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Conserved domains on  [gi|1720405414|ref|XP_030108723|]
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regulation of nuclear pre-mRNA domain-containing protein 2 isoform X1 [Mus musculus]

Protein Classification

epsin; LCP family protein( domain architecture ID 13017359)

epsin plays an important role as an accessory protein in clathrin-mediated endocytosis| LytR-CpsA-Psr (LCP) family protein is implicated in the attachment of anionic polymers to cell wall peptidoglycan in bacteria

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 27-146 7.18e-84

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: 269.86  E-value: 7.18e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd17001      6 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIVFRESFAEVLPE 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1720405414  107 AAALVKDPSVSKSIERIFKIWEDRNVYPEDMIVALREALS 146
Cdd:cd17001     86 AAALVKDASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
Herpes_BLLF1 super family cl37540
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 319-645 3.87e-08

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


The actual alignment was detected with superfamily member pfam05109:

Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 58.00  E-value: 3.87e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  319 SPVPSPSMDAPSPTgSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDvedmelsdveddgskiivedrkekpvEKPAV 398
Cdd:pfam05109  475 SPTPAGTTSGASPV-TPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATS--------------------------PTPAV 527

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  399 STGVPTKSTESVSKASPCAPPSVPT-TAAPPLPkplstALLSPSPTLVLPNLANVdlakisSILSSLTSVMKNTGVSSAS 477
Cdd:pfam05109  528 TTPTPNATSPTLGKTSPTSAVTTPTpNATSPTP-----AVTTPTPNATIPTLGKT------SPTSAVTTPTPNATSPTVG 596

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  478 RPSPGIPTSPSNLSSGLKTP----------APATTPSHNPLANILSKVEITPESILSALSKT----QTQSAPALQGLSSL 543
Cdd:pfam05109  597 ETSPQANTTNHTLGGTSSTPvvtsppknatSAVTTGQHNITSSSTSSMSLRPSSISETLSPStsdnSTSHMPLLTSAHPT 676

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  544 LQSVTANPVPASEVTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTTF 623
Cdd:pfam05109  677 GGENITQVTPASTSTHHVSTSSPAPRPGTTSQASGPGNSSTSTKPGEVNVTKGTPPKNATSPQAPSGQKTAVPTVTSTGG 756

                          330       340
                   ....*....|....*....|...
gi 1720405414  624 KLPSSSLG-FTGTHNPSPAAPPT 645
Cdd:pfam05109  757 KANSTTGGkHTTGHGARTSTEPT 779
PRK03918 super family cl35229
DNA double-strand break repair ATPase Rad50;
142-318 3.62e-04

DNA double-strand break repair ATPase Rad50;


The actual alignment was detected with superfamily member PRK03918:

Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.05  E-value: 3.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  142 REALSTTFKTQKQLKENLNKQpNKQWKKSQTStnpKAALKSKIVaEFRSQalIEELlmyKRSEDQIELKEKQLSTMRVDV 221
Cdd:PRK03918   223 LEKLEKEVKELEELKEEIEEL-EKELESLEGS---KRKLEEKIR-ELEER--IEEL---KKEIEELEEKVKELKELKEKA 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  222 CSTETLKCLKDKTggKKFSKEFEEASSKLEEFVNGLDKQVKNGPSLTEALENagifYEAQYKEVKVVANAYKTFA---NR 298
Cdd:PRK03918   293 EEYIKLSEFYEEY--LDELREIEKRLSRLEEEINGIEERIKELEEKEERLEE----LKKKLKELEKRLEELEERHelyEE 366

                          170       180
                   ....*....|....*....|..
gi 1720405414  299 VNNLKKKLDQLKSTLPD--PEE 318
Cdd:PRK03918   367 AKAKKEELERLKKRLTGltPEK 388
 
Name Accession Description Interval E-value
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 27-146 7.18e-84

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: 269.86  E-value: 7.18e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd17001      6 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIVFRESFAEVLPE 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1720405414  107 AAALVKDPSVSKSIERIFKIWEDRNVYPEDMIVALREALS 146
Cdd:cd17001     86 AAALVKDASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 27-138 4.24e-42

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: 150.05  E-value: 4.24e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:pfam04818    3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSEFADAFEPVLPE 82

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1720405414  107 AAALV---KDPSVSKSIERIFKIWEDRNVYPEDMI 138
Cdd:pfam04818   83 AFASAykkCDEKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
27-145 4.30e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 118.92  E-value: 4.30e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414    27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:smart00582    2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQD 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 1720405414   107 AAALVKDPSVS---KSIERIFKIWEDRNVYPEDMIVALREAL 145
Cdd:smart00582   82 ALRRVLGAAPEelkKKIRRLLNIWEERGIFPPEVLRPLREKL 123
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 319-645 3.87e-08

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 58.00  E-value: 3.87e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  319 SPVPSPSMDAPSPTgSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDvedmelsdveddgskiivedrkekpvEKPAV 398
Cdd:pfam05109  475 SPTPAGTTSGASPV-TPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATS--------------------------PTPAV 527

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  399 STGVPTKSTESVSKASPCAPPSVPT-TAAPPLPkplstALLSPSPTLVLPNLANVdlakisSILSSLTSVMKNTGVSSAS 477
Cdd:pfam05109  528 TTPTPNATSPTLGKTSPTSAVTTPTpNATSPTP-----AVTTPTPNATIPTLGKT------SPTSAVTTPTPNATSPTVG 596

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  478 RPSPGIPTSPSNLSSGLKTP----------APATTPSHNPLANILSKVEITPESILSALSKT----QTQSAPALQGLSSL 543
Cdd:pfam05109  597 ETSPQANTTNHTLGGTSSTPvvtsppknatSAVTTGQHNITSSSTSSMSLRPSSISETLSPStsdnSTSHMPLLTSAHPT 676

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  544 LQSVTANPVPASEVTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTTF 623
Cdd:pfam05109  677 GGENITQVTPASTSTHHVSTSSPAPRPGTTSQASGPGNSSTSTKPGEVNVTKGTPPKNATSPQAPSGQKTAVPTVTSTGG 756

                          330       340
                   ....*....|....*....|...
gi 1720405414  624 KLPSSSLG-FTGTHNPSPAAPPT 645
Cdd:pfam05109  757 KANSTTGGkHTTGHGARTSTEPT 779
PHA03247 PHA03247
large tegument protein UL36; Provisional
 314-668 1.76e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.02  E-value: 1.76e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  314 PDPEESPVPSPSMDAPSPTGSESPFQGMGGEEPQSPAMESDKSAtPEPVTDNRDVEDMELSDVEDDGSKIiveDRKEKPV 393
Cdd:PHA03247  2612 APPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDD-PAPGRVSRPRRARRLGRAAQASSPP---QRPRRRA 2687

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  394 EKPAVStgvptkstesvSKASPCAPPSVPTTAAPPlPKPLSTALLSPSPTLVLPNLANVDLAKISSILSSLTSVMKNTGV 473
Cdd:PHA03247  2688 ARPTVG-----------SLTSLADPPPPPPTPEPA-PHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPA 2755

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  474 SSASRPSPGIPTSPSNLSSGLKTPAPATTPshnPLANILSkveitpESILSALSKTQTQSAPALQGLSSLLQSVTANPVP 553
Cdd:PHA03247  2756 RPARPPTTAGPPAPAPPAAPAAGPPRRLTR---PAVASLS------ESRESLPSPWDPADPPAAVLAPAAALPPAASPAG 2826

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  554 ASEVTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTTFKLPSSSLGFT 633
Cdd:PHA03247  2827 PLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPE 2906

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1720405414  634 GTHNPSPAAPPTEVAVCQSSEVSKPKPESESTSPS 668
Cdd:PHA03247  2907 RPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQP 2941
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
142-318 3.62e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.05  E-value: 3.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  142 REALSTTFKTQKQLKENLNKQpNKQWKKSQTStnpKAALKSKIVaEFRSQalIEELlmyKRSEDQIELKEKQLSTMRVDV 221
Cdd:PRK03918   223 LEKLEKEVKELEELKEEIEEL-EKELESLEGS---KRKLEEKIR-ELEER--IEEL---KKEIEELEEKVKELKELKEKA 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  222 CSTETLKCLKDKTggKKFSKEFEEASSKLEEFVNGLDKQVKNGPSLTEALENagifYEAQYKEVKVVANAYKTFA---NR 298
Cdd:PRK03918   293 EEYIKLSEFYEEY--LDELREIEKRLSRLEEEINGIEERIKELEEKEERLEE----LKKKLKELEKRLEELEERHelyEE 366

                          170       180
                   ....*....|....*....|..
gi 1720405414  299 VNNLKKKLDQLKSTLPD--PEE 318
Cdd:PRK03918   367 AKAKKEELERLKKRLTGltPEK 388
 
Name Accession Description Interval E-value
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 27-146 7.18e-84

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: 269.86  E-value: 7.18e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd17001      6 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIVFRESFAEVLPE 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1720405414  107 AAALVKDPSVSKSIERIFKIWEDRNVYPEDMIVALREALS 146
Cdd:cd17001     86 AAALVKDASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 27-145 9.18e-56

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: 189.33  E-value: 9.18e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd16981      4 LEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGAPEFVEAFKKVLPE 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1720405414  107 AAALVK---DPSVSKSIERIFKIWEDRNVYPEDMIVALREAL 145
Cdd:cd16981     84 ALALVRsegDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 27-138 4.24e-42

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: 150.05  E-value: 4.24e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:pfam04818    3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSEFADAFEPVLPE 82

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1720405414  107 AAALV---KDPSVSKSIERIFKIWEDRNVYPEDMI 138
Cdd:pfam04818   83 AFASAykkCDEKLKKKLERLLNIWEERNVFSPEVI 117
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 27-145 7.82e-37

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: 135.46  E-value: 7.82e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAiIFRESFADVLPE 106
Cdd:cd17002      6 LEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGP-EFTKEFAPVLED 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1720405414  107 AAALV---KDPSVSKSIERIFKIWEDRNVYPEDMIVALREAL 145
Cdd:cd17002     85 AFKHVaklTDSEVLKALERILNIWKERQVYEKDFIEQLRAAL 126
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
27-145 4.30e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 118.92  E-value: 4.30e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414    27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:smart00582    2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQD 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 1720405414   107 AAALVKDPSVS---KSIERIFKIWEDRNVYPEDMIVALREAL 145
Cdd:smart00582   82 ALRRVLGAAPEelkKKIRRLLNIWEERGIFPPEVLRPLREKL 123
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 30-145 2.03e-26

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: 105.77  E-value: 2.03e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   30 KFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTY--PHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPEA 107
Cdd:cd17003      7 KLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSSVnsRRKLLLIYLANDVVQQAKAKKKTEFIDAFSKVLPEV 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1720405414  108 AALVK---DPSVSKSIERIFKIWEDRNVYPEDMIVALREAL 145
Cdd:cd17003     87 LEKIYpslPSDIKKKIKRVVNVWKQRQIFSKDVIDDIEERL 127
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 27-145 1.26e-25

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: 103.58  E-value: 1.26e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAiIFRESFADVLPE 106
Cdd:cd17011      6 LEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGP-EFTKDFAPVIVE 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1720405414  107 AAALVK---DPSVSKSIERIFKIWEDRNVYPEDMIVALREAL 145
Cdd:cd17011     85 AFKHVSsetDESCKKHLGRVLSIWEERSVYENDVLEQLKQAL 126
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 27-142 3.43e-24

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: 99.31  E-value: 3.43e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFREsFADVLPE 106
Cdd:cd17012      7 LEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTRE-FESVLVD 85

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1720405414  107 AAALVK---DPSVSKSIERIFKIWEDRNVYPEDMIVALR 142
Cdd:cd17012     86 AFSHVAreaDEGCKKPLERLLNIWQERSVYGGDFIQQLK 124
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 36-144 3.07e-14

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: 70.62  E-value: 3.07e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   36 NTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAiIFRESFADVLPEA---AALVK 112
Cdd:cd03562     13 LSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKGP-EFTKDFSPVIVELfkhVYSET 91

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1720405414  113 DPSVSKSIERIFKIWEDRNVYPEDMIVALREA 144
Cdd:cd03562     92 DEDCKKKLGRVLSIWEERNVFENSVLEQLKQA 123
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 319-645 3.87e-08

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 58.00  E-value: 3.87e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  319 SPVPSPSMDAPSPTgSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDvedmelsdveddgskiivedrkekpvEKPAV 398
Cdd:pfam05109  475 SPTPAGTTSGASPV-TPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATS--------------------------PTPAV 527

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  399 STGVPTKSTESVSKASPCAPPSVPT-TAAPPLPkplstALLSPSPTLVLPNLANVdlakisSILSSLTSVMKNTGVSSAS 477
Cdd:pfam05109  528 TTPTPNATSPTLGKTSPTSAVTTPTpNATSPTP-----AVTTPTPNATIPTLGKT------SPTSAVTTPTPNATSPTVG 596

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  478 RPSPGIPTSPSNLSSGLKTP----------APATTPSHNPLANILSKVEITPESILSALSKT----QTQSAPALQGLSSL 543
Cdd:pfam05109  597 ETSPQANTTNHTLGGTSSTPvvtsppknatSAVTTGQHNITSSSTSSMSLRPSSISETLSPStsdnSTSHMPLLTSAHPT 676

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  544 LQSVTANPVPASEVTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTTF 623
Cdd:pfam05109  677 GGENITQVTPASTSTHHVSTSSPAPRPGTTSQASGPGNSSTSTKPGEVNVTKGTPPKNATSPQAPSGQKTAVPTVTSTGG 756

                          330       340
                   ....*....|....*....|...
gi 1720405414  624 KLPSSSLG-FTGTHNPSPAAPPT 645
Cdd:pfam05109  757 KANSTTGGkHTTGHGARTSTEPT 779
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 41-144 4.11e-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: 53.38  E-value: 4.11e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414   41 IQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAII---FRESFADVL-PEAAALVKDPSV 116
Cdd:cd16983     22 INAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQYGKEkdvYAPRFAKNLsKTFLNLLKCPEK 101

                           90       100
                   ....*....|....*....|....*....
gi 1720405414  117 SKS-IERIFKIWEDRNVYPEDMIVALREA 144
Cdd:cd16983    102 DKPkVKRVLNLWQKNGVFPKEIIQPLLDA 130
PHA03247 PHA03247
large tegument protein UL36; Provisional
 314-668 1.76e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.02  E-value: 1.76e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  314 PDPEESPVPSPSMDAPSPTGSESPFQGMGGEEPQSPAMESDKSAtPEPVTDNRDVEDMELSDVEDDGSKIiveDRKEKPV 393
Cdd:PHA03247  2612 APPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDD-PAPGRVSRPRRARRLGRAAQASSPP---QRPRRRA 2687

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  394 EKPAVStgvptkstesvSKASPCAPPSVPTTAAPPlPKPLSTALLSPSPTLVLPNLANVDLAKISSILSSLTSVMKNTGV 473
Cdd:PHA03247  2688 ARPTVG-----------SLTSLADPPPPPPTPEPA-PHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPA 2755

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  474 SSASRPSPGIPTSPSNLSSGLKTPAPATTPshnPLANILSkveitpESILSALSKTQTQSAPALQGLSSLLQSVTANPVP 553
Cdd:PHA03247  2756 RPARPPTTAGPPAPAPPAAPAAGPPRRLTR---PAVASLS------ESRESLPSPWDPADPPAAVLAPAAALPPAASPAG 2826

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  554 ASEVTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTTFKLPSSSLGFT 633
Cdd:PHA03247  2827 PLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPE 2906

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1720405414  634 GTHNPSPAAPPTEVAVCQSSEVSKPKPESESTSPS 668
Cdd:PHA03247  2907 RPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQP 2941
PHA03247 PHA03247
large tegument protein UL36; Provisional
 314-577 1.33e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.32  E-value: 1.33e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  314 PDPEESPVPSPSMDAP-SPTGSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDVEDMELSDVEDDGSKiivedrkeKP 392
Cdd:PHA03247  2733 PALPAAPAPPAVPAGPaTPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPW--------DP 2804

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  393 VEKPAVSTGVPTKSTESVSKASPCAPPSVPTTAAPPLPKPLSTALLSPSPTLVlpnlANVDLAKISSILSSLTSVMKNTG 472
Cdd:PHA03247  2805 ADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVA----PGGDVRRRPPSRSPAAKPAAPAR 2880

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  473 VSSASRPSPGIPTSPSNLSSGLKTPAPATTPSHNPLANILSKVEITPesilsalsktQTQSAPALQGLSSLLQSVTANPV 552
Cdd:PHA03247  2881 PPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPP----------QPQPPPPPPPRPQPPLAPTTDPA 2950

                          250       260
                   ....*....|....*....|....*
gi 1720405414  553 PASEvtsqSTTASPASTTGSAVKGR 577
Cdd:PHA03247  2951 GAGE----PSGAVPQPWLGALVPGR 2971
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 396-715 9.50e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 47.22  E-value: 9.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  396 PAVSTGVPTKSTESVSKASPCAPPSVPTTAAPPLPKPLST----ALLSPSPTlvlpNLANVDLAKISSILSSLTSVmkNT 471
Cdd:pfam05109  442 PNTTTGLPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTtsgaSPVTPSPS----PRDNGTESKAPDMTSPTSAV--TT 515

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  472 GVSSASRPSPGIPTSPSNLSS---GLKTPAPA-TTPSHNPLANILSKVEITPESILSALSKTQTQSA---PALQGLSSLL 544
Cdd:pfam05109  516 PTPNATSPTPAVTTPTPNATSptlGKTSPTSAvTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAvttPTPNATSPTV 595

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  545 -----QSVTANPVPASEVTSQSTTASPASTTGSAVKGRNLLSSTQSfipkSFNYSPSSSTSEVSSTSASKASVGQSPVL- 618
Cdd:pfam05109  596 getspQANTTNHTLGGTSSTPVVTSPPKNATSAVTTGQHNITSSST----SSMSLRPSSISETLSPSTSDNSTSHMPLLt 671

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  619 ---PSTTFKLPSSSLGFTGTHNPSPAAPPTEVAVcqSSEVSKPKPESESTSPSLEmkihNFLKGNP--------GFSGLN 687
Cdd:pfam05109  672 sahPTGGENITQVTPASTSTHHVSTSSPAPRPGT--TSQASGPGNSSTSTKPGEV----NVTKGTPpknatspqAPSGQK 745

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1720405414  688 LNIPILSSLGSSAPS-------EGHASDFQRGPTS 715
Cdd:pfam05109  746 TAVPTVTSTGGKANSttggkhtTGHGARTSTEPTT 780
PRK11901 PRK11901
hypothetical protein; Reviewed
 399-579 3.58e-04

hypothetical protein; Reviewed


Pssm-ID: 237015 [Multi-domain]  Cd Length: 327  Bit Score: 44.29  E-value: 3.58e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  399 STGVPTKSTESVSKASPCAPPSVPTTAAPPL-PKPLSTALLSPSPTLVLPNLAN-----VDLAKISSILSSLTSVMKNTG 472
Cdd:PRK11901    84 SSSLSSGNQSSPSAANNTSDGHDASGVKNTApPQDISAPPISPTPTQAAPPQTPngqqrIELPGNISDALSQQQGQVNAA 163

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  473 VSSASRPSPGIPTSPSNLSSGLKTPAPATTPSHN--PLANILSKVEITPESILSALSKTQTQSAP-ALQGLSSLLQSvta 549
Cdd:PRK11901   164 SQNAQGNTSTLPTAPATVAPSKGAKVPATAETHPtpPQKPATKKPAVNHHKTATVAVPPATSGKPkSGAASARALSS--- 240

                          170       180       190
                   ....*....|....*....|....*....|
gi 1720405414  550 npVPASEVTSQSTTASPASTTGSAVKGRNL 579
Cdd:PRK11901   241 --APASHYTLQLSSASRSDTLNAYAKKQNL 268
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
142-318 3.62e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.05  E-value: 3.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  142 REALSTTFKTQKQLKENLNKQpNKQWKKSQTStnpKAALKSKIVaEFRSQalIEELlmyKRSEDQIELKEKQLSTMRVDV 221
Cdd:PRK03918   223 LEKLEKEVKELEELKEEIEEL-EKELESLEGS---KRKLEEKIR-ELEER--IEEL---KKEIEELEEKVKELKELKEKA 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  222 CSTETLKCLKDKTggKKFSKEFEEASSKLEEFVNGLDKQVKNGPSLTEALENagifYEAQYKEVKVVANAYKTFA---NR 298
Cdd:PRK03918   293 EEYIKLSEFYEEY--LDELREIEKRLSRLEEEINGIEERIKELEEKEERLEE----LKKKLKELEKRLEELEERHelyEE 366

                          170       180
                   ....*....|....*....|..
gi 1720405414  299 VNNLKKKLDQLKSTLPD--PEE 318
Cdd:PRK03918   367 AKAKKEELERLKKRLTGltPEK 388
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 314-577 5.47e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.78  E-value: 5.47e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  314 PDPEESPVPSPSMDAP-SPTGSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDVEDMELSDVEDDGSKIIVEDRKEKP 392
Cdd:PHA03307    82 NESRSTPTWSLSTLAPaSPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAA 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  393 VEKPAVSTG-------VPTKSTESVSKASPCAPPSVPTTAAPPLPKPLST--ALLSPSPTLVLPNLANVDLAKISSILSS 463
Cdd:PHA03307   162 VASDAASSRqaalplsSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSpiSASASSPAPAPGRSAADDAGASSSDSSS 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  464 LTSVMKN-------------------------TGVSSASRPSPGIPTSPSNLSSGLKTPAPATTPSHNPLANILSKVEIT 518
Cdd:PHA03307   242 SESSGCGwgpenecplprpapitlptriweasGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSS 321

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720405414  519 PESILSALSKTQTQSAPALQGLSSLLQSVTAN----PVPASEVTSQSTTASPASTTGSAVKGR 577
Cdd:PHA03307   322 RESSSSSTSSSSESSRGAAVSPGPSPSRSPSPsrppPPADPSSPRKRPRPSRAPSSPAASAGR 384
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 307-442 1.15e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.62  E-value: 1.15e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  307 DQLKSTLPDPEESPVPSPSMDAPSPTGSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDVEDMELSDVEDDGSKIIVE 386
Cdd:PHA03307   793 EAAFRRPGRLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAAARPPPARSSESSKSKPAAAGGRARGKNGRR 872

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1720405414  387 DrkekpvekpavSTGVPTKSTESVSKASPCAPPSVPTTAAPPLPKPLSTALLSPSP 442
Cdd:PHA03307   873 R-----------PRPPEPRARPGAAAPPKAAAAAPPAGAPAPRPRPAPRVKLGPMP 917
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 405-670 1.37e-03

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 43.02  E-value: 1.37e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  405 KSTESVSKASPCAPPSVPTTAAPPLP---KPLSTALLSPSPTLVLPNLANVDLAKISSILSSLTSVMKNTGVSSAsrPSP 481
Cdd:pfam17823  128 QSLPAAIAALPSEAFSAPRAAACRANasaAPRAAIAAASAPHAASPAPRTAASSTTAASSTTAASSAPTTAASSA--PAT 205

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  482 GIPTSPSNLSS-GLKTPAPATT----PSHNPLANILSKVEITPESILSALSKTQTQSAPALQGLSSLLQSVTANPVPASE 556
Cdd:pfam17823  206 LTPARGISTAAtATGHPAAGTAlaavGNSSPAAGTVTAAVGTVTPAALATLAAAAGTVASAAGTINMGDPHARRLSPAKH 285

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  557 VTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTT---FKLPSSSlgft 633
Cdd:pfam17823  286 MPSDTMARNPAAPMGAQAQGPIIQVSTDQPVHNTAGEPTPSPSNTTLEPNTPKSVASTNLAVVTTTkaqAKEPSAS---- 361

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 1720405414  634 gthnPSPaAPPTEVAvcqssevskpkPESESTSPSLE 670
Cdd:pfam17823  362 ----PVP-VLHTSMI-----------PEVEATSPTTQ 382
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 311-504 1.65e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 1.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  311 STLPDPEESPVPSPSMDAPSPTGSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDVEDMELSDVEDDGSKIIVEDRKE 390
Cdd:PHA03307   177 SSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECP 256

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  391 KPVEKPAVSTGVPTKSTESVSKASPCAPPSVPTTAAPPLPKPLSTALLSPSPTLVLPNLANV------DLAKISSILSSL 464
Cdd:PHA03307   257 LPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSsssresSSSSTSSSSESS 336

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1720405414  465 TSVMKNTGVSSASRPSPGIPTSPSNLSSGLKTPAPATTPS 504
Cdd:PHA03307   337 RGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPS 376
PHA03247 PHA03247
large tegument protein UL36; Provisional
 314-665 1.90e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 1.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  314 PDPEESPVPSPsmDAPSPTGSESP--FQGMGGEEPQSPAM----------ESDKSATPEP--------VTDNRDVEDmel 373
Cdd:PHA03247  2496 PDPGGGGPPDP--DAPPAPSRLAPaiLPDEPVGEPVHPRMltwirgleelASDDAGDPPPplppaappAAPDRSVPP--- 2570

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  374 SDVEDDGSKIIVEDRKEKPVEKPAVSTGVPTKSTESVSKASPCAPPSVPTTAAPPLPKPlstallSPSP---TLVLPNLA 450
Cdd:PHA03247  2571 PRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPP------SPSPaanEPDPHPPP 2644

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  451 NVDLAKISSILSSLTSVMKNTGVSSASRPS-----------PGIPTSPSNLSSGLKTPAPATTPSHNPLAnilskveITP 519
Cdd:PHA03247  2645 TVPPPERPRDDPAPGRVSRPRRARRLGRAAqassppqrprrRAARPTVGSLTSLADPPPPPPTPEPAPHA-------LVS 2717

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  520 ESILSALSKTQTQSAPALQGLSSLLQSVTANPVPASE--VTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSS 597
Cdd:PHA03247  2718 ATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGParPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRES 2797

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1720405414  598 STSEVSSTSASKASVGQSPVLPSTTfkLPSsslgftgthnpSPAAPPTEVAVCQSSEVSKPKPESEST 665
Cdd:PHA03247  2798 LPSPWDPADPPAAVLAPAAALPPAA--SPA-----------GPLPPPTSAQPTAPPPPPGPPPPSLPL 2852
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 312-669 2.81e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 42.47  E-value: 2.81e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  312 TLPDPEESPVPSPSMDAPSPTGSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDvedmelSDVEDDGSKIIVEDRKEK 391
Cdd:PHA03307    69 TGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPA------SPPPSPAPDLSEMLRPVG 142

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  392 PVEKPAVSTGVPTksteSVSKASPCAPPSVPTTAAPPLPKPLSTALLSPSPTLVLPNLANvdlakissilssltsvmknt 471
Cdd:PHA03307   143 SPGPPPAASPPAA----GASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTP-------------------- 198

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  472 gvSSASRPSPGIPTSPSNLSSGLKTPAPATTP-SHNPLANILSKVEITPESILSALSKTQTQSAPALQGLSSLLQSVTAN 550
Cdd:PHA03307   199 --PAAASPRPPRRSSPISASASSPAPAPGRSAaDDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWN 276

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720405414  551 PvPASEVTSQSTTASPASTTGSAVKGRNLLSSTQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTTFKLPSSSL 630
Cdd:PHA03307   277 G-PSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSR 355

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1720405414  631 GFTGTHNPSPAAPPTEVAVCQSSEVSKPKPESESTSPSL 669
Cdd:PHA03307   356 PPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAV 394
 
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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