAPYSGHEE 753

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 193202742  526 VQKPQLV--------SPQIQNNGYQARFEQSQLSPSIP 555
Cdd:PHA03377  754 PQAQQAPypgyweprPPQAPYLGYQEPQAQGVQVSSYP 791
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
370-514 1.76e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 41.30  E-value: 1.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742 370 ADTPLPSTFQPPPSKPAVINASkfSMPPPAITSAPLSDPRIRSDGEGPSQYAIALKQHGLPP-----PTGQQPVQNRMNA 444
Cdd:PRK14971 366 GDDASGGRGPKQHIKPVFTQPA--AAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPtvsvdPPAAVPVNPPSTA 443

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 193202742 445 PPPAQPSPYQAIPQKPVEQTVYQGQF--GGARDPRLANSVTPQSVAVAQQPPI-TGYQAQYEQIRDPRILQQA 514
Cdd:PRK14971 444 PQAVRPAQFKEEKKIPVSKVSSLGPStlRPIQEKAEQATGNIKEAPTGTQKEIfTEEDLQYYWQEFAGTRPQE 516
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 379-540 1.77e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 41.61  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  379 QPPPSKPAVINASKFSmPPPAIT----SAPLSDPRIRSDGEgPSQYAIALKQHGLPpptgQQPVqnrmnAPPPAQPSPYQ 454
Cdd:PRK10263  715 QPAGANPFSLDDFEFS-PMKALLddgpHEPLFTPIVEPVQQ-PQQPVAPQQQYQQP----QQPV-----APQPQYQQPQQ 783

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  455 AIPQKPVEQTVYQGQFGGARDPRLANSVTPQSVAVAQQPPITGyQAQYEQIRdprilQQAAPQqgyqatfevqkPQ--LV 532
Cdd:PRK10263  784 PVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAP-QPQYQQPQ-----QPVAPQ-----------PQdtLL 846


                  ....*...
gi 193202742  533 SPQIQNNG 540
Cdd:PRK10263  847 HPLLMRNG 854
PHA03378 PHA03378
EBNA-3B; Provisional
 375-537 2.70e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 41.21  E-value: 2.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742 375 PSTFQPPPSKPAVIN-------------ASKFSMPPPAITSAPLSDPRIRSDGEGPSQYAIALKQHGLPPPTGQQPVQNR 441
Cdd:PHA03378 691 PGTMQPPPRAPTPMRppaappgraqrpaAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAA 770

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742 442 MNAPPPAQPspyqaiPQKPveqTVYQGQFGGARDPRLANSVTPQSVAVAqQPPITGYQAQYEQIRDPRI---LQQAAPQQ 518
Cdd:PHA03378 771 PGAPTPQPP------PQAP---PAPQQRPRGAPTPQPPPQAGPTSMQLM-PRAAPGQQGPTKQILRQLLtggVKRGRPSL 840

                        170
                 ....*....|....*....
gi 193202742 519 GYQATFEVQKPQLVSPQIQ 537
Cdd:PHA03378 841 KKPAALERQAAAGPTPSPG 859
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 373-535 2.99e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 40.84  E-value: 2.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  373 PLPSTfQPPPSKPAVI--NASKFSMPPPAITSAPLSDPRIrsdgegpSQYAIALKQHGLPpptGQQPVqnrmnapPPAQP 450
Cdd:PRK10263  345 PVASV-DVPPAQPTVAwqPVPGPQTGEPVIAPAPEGYPQQ-------SQYAQPAVQYNEP---LQQPV-------QPQQP 406

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  451 SPYQAIPQKPVEQTVYQGQFGGARDPRLANSVTPQSVAVAQQPPITGYQAQYEQIRDPR--ILQQAAPQQGYQATFEVQK 528
Cdd:PRK10263  407 YYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEqtYQQPAAQEPLYQQPQPVEQ 486


                  ....*..
gi 193202742  529 PQLVSPQ 535
Cdd:PRK10263  487 QPVVEPE 493
PHA03247 PHA03247
large tegument protein UL36; Provisional
 364-492 3.26e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.08  E-value: 3.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  364 PTTTTTADTPLPSTFQPPPSKP--AVINASKF-----SMPPPAITSAPlSDPRIRSDGEGPSQYAIalKQHGLPPPTGQQ 436
Cdd:PHA03247 2831 PTSAQPTAPPPPPGPPPPSLPLggSVAPGGDVrrrppSRSPAAKPAAP-ARPPVRRLARPAVSRST--ESFALPPDQPER 2907

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 193202742  437 PVQNRMNAPPPAQPSPYQAIPQKPVEQTVYQGQFGGARDPRLANSVTPQSVAVAQQ 492
Cdd:PHA03247 2908 PPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPW 2963
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 373-536 6.12e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 40.07  E-value: 6.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  373 PLPSTFQPPP--SKPAVINASKFSMPPPAITSAPLSDPRIRSDGEGPSQYAIALKQHGLPPPTGQQPVQNRMNAPPPA-- 448
Cdd:PRK10263  375 PAPEGYPQQSqyAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQqs 454

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  449 --QPSPYQAiPQKPVEQTVYQGQFGGARDPRLANSVTPQSVAVAQQPPITGYQAQYEQIRDPRILQQAAPQQGYQATFE- 525
Cdd:PRK10263  455 tfAPQSTYQ-TEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPVVEETKPARPPLYYFEEVEEKRAREREQLAAWYQPIPEp 533

                         170
                  ....*....|.
gi 193202742  526 VQKPQLVSPQI 536
Cdd:PRK10263  534 VKEPEPIKSSL 544
PHA03377 PHA03377
EBNA-3C; Provisional
 376-559 8.21e-03

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 39.65  E-value: 8.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  376 STFQPPPSKPAVInASKFSMPP-PAITSAPLSDPRIRS-DGEGPSQYAIALKQHGLPPPT--GQQPVQnrmnAPPPAQPS 451
Cdd:PHA03377  672 PATQSTPPRPSWL-PSVFVLPSvDAGRAQPSEESHLSSmSPTQPISHEEQPRYEDPDDPLdlSLHPDQ----APPPSHQA 746

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193202742  452 PYQAIPQKPVEQTVYQG---------QFGGARDPrlansvTPQSVAVAQQPPITG---YQAQYEQIRDPRILQQAAPQQG 519
Cdd:PHA03377  747 PYSGHEEPQAQQAPYPGyweprppqaPYLGYQEP------QAQGVQVSSYPGYAGpwgLRAQHPRYRHSWAYWSQYPGHG 820

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 193202742  520 YQATFEVQKPQLVSPQIQNNGYQARFEQSQLSPSIPQHQP 559
Cdd:PHA03377  821 HPQGPWAPRPPHLPPQWDGSAGHGQDQVSQFPHLQSETGP 860
 
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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