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Conserved domains on  [gi|1297636736|ref|XP_023065709|]
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retinoblastoma-like protein 2 isoform X4 [Piliocolobus tephrosceles]

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 ...
 704-893 3.68e-134

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: 401.58  E-value: 3.68e-134
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  704 SLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:cd20606      1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  784 CYRTQPQARSQVYRSVLIKGKRKRRNSGSSDSRSHQNsPTELNKDRTSRDSSPVMRSSSTLPVPQPSSAPPTPTRLTGAN 863
Cdd:cd20606     81 CYRTQPQASSSVYRSVLIKGRRRRRSGSSDDSGSQSS-SSEENRERTSRDSSPVMRSSSTLPVPQPNSAPPTPTRLTGAN 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 1297636736  864 SDMEEEERGDLIQFYNNIYIKQIKTFAMKY 893
Cdd:cd20606    160 SDMEEEERGDLIQFYNNIYIEQIKEFALKY 189
RB_A pfam01858
Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
 286-478 1.49e-99

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


:

Pssm-ID: 460364  Cd Length: 195  Bit Score: 311.05  E-value: 1.49e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  286 TPVSTATHSLSRLHTMLTGLRNAPSEKLEQILRTCSRDPTQAIANRLKEMFEIYSQHF-QPDEDFSNCAKEIASKHFRFA 364
Cdd:pfam01858    1 TPVSSAMQTVSWLQTLLSGLSDEPSEKLLRIFKSCSRDPTETILKRVKELGEIFCQKYtEASGEHPSFCIEIAEQRFRLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  365 EMLYYKVLESVIEQEQKRLGDMDLSGILEQDAFHRSLLACCLEVVTFSYKPPG-NFPFITEIFEVPLYHFYKVIEVFIRA 443
Cdd:pfam01858   81 EKLYYKVLESILKSEKKRLPGNDLSSLLSNDIFHRSLLACCLEIVLFAYNSERlSFPWILEVFGLPPFDFYKVIESFIRA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1297636736  444 EDGLCREVVKHLNQIEEQILDHLAWKPESPLWEKI 478
Cdd:pfam01858  161 EDGLPRELVKHLNSIEEQILESLAWKSDSPLWELL 195
DUF3452 pfam11934
Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. ...
 1-108 2.16e-43

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: 153.90  E-value: 2.16e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736    1 MKKWEDMANLPPHFRERTERLERNFTVSAVIFKKYEPIFQDIFKYPQEEQPRQQRGRKQRrqPCTVSEIFHFCWVLFIYA 80
Cdd:pfam11934   29 MKQWADMANLDWEFRLEIKELERNFSVTTVLFKKYKRIFNELFLSPPPKEPKRSKKSRPA--PCSYSDLFEFGWLLFLAA 106

                           90       100
                   ....*....|....*....|....*...
gi 1297636736   81 KGNFPMISDDLVNSYHLLLCALDLVYGN 108
Cdd:pfam11934  107 KNEFPSISKDLVTSYHLLLCCLDLVYVN 134
SP1-4_N super family cl41773
N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; Specificity Proteins ...
 539-679 1.18e-06

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: 51.95  E-value: 1.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  539 YSSPPASTT-----RRRLFVEndSPSDGGTPGRMPPQPLVNA-----VPVQNVSGEPVSVTPVPGQTLVTMATATVTAN- 607
Cdd:cd22553     67 YSVSPAVQTvtvdgHEAIFIP--ANSGLLQTNNQQAIQLAPGgtqaiLANQQTLIRPNTVQGQANASNVLQNIAQIASGg 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  608 -------NGQTVTIPVQ-GIANENGGITF----FPVQV----NVGGQAQAVTGSIQPLSAQAlaGSLSSQQMAgttlQVP 671
Cdd:cd22553    145 navqlplNNMTQTIPVQvPVSTANGQTVYqtiqVPIQAiqsgNAGGGNQALQAQVIPQLAQA--AQLQPQQLA----QVS 218


                   ....*...
gi 1297636736  672 GQVAIQQI 679
Cdd:cd22553    219 SQGYIQQI 226
 
Name Accession Description Interval E-value
CYCLIN_RBL2 cd20606
cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also ...
 704-893 3.68e-134

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: 401.58  E-value: 3.68e-134
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  704 SLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:cd20606      1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  784 CYRTQPQARSQVYRSVLIKGKRKRRNSGSSDSRSHQNsPTELNKDRTSRDSSPVMRSSSTLPVPQPSSAPPTPTRLTGAN 863
Cdd:cd20606     81 CYRTQPQASSSVYRSVLIKGRRRRRSGSSDDSGSQSS-SSEENRERTSRDSSPVMRSSSTLPVPQPNSAPPTPTRLTGAN 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 1297636736  864 SDMEEEERGDLIQFYNNIYIKQIKTFAMKY 893
Cdd:cd20606    160 SDMEEEERGDLIQFYNNIYIEQIKEFALKY 189
RB_A pfam01858
Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
 286-478 1.49e-99

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


Pssm-ID: 460364  Cd Length: 195  Bit Score: 311.05  E-value: 1.49e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  286 TPVSTATHSLSRLHTMLTGLRNAPSEKLEQILRTCSRDPTQAIANRLKEMFEIYSQHF-QPDEDFSNCAKEIASKHFRFA 364
Cdd:pfam01858    1 TPVSSAMQTVSWLQTLLSGLSDEPSEKLLRIFKSCSRDPTETILKRVKELGEIFCQKYtEASGEHPSFCIEIAEQRFRLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  365 EMLYYKVLESVIEQEQKRLGDMDLSGILEQDAFHRSLLACCLEVVTFSYKPPG-NFPFITEIFEVPLYHFYKVIEVFIRA 443
Cdd:pfam01858   81 EKLYYKVLESILKSEKKRLPGNDLSSLLSNDIFHRSLLACCLEIVLFAYNSERlSFPWILEVFGLPPFDFYKVIESFIRA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1297636736  444 EDGLCREVVKHLNQIEEQILDHLAWKPESPLWEKI 478
Cdd:pfam01858  161 EDGLPRELVKHLNSIEEQILESLAWKSDSPLWELL 195
RB_B pfam01857
Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a ...
 704-887 3.51e-73

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: 237.46  E-value: 3.51e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  704 SLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:pfam01857    1 SLNLFFRKVYHLAAVRLQDLCSRLDLSSDLREKIWTCFEHSLVHQTDLMKDRHLDQILLCAIYVICKVTKEELTFKEIMK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  784 CYRTQPQARSQVYRSVLIKGKRKRRNSGSSdsrshqnsptelnkdrtsrdsspvmrssstlpvpqpssapptptrltgan 863
Cdd:pfam01857   81 CYRKQPQASSHVYRSVLIRRRERERNGKNN-------------------------------------------------- 110

                          170       180
                   ....*....|....*....|....
gi 1297636736  864 sdmEEEERGDLIQFYNNIYIKQIK 887
Cdd:pfam01857  111 ---EEEERGDIIKFYNKVFVPAMK 131
DUF3452 pfam11934
Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. ...
 1-108 2.16e-43

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: 153.90  E-value: 2.16e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736    1 MKKWEDMANLPPHFRERTERLERNFTVSAVIFKKYEPIFQDIFKYPQEEQPRQQRGRKQRrqPCTVSEIFHFCWVLFIYA 80
Cdd:pfam11934   29 MKQWADMANLDWEFRLEIKELERNFSVTTVLFKKYKRIFNELFLSPPPKEPKRSKKSRPA--PCSYSDLFEFGWLLFLAA 106

                           90       100
                   ....*....|....*....|....*...
gi 1297636736   81 KGNFPMISDDLVNSYHLLLCALDLVYGN 108
Cdd:pfam11934  107 KNEFPSISKDLVTSYHLLLCCLDLVYVN 134
SP1-4_arthropods_N cd22553
N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; ...
 539-679 1.18e-06

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: 51.95  E-value: 1.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  539 YSSPPASTT-----RRRLFVEndSPSDGGTPGRMPPQPLVNA-----VPVQNVSGEPVSVTPVPGQTLVTMATATVTAN- 607
Cdd:cd22553     67 YSVSPAVQTvtvdgHEAIFIP--ANSGLLQTNNQQAIQLAPGgtqaiLANQQTLIRPNTVQGQANASNVLQNIAQIASGg 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  608 -------NGQTVTIPVQ-GIANENGGITF----FPVQV----NVGGQAQAVTGSIQPLSAQAlaGSLSSQQMAgttlQVP 671
Cdd:cd22553    145 navqlplNNMTQTIPVQvPVSTANGQTVYqtiqVPIQAiqsgNAGGGNQALQAQVIPQLAQA--AQLQPQQLA----QVS 218


                   ....*...
gi 1297636736  672 GQVAIQQI 679
Cdd:cd22553    219 SQGYIQQI 226
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 718-801 9.18e-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: 41.81  E-value: 9.18e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736   718 VRLRDLCAKLDISDELRKKIWTCFEFSIIQCPelMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMRCYRTQPqaRSQVYR 797
Cdd:smart00385    1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYK--FLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT--EEEILR 76


                    ....
gi 1297636736   798 SVLI 801
Cdd:smart00385   77 MERL 80
 
Name Accession Description Interval E-value
CYCLIN_RBL2 cd20606
cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also ...
 704-893 3.68e-134

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: 401.58  E-value: 3.68e-134
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  704 SLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:cd20606      1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  784 CYRTQPQARSQVYRSVLIKGKRKRRNSGSSDSRSHQNsPTELNKDRTSRDSSPVMRSSSTLPVPQPSSAPPTPTRLTGAN 863
Cdd:cd20606     81 CYRTQPQASSSVYRSVLIKGRRRRRSGSSDDSGSQSS-SSEENRERTSRDSSPVMRSSSTLPVPQPNSAPPTPTRLTGAN 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 1297636736  864 SDMEEEERGDLIQFYNNIYIKQIKTFAMKY 893
Cdd:cd20606    160 SDMEEEERGDLIQFYNNIYIEQIKEFALKY 189
RB_A pfam01858
Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
 286-478 1.49e-99

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


Pssm-ID: 460364  Cd Length: 195  Bit Score: 311.05  E-value: 1.49e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  286 TPVSTATHSLSRLHTMLTGLRNAPSEKLEQILRTCSRDPTQAIANRLKEMFEIYSQHF-QPDEDFSNCAKEIASKHFRFA 364
Cdd:pfam01858    1 TPVSSAMQTVSWLQTLLSGLSDEPSEKLLRIFKSCSRDPTETILKRVKELGEIFCQKYtEASGEHPSFCIEIAEQRFRLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  365 EMLYYKVLESVIEQEQKRLGDMDLSGILEQDAFHRSLLACCLEVVTFSYKPPG-NFPFITEIFEVPLYHFYKVIEVFIRA 443
Cdd:pfam01858   81 EKLYYKVLESILKSEKKRLPGNDLSSLLSNDIFHRSLLACCLEIVLFAYNSERlSFPWILEVFGLPPFDFYKVIESFIRA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1297636736  444 EDGLCREVVKHLNQIEEQILDHLAWKPESPLWEKI 478
Cdd:pfam01858  161 EDGLPRELVKHLNSIEEQILESLAWKSDSPLWELL 195
RB_B pfam01857
Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a ...
 704-887 3.51e-73

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: 237.46  E-value: 3.51e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  704 SLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:pfam01857    1 SLNLFFRKVYHLAAVRLQDLCSRLDLSSDLREKIWTCFEHSLVHQTDLMKDRHLDQILLCAIYVICKVTKEELTFKEIMK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  784 CYRTQPQARSQVYRSVLIKGKRKRRNSGSSdsrshqnsptelnkdrtsrdsspvmrssstlpvpqpssapptptrltgan 863
Cdd:pfam01857   81 CYRKQPQASSHVYRSVLIRRRERERNGKNN-------------------------------------------------- 110

                          170       180
                   ....*....|....*....|....
gi 1297636736  864 sdmEEEERGDLIQFYNNIYIKQIK 887
Cdd:pfam01857  111 ---EEEERGDIIKFYNKVFVPAMK 131
CYCLIN_RBL1 cd20605
cyclin box found in retinoblastoma-like protein 1 (RBL1) and similar proteins; RBL1, also ...
 698-893 1.70e-66

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: 218.99  E-value: 1.70e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  698 RPRKTSSLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKS 777
Cdd:cd20605      1 KPKKTGSLALFYRKVYHLASVRLRDLCLKLDVSNELRRKIWTCFEFSLVHCTDLMKDRHLDQLLLCAFYIMAKVTKEERT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  778 FQNIMRCYRTQPQARSQVYRSVLIKgkrkrrnsgssdsrshqnsptelnkdrtsrdsspvmrssstlpvpqpssapptpt 857
Cdd:cd20605     81 FQDIMKCYRNQPQANSHVYRSVLLK------------------------------------------------------- 105

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1297636736  858 rltgansdmeeEERGDLIQFYNNIYIKQIKTFAMKY 893
Cdd:cd20605    106 -----------EERGDLIKFYNTIYVGRVKSFALKY 130
CYCLIN_RBL cd20600
cyclin box found in retinoblastoma-like protein (RBL) subfamily; The RBL subfamily includes ...
 704-893 2.86e-66

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: 217.66  E-value: 2.86e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  704 SLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:cd20600      1 SLGLFFRKVYHLASVRLRDLCEKLEISEELRRKIWTCFEHSLVHHIELMRDRHLDQLLMCAVYVIAKVTKQDKSFQEIMK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  784 CYRTQPQARSqvyrsvlikgkrkrrnsgssdsrshqnsptelnkdrtsrdsspvmrssstlpvpqpssapptptrltgan 863
Cdd:cd20600     81 CYRLQPQAQS---------------------------------------------------------------------- 90

                          170       180       190
                   ....*....|....*....|....*....|
gi 1297636736  864 sdmeeeerGDLIQFYNNIYIKQIKTFAMKY 893
Cdd:cd20600     91 --------GDLIQFYNSVYVKKMKEFALKF 112
DUF3452 pfam11934
Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. ...
 1-108 2.16e-43

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: 153.90  E-value: 2.16e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736    1 MKKWEDMANLPPHFRERTERLERNFTVSAVIFKKYEPIFQDIFKYPQEEQPRQQRGRKQRrqPCTVSEIFHFCWVLFIYA 80
Cdd:pfam11934   29 MKQWADMANLDWEFRLEIKELERNFSVTTVLFKKYKRIFNELFLSPPPKEPKRSKKSRPA--PCSYSDLFEFGWLLFLAA 106

                           90       100
                   ....*....|....*....|....*...
gi 1297636736   81 KGNFPMISDDLVNSYHLLLCALDLVYGN 108
Cdd:pfam11934  107 KNEFPSISKDLVTSYHLLLCCLDLVYVN 134
CYCLIN_RB-like cd20548
cyclin box found in retinoblastoma-associated protein (RB) family; The RB family includes ...
 705-882 4.86e-37

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: 135.13  E-value: 4.86e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  705 LSLFFRKVYHLAAVRLRDLCAKLD-ISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:cd20548      1 LQLFFRKLYRLAAARLQDLCKRLDlLSPPLRERIWTVFKHILSEETELLFDRHLDQIILCSIYAVCKVNNENLTFKEILD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  784 CYRTQPQARSQVYRSVLIkgkrKRRNSGSSDsrshqnsptelnkdrtsrdsspvmrssstlpvpqpssapptptrltgan 863
Cdd:cd20548     81 AYRKQPQAESEVYRSVLP----LFRSVGSDD------------------------------------------------- 107

                          170
                   ....*....|....*....
gi 1297636736  864 sdmeEEERGDLIQFYNNIY 882
Cdd:cd20548    108 ----EGESGDIIKFYNQVF 122
CYCLIN_RB cd20599
cyclin box found in retinoblastoma-associated protein (RB) and similar proteins; RB, also ...
 704-806 1.56e-36

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: 133.95  E-value: 1.56e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  704 SLSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 783
Cdd:cd20599      2 SLSLFYKKVYRLAYLRLNTLCDLLLLHPDLEHRIWTCFEHCLQNRYELLKDRHLDQIMMCSMYGICKVKNKDLRFKTIVT 81

                           90       100
                   ....*....|....*....|...
gi 1297636736  784 CYRTQPQARSQVYRSVLIKGKRK 806
Cdd:cd20599     82 AYKDLPHASQEVYKRVLIRGEEY 104
CYCLIN_AtRBR_like cd20601
cyclin box found in Arabidopsis thaliana retinoblastoma-related protein 1 (AtRBR1) and similar ...
 705-891 5.18e-26

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: 104.01  E-value: 5.18e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  705 LSLFFRKVYHLAAVRLRDLCAKLDISDELRKKIWTCFEFSIIQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMRC 784
Cdd:cd20601      1 INVFFQKVLKLAAIRIADLCERLQQPQLVVEQVYRLIEHVLYEQTGLFFNRHIDQIILCCLYGVCKVHKLNVTFREIIYQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  785 YRTQPQARSQVYRSVLIKGKRKRrnsgssdsrshqnsptelnkdrtsrdsspvmrssstlpvpqpssapptptrltgans 864
Cdd:cd20601     81 YRKQPQCKPDVFRNVVIEQRRPT--------------------------------------------------------- 103

                          170       180
                   ....*....|....*....|....*..
gi 1297636736  865 dMEEEERGDLIQFYNNIYIKQIKTFAM 891
Cdd:cd20601    104 -LGGPDHGDIIAFYNEVFVPATKPFLL 129
SP1-4_arthropods_N cd22553
N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; ...
 539-679 1.18e-06

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: 51.95  E-value: 1.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  539 YSSPPASTT-----RRRLFVEndSPSDGGTPGRMPPQPLVNA-----VPVQNVSGEPVSVTPVPGQTLVTMATATVTAN- 607
Cdd:cd22553     67 YSVSPAVQTvtvdgHEAIFIP--ANSGLLQTNNQQAIQLAPGgtqaiLANQQTLIRPNTVQGQANASNVLQNIAQIASGg 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736  608 -------NGQTVTIPVQ-GIANENGGITF----FPVQV----NVGGQAQAVTGSIQPLSAQAlaGSLSSQQMAgttlQVP 671
Cdd:cd22553    145 navqlplNNMTQTIPVQvPVSTANGQTVYqtiqVPIQAiqsgNAGGGNQALQAQVIPQLAQA--AQLQPQQLA----QVS 218


                   ....*...
gi 1297636736  672 GQVAIQQI 679
Cdd:cd22553    219 SQGYIQQI 226
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 718-801 9.18e-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: 41.81  E-value: 9.18e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1297636736   718 VRLRDLCAKLDISDELRKKIWTCFEFSIIQCPelMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMRCYRTQPqaRSQVYR 797
Cdd:smart00385    1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYK--FLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFT--EEEILR 76


                    ....
gi 1297636736   798 SVLI 801
Cdd:smart00385   77 MERL 80
 
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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