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Conserved domains on  [gi|564394744|ref|XP_006255261|]
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retinoblastoma-like protein 2 isoform X1 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_RBL2 cd20606
cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also ...
 831-1018 3.23e-123

cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also called 130 kDa retinoblastoma-associated protein (p130), retinoblastoma-related protein 2 (RBR-2), or pRb2, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL2 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. It probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL2 contains one cyclin box. The cyclin box is a protein binding domain.


:

Pssm-ID: 410309  Cd Length: 189  Bit Score: 375.78  E-value: 3.23e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20606     1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  911 CYRTQPQARSQVYRSVLIKG-KRRNSGSCENRSHQNSPTELNTDRASRDSSPVMRSNSTLPVPQPSSAPPTPTRLTGANS 989
Cdd:cd20606    81 CYRTQPQASSSVYRSVLIKGrRRRRSGSSDDSGSQSSSSEENRERTSRDSSPVMRSSSTLPVPQPNSAPPTPTRLTGANS 160

                         170       180
                  ....*....|....*....|....*....
gi 564394744  990 DIEEEERGDLIQFYNNIYRKQIQTFAMKY 1018
Cdd:cd20606   161 DMEEEERGDLIQFYNNIYIEQIKEFALKY 189
RB_A pfam01858
Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
 414-606 4.41e-97

Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.


:

Pssm-ID: 460364  Cd Length: 195  Bit Score: 306.43  E-value: 4.41e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   414 TPVSTATHSLNRLHTMLAGLRNAPSEKLEQILRSCSRDPTRAIADRLREMYEIYSQHF-QPDENVSNCAKEMANKHFRFA 492
Cdd:pfam01858    1 TPVSSAMQTVSWLQTLLSGLSDEPSEKLLRIFKSCSRDPTETILKRVKELGEIFCQKYtEASGEHPSFCIEIAEQRFRLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   493 EMLYYKVLESVIEQEQKRLGDMDLSGVLEQDAFHKSLLACCLEVVAFSYKPPG-NFPFIAEIFDVPHYHFYKVIEVFIRA 571
Cdd:pfam01858   81 EKLYYKVLESILKSEKKRLPGNDLSSLLSNDIFHRSLLACCLEIVLFAYNSERlSFPWILEVFGLPPFDFYKVIESFIRA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 564394744   572 EDGLCREVVKHLNQIEEQILDHLAWKTKSPLWDRI 606
Cdd:pfam01858  161 EDGLPRELVKHLNSIEEQILESLAWKSDSPLWELL 195
DUF3452 pfam11934
Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. ...
 101-236 1.54e-59

Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with pfam01858, pfam01857. This domain has a single completely conserved residue W that may be functionally important.


:

Pssm-ID: 463402  Cd Length: 134  Bit Score: 200.13  E-value: 1.54e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   101 KGTAEGNYVSLTRILRCSEQSLIEFFNKMKKWEDMANLPPHFRERTERLERNFTVSAVIFKKYEPIFQDIFKYPQEEqpR 180
Cdd:pfam11934    1 DGTVEGNCVSLTRLLRACKLSIIDFFKKMKQWADMANLDWEFRLEIKELERNFSVTTVLFKKYKRIFNELFLSPPPK--E 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 564394744   181 QQRGRKQRRQPCTTSEIFHFCWVLFIYAKGNFPMISDDLVNSYHLLLCALDLVYGN 236
Cdd:pfam11934   79 PKRSKKSRPAPCSYSDLFEFGWLLFLAAKNEFPSISKDLVTSYHLLLCCLDLVYVN 134
SP1-4_N super family cl41773
N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; Specificity Proteins ...
 696-834 5.12e-04

N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. SPs belong to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (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. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP1-4.


The actual alignment was detected with superfamily member cd22553:

Pssm-ID: 425404 [Multi-domain]  Cd Length: 384  Bit Score: 43.86  E-value: 5.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  696 PQPLVNA-----VPVQNVSGETVSVTPVPGQTLVTMATATVTANNGQTV--TI--PVQGIANENGGITFFPVQVNVGGQA 766
Cdd:cd22553   124 VQGQANAsnvlqNIAQIASGGNAVQLPLNNMTQTIPVQVPVSTANGQTVyqTIqvPIQAIQSGNAGGGNQALQAQVIPQL 203

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564394744  767 qAVTGSIQPlsaQALAgSLSSQqvtGTTLQVPGPVA-----IQQISPGGQQQNQGQPLTSSSIRPRKTSSLSL 834
Cdd:cd22553   204 -AQAAQLQP---QQLA-QVSSQ---GYIQQIPANASqqqpqMVQQGPNQSGQIIGQVASASSIQAAAIPLTVY 268
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 41-131 1.76e-03

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


:

Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 38.55  E-value: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   41 QIQQRFEELCSRLNMDEAARAEAWSSYRSMSESYTLEGNDLHWLACA-LYVACRKsvptvskgtaEGNYVSLTRILRCSE 119
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAAcLYLACKL----------EELPRTLKEIAKVSG 70

                          90
                  ....*....|..
gi 564394744  120 QSLIEFFNKMKK 131
Cdd:cd00043    71 VSEKELRKAEKE 82
 
Name Accession Description Interval E-value
CYCLIN_RBL2 cd20606
cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also ...
 831-1018 3.23e-123

cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also called 130 kDa retinoblastoma-associated protein (p130), retinoblastoma-related protein 2 (RBR-2), or pRb2, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL2 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. It probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL2 contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410309  Cd Length: 189  Bit Score: 375.78  E-value: 3.23e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20606     1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  911 CYRTQPQARSQVYRSVLIKG-KRRNSGSCENRSHQNSPTELNTDRASRDSSPVMRSNSTLPVPQPSSAPPTPTRLTGANS 989
Cdd:cd20606    81 CYRTQPQASSSVYRSVLIKGrRRRRSGSSDDSGSQSSSSEENRERTSRDSSPVMRSSSTLPVPQPNSAPPTPTRLTGANS 160

                         170       180
                  ....*....|....*....|....*....
gi 564394744  990 DIEEEERGDLIQFYNNIYRKQIQTFAMKY 1018
Cdd:cd20606   161 DMEEEERGDLIQFYNNIYIEQIKEFALKY 189
RB_A pfam01858
Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
 414-606 4.41e-97

Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.


Pssm-ID: 460364  Cd Length: 195  Bit Score: 306.43  E-value: 4.41e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   414 TPVSTATHSLNRLHTMLAGLRNAPSEKLEQILRSCSRDPTRAIADRLREMYEIYSQHF-QPDENVSNCAKEMANKHFRFA 492
Cdd:pfam01858    1 TPVSSAMQTVSWLQTLLSGLSDEPSEKLLRIFKSCSRDPTETILKRVKELGEIFCQKYtEASGEHPSFCIEIAEQRFRLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   493 EMLYYKVLESVIEQEQKRLGDMDLSGVLEQDAFHKSLLACCLEVVAFSYKPPG-NFPFIAEIFDVPHYHFYKVIEVFIRA 571
Cdd:pfam01858   81 EKLYYKVLESILKSEKKRLPGNDLSSLLSNDIFHRSLLACCLEIVLFAYNSERlSFPWILEVFGLPPFDFYKVIESFIRA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 564394744   572 EDGLCREVVKHLNQIEEQILDHLAWKTKSPLWDRI 606
Cdd:pfam01858  161 EDGLPRELVKHLNSIEEQILESLAWKSDSPLWELL 195
RB_B pfam01857
Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a ...
 831-1012 4.09e-70

Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B domain. The B domain has a cyclin fold.


Pssm-ID: 460363  Cd Length: 131  Bit Score: 229.76  E-value: 4.09e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:pfam01857    1 SLNLFFRKVYHLAAVRLQDLCSRLDLSSDLREKIWTCFEHSLVHQTDLMKDRHLDQILLCAIYVICKVTKEELTFKEIMK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   911 CYRTQPQARSQVYRSVLIKGKRRNsgscenrshqnsptelntdrasrdsspvmrsnstlpvpqpssapptptrltGANSD 990
Cdd:pfam01857   81 CYRKQPQASSHVYRSVLIRRRERE---------------------------------------------------RNGKN 109

                          170       180
                   ....*....|....*....|..
gi 564394744   991 IEEEERGDLIQFYNNIYRKQIQ 1012
Cdd:pfam01857  110 NEEEERGDIIKFYNKVFVPAMK 131
DUF3452 pfam11934
Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. ...
 101-236 1.54e-59

Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with pfam01858, pfam01857. This domain has a single completely conserved residue W that may be functionally important.


Pssm-ID: 463402  Cd Length: 134  Bit Score: 200.13  E-value: 1.54e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   101 KGTAEGNYVSLTRILRCSEQSLIEFFNKMKKWEDMANLPPHFRERTERLERNFTVSAVIFKKYEPIFQDIFKYPQEEqpR 180
Cdd:pfam11934    1 DGTVEGNCVSLTRLLRACKLSIIDFFKKMKQWADMANLDWEFRLEIKELERNFSVTTVLFKKYKRIFNELFLSPPPK--E 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 564394744   181 QQRGRKQRRQPCTTSEIFHFCWVLFIYAKGNFPMISDDLVNSYHLLLCALDLVYGN 236
Cdd:pfam11934   79 PKRSKKSRPAPCSYSDLFEFGWLLFLAAKNEFPSISKDLVTSYHLLLCCLDLVYVN 134
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 845-928 2.39e-05

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 43.74  E-value: 2.39e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744    845 VRLRDLCTKLDISDELRKKIWTCFEFSIVQCPelMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMRCYRTQPqaRSQVYR 924
Cdd:smart00385    1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYK--FLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT--EEEILR 76


                    ....
gi 564394744    925 SVLI 928
Cdd:smart00385   77 MERL 80
SP1-4_arthropods_N cd22553
N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; ...
 696-834 5.12e-04

N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. One SP is clade SP1-4, which is expressed ubiquitously throughout development. SP1-4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (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. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. This model represents the N-terminal domain of SP1-4 from arthropods.


Pssm-ID: 411778 [Multi-domain]  Cd Length: 384  Bit Score: 43.86  E-value: 5.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  696 PQPLVNA-----VPVQNVSGETVSVTPVPGQTLVTMATATVTANNGQTV--TI--PVQGIANENGGITFFPVQVNVGGQA 766
Cdd:cd22553   124 VQGQANAsnvlqNIAQIASGGNAVQLPLNNMTQTIPVQVPVSTANGQTVyqTIqvPIQAIQSGNAGGGNQALQAQVIPQL 203

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564394744  767 qAVTGSIQPlsaQALAgSLSSQqvtGTTLQVPGPVA-----IQQISPGGQQQNQGQPLTSSSIRPRKTSSLSL 834
Cdd:cd22553   204 -AQAAQLQP---QQLA-QVSSQ---GYIQQIPANASqqqpqMVQQGPNQSGQIIGQVASASSIQAAAIPLTVY 268
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 41-131 1.76e-03

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 38.55  E-value: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   41 QIQQRFEELCSRLNMDEAARAEAWSSYRSMSESYTLEGNDLHWLACA-LYVACRKsvptvskgtaEGNYVSLTRILRCSE 119
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAAcLYLACKL----------EELPRTLKEIAKVSG 70

                          90
                  ....*....|..
gi 564394744  120 QSLIEFFNKMKK 131
Cdd:cd00043    71 VSEKELRKAEKE 82
 
Name Accession Description Interval E-value
CYCLIN_RBL2 cd20606
cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also ...
 831-1018 3.23e-123

cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also called 130 kDa retinoblastoma-associated protein (p130), retinoblastoma-related protein 2 (RBR-2), or pRb2, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL2 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. It probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL2 contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410309  Cd Length: 189  Bit Score: 375.78  E-value: 3.23e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20606     1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  911 CYRTQPQARSQVYRSVLIKG-KRRNSGSCENRSHQNSPTELNTDRASRDSSPVMRSNSTLPVPQPSSAPPTPTRLTGANS 989
Cdd:cd20606    81 CYRTQPQASSSVYRSVLIKGrRRRRSGSSDDSGSQSSSSEENRERTSRDSSPVMRSSSTLPVPQPNSAPPTPTRLTGANS 160

                         170       180
                  ....*....|....*....|....*....
gi 564394744  990 DIEEEERGDLIQFYNNIYRKQIQTFAMKY 1018
Cdd:cd20606   161 DMEEEERGDLIQFYNNIYIEQIKEFALKY 189
RB_A pfam01858
Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
 414-606 4.41e-97

Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.


Pssm-ID: 460364  Cd Length: 195  Bit Score: 306.43  E-value: 4.41e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   414 TPVSTATHSLNRLHTMLAGLRNAPSEKLEQILRSCSRDPTRAIADRLREMYEIYSQHF-QPDENVSNCAKEMANKHFRFA 492
Cdd:pfam01858    1 TPVSSAMQTVSWLQTLLSGLSDEPSEKLLRIFKSCSRDPTETILKRVKELGEIFCQKYtEASGEHPSFCIEIAEQRFRLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   493 EMLYYKVLESVIEQEQKRLGDMDLSGVLEQDAFHKSLLACCLEVVAFSYKPPG-NFPFIAEIFDVPHYHFYKVIEVFIRA 571
Cdd:pfam01858   81 EKLYYKVLESILKSEKKRLPGNDLSSLLSNDIFHRSLLACCLEIVLFAYNSERlSFPWILEVFGLPPFDFYKVIESFIRA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 564394744   572 EDGLCREVVKHLNQIEEQILDHLAWKTKSPLWDRI 606
Cdd:pfam01858  161 EDGLPRELVKHLNSIEEQILESLAWKSDSPLWELL 195
RB_B pfam01857
Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a ...
 831-1012 4.09e-70

Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B domain. The B domain has a cyclin fold.


Pssm-ID: 460363  Cd Length: 131  Bit Score: 229.76  E-value: 4.09e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:pfam01857    1 SLNLFFRKVYHLAAVRLQDLCSRLDLSSDLREKIWTCFEHSLVHQTDLMKDRHLDQILLCAIYVICKVTKEELTFKEIMK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   911 CYRTQPQARSQVYRSVLIKGKRRNsgscenrshqnsptelntdrasrdsspvmrsnstlpvpqpssapptptrltGANSD 990
Cdd:pfam01857   81 CYRKQPQASSHVYRSVLIRRRERE---------------------------------------------------RNGKN 109

                          170       180
                   ....*....|....*....|..
gi 564394744   991 IEEEERGDLIQFYNNIYRKQIQ 1012
Cdd:pfam01857  110 NEEEERGDIIKFYNKVFVPAMK 131
CYCLIN_RBL cd20600
cyclin box found in retinoblastoma-like protein (RBL) subfamily; The RBL subfamily includes ...
 831-1018 2.00e-64

cyclin box found in retinoblastoma-like protein (RBL) subfamily; The RBL subfamily includes two retinoblastoma-like proteins, RBL1 and RBL2. They are key regulators of entry into cell division and are directly involved in heterochromatin formation by maintaining overall chromatin structure. RBL1 and RBL2 recruit and target histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. They control histone H4 'Lys-20' trimethylation and probably act as transcription repressors by recruiting chromatin-modifying enzymes to promoters. They may also act as tumor suppressors. Members of this family contain one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410303  Cd Length: 112  Bit Score: 213.03  E-value: 2.00e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20600     1 SLGLFFRKVYHLASVRLRDLCEKLEISEELRRKIWTCFEHSLVHHIELMRDRHLDQLLMCAVYVIAKVTKQDKSFQEIMK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  911 CYRTQPQARSqvyrsvlikgkrrnsgscenrshqnsptelntdrasrdsspvmrsnstlpvpqpssapptptrltgansd 990
Cdd:cd20600    81 CYRLQPQAQS---------------------------------------------------------------------- 90

                         170       180
                  ....*....|....*....|....*...
gi 564394744  991 ieeeerGDLIQFYNNIYRKQIQTFAMKY 1018
Cdd:cd20600    91 ------GDLIQFYNSVYVKKMKEFALKF 112
CYCLIN_RBL1 cd20605
cyclin box found in retinoblastoma-like protein 1 (RBL1) and similar proteins; RBL1, also ...
 825-1018 2.38e-64

cyclin box found in retinoblastoma-like protein 1 (RBL1) and similar proteins; RBL1, also called 107 kDa retinoblastoma-associated protein (p107), retinoblastoma-related protein 1 (RBR-1), or pRb1, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL1 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. RBL1 probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL1 contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410308  Cd Length: 130  Bit Score: 213.59  E-value: 2.38e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  825 RPRKTSSLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKS 904
Cdd:cd20605     1 KPKKTGSLALFYRKVYHLASVRLRDLCLKLDVSNELRRKIWTCFEFSLVHCTDLMKDRHLDQLLLCAFYIMAKVTKEERT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  905 FQNIMRCYRTQPQARSQVYRSVLIKgkrrnsgscenrshqnsptelntdrasrdsspvmrsnstlpvpqpssapptptrl 984
Cdd:cd20605    81 FQDIMKCYRNQPQANSHVYRSVLLK------------------------------------------------------- 105

                         170       180       190
                  ....*....|....*....|....*....|....
gi 564394744  985 tgansdieeEERGDLIQFYNNIYRKQIQTFAMKY 1018
Cdd:cd20605   106 ---------EERGDLIKFYNTIYVGRVKSFALKY 130
DUF3452 pfam11934
Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. ...
 101-236 1.54e-59

Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with pfam01858, pfam01857. This domain has a single completely conserved residue W that may be functionally important.


Pssm-ID: 463402  Cd Length: 134  Bit Score: 200.13  E-value: 1.54e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   101 KGTAEGNYVSLTRILRCSEQSLIEFFNKMKKWEDMANLPPHFRERTERLERNFTVSAVIFKKYEPIFQDIFKYPQEEqpR 180
Cdd:pfam11934    1 DGTVEGNCVSLTRLLRACKLSIIDFFKKMKQWADMANLDWEFRLEIKELERNFSVTTVLFKKYKRIFNELFLSPPPK--E 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 564394744   181 QQRGRKQRRQPCTTSEIFHFCWVLFIYAKGNFPMISDDLVNSYHLLLCALDLVYGN 236
Cdd:pfam11934   79 PKRSKKSRPAPCSYSDLFEFGWLLFLAAKNEFPSISKDLVTSYHLLLCCLDLVYVN 134
CYCLIN_RB cd20599
cyclin box found in retinoblastoma-associated protein (RB) and similar proteins; RB, also ...
 831-935 7.46e-37

cyclin box found in retinoblastoma-associated protein (RB) and similar proteins; RB, also called p105-Rb, pRb, or pp110, is a key regulator of entry into cell division and also acts as a tumor suppressor. It promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. It also acts as a transcription repressor of E2F1 target genes. RB is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. It recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. RB contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410302  Cd Length: 126  Bit Score: 135.11  E-value: 7.46e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20599     2 SLSLFYKKVYRLAYLRLNTLCDLLLLHPDLEHRIWTCFEHCLQNRYELLKDRHLDQIMMCSMYGICKVKNKDLRFKTIVT 81

                          90       100
                  ....*....|....*....|....*
gi 564394744  911 CYRTQPQARSQVYRSVLIKGKRRNS 935
Cdd:cd20599    82 AYKDLPHASQEVYKRVLIRGEEYDS 106
CYCLIN_RB-like cd20548
cyclin box found in retinoblastoma-associated protein (RB) family; The RB family includes ...
 832-1007 2.27e-36

cyclin box found in retinoblastoma-associated protein (RB) family; The RB family includes retinoblastoma-associated protein (RB), and two retinoblastoma-like proteins, RBL1 and RBL2. RB, also called p105-Rb, pRb, or pp110, is a key regulator of entry into cell division, and also acts as a tumor suppressor. It promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. It also acts as a transcription repressor of E2F1 target genes. RB is directly involved in heterochromatin formation by maintaining overall chromatin structure. It recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. RBL1 and RBL2 are also key regulators of entry into cell division. RBL1 and RBL2 recruit and target histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. They control histone H4 'Lys-20' trimethylation and probably act as transcription repressors by recruiting chromatin-modifying enzymes to promoters. They may also act as tumor suppressors. Members of this family contain one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410251  Cd Length: 122  Bit Score: 133.59  E-value: 2.27e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  832 LSLFFRKVYYLAGVRLRDLCTKLD-ISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20548     1 LQLFFRKLYRLAAARLQDLCKRLDlLSPPLRERIWTVFKHILSEETELLFDRHLDQIILCSIYAVCKVNNENLTFKEILD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  911 CYRTQPQARSQVYRSVLIKGKRRNSGScenrshqnsptelntdrasrdsspvmrsnstlpvpqpssapptptrltgansd 990
Cdd:cd20548    81 AYRKQPQAESEVYRSVLPLFRSVGSDD----------------------------------------------------- 107

                         170
                  ....*....|....*..
gi 564394744  991 ieEEERGDLIQFYNNIY 1007
Cdd:cd20548   108 --EGESGDIIKFYNQVF 122
CYCLIN_AtRBR_like cd20601
cyclin box found in Arabidopsis thaliana retinoblastoma-related protein 1 (AtRBR1) and similar ...
 832-933 1.74e-24

cyclin box found in Arabidopsis thaliana retinoblastoma-related protein 1 (AtRBR1) and similar proteins; AtRBR1 is a key regulator of entry into cell division. It acts as a transcription repressor of E2F target genes, whose activity is required for progress from the G1 to the S phase of the cell cycle. AtRBR1 plays a central role in the mechanism controlling meristem cell differentiation, cell fate establishment and cell fate maintenance during organogenesis and gametogenesis. AtRBR1 contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410304  Cd Length: 129  Bit Score: 99.77  E-value: 1.74e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  832 LSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMRC 911
Cdd:cd20601     1 INVFFQKVLKLAAIRIADLCERLQQPQLVVEQVYRLIEHVLYEQTGLFFNRHIDQIILCCLYGVCKVHKLNVTFREIIYQ 80

                          90       100
                  ....*....|....*....|..
gi 564394744  912 YRTQPQARSQVYRSVLIKGKRR 933
Cdd:cd20601    81 YRKQPQCKPDVFRNVVIEQRRP 102
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 845-928 2.39e-05

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 43.74  E-value: 2.39e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744    845 VRLRDLCTKLDISDELRKKIWTCFEFSIVQCPelMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMRCYRTQPqaRSQVYR 924
Cdd:smart00385    1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYK--FLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT--EEEILR 76


                    ....
gi 564394744    925 SVLI 928
Cdd:smart00385   77 MERL 80
SP1-4_arthropods_N cd22553
N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; ...
 696-834 5.12e-04

N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. One SP is clade SP1-4, which is expressed ubiquitously throughout development. SP1-4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (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. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. This model represents the N-terminal domain of SP1-4 from arthropods.


Pssm-ID: 411778 [Multi-domain]  Cd Length: 384  Bit Score: 43.86  E-value: 5.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744  696 PQPLVNA-----VPVQNVSGETVSVTPVPGQTLVTMATATVTANNGQTV--TI--PVQGIANENGGITFFPVQVNVGGQA 766
Cdd:cd22553   124 VQGQANAsnvlqNIAQIASGGNAVQLPLNNMTQTIPVQVPVSTANGQTVyqTIqvPIQAIQSGNAGGGNQALQAQVIPQL 203

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564394744  767 qAVTGSIQPlsaQALAgSLSSQqvtGTTLQVPGPVA-----IQQISPGGQQQNQGQPLTSSSIRPRKTSSLSL 834
Cdd:cd22553   204 -AQAAQLQP---QQLA-QVSSQ---GYIQQIPANASqqqpqMVQQGPNQSGQIIGQVASASSIQAAAIPLTVY 268
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 41-131 1.76e-03

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 38.55  E-value: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394744   41 QIQQRFEELCSRLNMDEAARAEAWSSYRSMSESYTLEGNDLHWLACA-LYVACRKsvptvskgtaEGNYVSLTRILRCSE 119
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAAcLYLACKL----------EELPRTLKEIAKVSG 70

                          90
                  ....*....|..
gi 564394744  120 QSLIEFFNKMKK 131
Cdd:cd00043    71 VSEKELRKAEKE 82
 
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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