Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1730154169 527 PEEQLKCELLLLTIYCYPKSGFFIPKPKQRKEKFPDLREHMWLNKIKNRLNKKAYHSVRRFVEDMRLIFHNHSIFYKK-R 605
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDdD 80

                          90       100
                  ....*....|....*....|..
gi 1730154169 606 FKNLGIIVGKKFEKNFKRIFSI 627
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1730154169 357 DFGGAELPVVCGNAQGFLDKEKFKQGIYVRSIRGKtGRLFTPMDFEIEGNCEKAKNWRQSIRCKGWTLRELIQKGVL 433
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNE-DSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1730154169 527 PEEQLKCELLLLTIYCYPKSGFFIPKPKQRKEKFPDLREHMWLNKIKNRLNKKAYHSVRRFVEDMRLIFHNHSIFYKK-R 605
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDdD 80

                          90       100
                  ....*....|....*....|..
gi 1730154169 606 FKNLGIIVGKKFEKNFKRIFSI 627
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1730154169 357 DFGGAELPVVCGNAQGFLDKEKFKQGIYVRSIRGKtGRLFTPMDFEIEGNCEKAKNWRQSIRCKGWTLRELIQKGVL 433
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNE-DSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1730154169 459 ACKVCGQPRKVHPCTACKEFYHKNCHIPPVEDKSRSWHCAFC 500
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1730154169 548 FFIPKPKQRKEKFPDLREH-MWLNKIKNRLNKKAYHSVRRFVEDMRLIFHNHSIFYKKRF 606
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKKpMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGS 76

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1730154169 527 PEEQLKCELLLLTIYCYPKSGFFIPKPKQRKEKFPDLREHMWLNKIKNRLNKKAYHSVRRFVEDMRLIFHNHSIFYKK-R 605
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDdD 80

                          90       100
                  ....*....|....*....|..
gi 1730154169 606 FKNLGIIVGKKFEKNFKRIFSI 627
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1730154169 357 DFGGAELPVVCGNAQGFLDKEKFKQGIYVRSIRGKtGRLFTPMDFEIEGNCEKAKNWRQSIRCKGWTLRELIQKGVL 433
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNE-DSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1730154169 459 ACKVCGQPRKVHPCTACKEFYHKNCHIPPVEDKSRSWHCAFC 500
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1730154169 529 EQLKCELLLLTIYCY--PKSGFFIPKPKqrKEKFPD----LREHMWLNKIKNRLNKKAYHSVRRFVEDMRLIFHNHSIFY 602
Cdd:cd04369     1 LKKKLRSLLDALKKLkrDLSEPFLEPVD--PKEAPDyyevIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYN 78

                          90       100
                  ....*....|....*....|...
gi 1730154169 603 KKrfKNLGIIVGKKFEKNFKRIF 625
Cdd:cd04369    79 GP--GSPIYKDAKKLEKLFEKLL 99

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1730154169 548 FFIPKPKQRKEKFPDLREH-MWLNKIKNRLNKKAYHSVRRFVEDMRLIFHNHSIFYKKRF 606
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKKpMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGS 76

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1730154169 460 CKVCGQPRKVHPCTACKEFYHKNCHIPPVED-KSRSWHCAFC 500
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEvPGEDWKCLLC 43

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1730154169 459 ACKVCGQP------RKVHpCTACKEFYHKNCHIPPVEDKSRS-----WHCAFC 500
Cdd:cd15501     1 SCVVCKQMdvtsgnQLVE-CQECHNLYHQECHKPPVTDKDVNdprlvWYCSRC 52

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1730154169 460 CKVCGQPRKVH---PCTACKEFYHKNCHIPPVE---DKSRS--WHCAFC 500
Cdd:cd15562     2 CGICKKSNDQHllaLCDTCKLYYHLGCLDPPLTrmpKKTKNsgWQCSEC 50

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1730154169 459 ACKVC---GQPRKVHPCTACKEFYHKNCHIPPV-EDKSRSWHCAFC 500
Cdd:cd15527     1 TCSVCqdsGNADNLLFCDACDKGFHMECHDPPLtRMPKGKWVCQIC 46

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1730154169 529 EQLKCELLLLTIYCYPKSG-FFIPKPKQRKEKFPDLREH-MWLNKIKNRLNKKAYHSVRRFVEDMRLIFHNHSIFY 602
Cdd:cd05505     1 ELQKCEEILSKILKYRFSWpFREPVTADEAEDYKKVITNpMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1730154169 460 CKVCGQPRKVHP-----CTACKEFYHKNCHIPPVEDKSRS----WHCAFC 500
Cdd:cd15578     2 CTVCQDGSSESPneivlCDKCGQGYHQLCHNPKIDSSVLDpdvpWLCRQC 51

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1730154169 460 CKVCGQP---RKVHPCTACKEFYHKNCHIPPVED-KSRSWHCAFC 500
Cdd:cd15595     2 CQTCRKPgedSKMLVCEACDKGYHTFCLKPAMESlPTDSWKCKAC 46