PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 283 YPCSPNHELVWARMKGFGYWPAKVMQREGNQVDVRFFGHQHQRAWIPSDNIQDITVSVQQLQVKRSSGWKKACDELELHQ 362
Cdd:cd20159     1 KPCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGGHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQ 80

                  ....*
gi 1207165765 363 RFVRE 367
Cdd:cd20159    81 ELLEE 85

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1207165765 110 YCFECHLPGDVMECDGCFRVYHLRCVSEDHRPrDTTSHWQCGIC 153
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDCLSEDFRP-DSTSHWTCPVC 43

recombination and DNA strand exchange inhibitor protein; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 509 MKAENK-RETERVLKEAlDKLRGEMEEEK--------------RQAVNKAVSSTQAEMERKCKQVKEKC-------KEEL 566
Cdd:PRK00409  530 RELEQKaEEAEALLKEA-EKLKEELEEKKeklqeeedklleeaEKEAQQAIKEAKKEADEIIKELRQLQkggyasvKAHE 608

                          90       100
                  ....*....|....*....|..
gi 1207165765 567 MEEMKKMVSQHKQLLSQTKKKQ 588
Cdd:PRK00409  609 LIEARKRLNKANEKKEKKKKKQ 630

PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 283 YPCSPNHELVWARMKGFGYWPAKVMQREGNQVDVRFFGHQHQRAWIPSDNIQDITVSVQQLQVKRSSGWKKACDELELHQ 362
Cdd:cd20159     1 KPCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGGHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQ 80

                  ....*
gi 1207165765 363 RFVRE 367
Cdd:cd20159    81 ELLEE 85

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1207165765 110 YCFECHLPGDVMECDGCFRVYHLRCVSEDHRPrDTTSHWQCGIC 153
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDCLSEDFRP-DSTSHWTCPVC 43

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207165765  287 PNHELVWARMKGFGYWPAKVMQRE------------GNQVDVRFFGHQHQrAWIPSDNIQDIT 337
Cdd:smart00293   2 KPGDLVWAKMKGFPWWPALVISPKmtpdnimkrksdENLYPVLFFGDKDT-AWIPSSKLFPLT 63

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 290 ELVWARMKGFGYWPAKVMQRE------------GNQVDVRFFGHQHqRAWIPSDNIQDITVSVQQLQVKRSSG------W 351
Cdd:pfam00855   2 DLVWAKLKGYPWWPARVVDPEelpenvlkpkkkDGEYLVRFFGDSE-FAWVKPKDLKPFDEGDEFEYLKKKKKkkkkkaF 80

                          90
                  ....*....|
gi 1207165765 352 KKACDELELH 361
Cdd:pfam00855  81 KKALEEAEEA 90

MYND finger;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1207165765 590 CYNCEEEA--MYHC--CWNTSYCSIKCQQEHWhADHKRTC 625
Cdd:pfam01753   1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADW-PYHKKEC 39

recombination and DNA strand exchange inhibitor protein; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 509 MKAENK-RETERVLKEAlDKLRGEMEEEK--------------RQAVNKAVSSTQAEMERKCKQVKEKC-------KEEL 566
Cdd:PRK00409  530 RELEQKaEEAEALLKEA-EKLKEELEEKKeklqeeedklleeaEKEAQQAIKEAKKEADEIIKELRQLQkggyasvKAHE 608

                          90       100
                  ....*....|....*....|..
gi 1207165765 567 MEEMKKMVSQHKQLLSQTKKKQ 588
Cdd:PRK00409  609 LIEARKRLNKANEKKEKKKKKQ 630

PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 283 YPCSPNHELVWARMKGFGYWPAKVMQREGNQVDVRFFGHQHQRAWIPSDNIQDITVSVQQLQVKRSSGWKKACDELELHQ 362
Cdd:cd20159     1 KPCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGGHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQ 80

                  ....*
gi 1207165765 363 RFVRE 367
Cdd:cd20159    81 ELLEE 85

PWWP domain found in protein BS69, protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. BS69 is a multi-domain protein, containing bromo, plant homeodomain (PHD), proline-tryptophan-tryptophan-proline (PWWP), and MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a PHD finger, a bromodomain, and a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 283 YPCSPNHELVWARMKGFGYWPAKVMQREGNQVDVRFFGhQHQRAWIPSDNIQDIT-----VSVQQLQVKRSSGWKKACDE 357
Cdd:cd05841     1 KPCPVVHPLVWVKLDGFPFWPAKVMGTKDGQVDVRFFG-DYDRAWLPSKNVTLHTreivsTLPDSSESKDKRTLKKAIKE 79

                          90
                  ....*....|
gi 1207165765 358 LELHQRFVRE 367
Cdd:cd05841    80 LERHIALLRQ 89

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1207165765 110 YCFECHLPGDVMECDGCFRVYHLRCVSEDHRPrDTTSHWQCGIC 153
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDCLSEDFRP-DSTSHWTCPVC 43

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207165765  287 PNHELVWARMKGFGYWPAKVMQRE------------GNQVDVRFFGHQHQrAWIPSDNIQDIT 337
Cdd:smart00293   2 KPGDLVWAKMKGFPWWPALVISPKmtpdnimkrksdENLYPVLFFGDKDT-AWIPSSKLFPLT 63

PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 290 ELVWARMKGFGYWPAKVMQ---------REGNQVDVRFFG-HQHqrAWIPSDNIQDITVSVQQ-LQVKRSSGWKKACDEL 358
Cdd:cd05836     5 DLVWAKMKGFPPWPGKIVNpppdlkkppRKKKMHCVYFFGsENY--AWIEDENIKPYEEFKEEmLKSKKSAGFKDAVEAI 82

                  ...
gi 1207165765 359 ELH 361
Cdd:cd05836    83 EEY 85

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 1207165765 163 KQEMTTYLKFILGRMKERAVDLHKRGKEAKQPIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHNTAILHGVN 242
Cdd:cd04369     2 KKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPG 81

                          90
                  ....*....|....*...
gi 1207165765 243 SDQTEIARLLYNDTCHEL 260
Cdd:cd04369    82 SPIYKDAKKLEKLFEKLL 99

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. 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 1207165765 170 LKFILG------RMKERAVDLHKRGKEAKQPIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHNTAILHGVNS 243
Cdd:cd05511     1 LSFILDeivnelKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80

                  ....*..
gi 1207165765 244 DQTEIAR 250
Cdd:cd05511    81 VYTKKAK 87

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. 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
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1207165765 194 PIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHNTAILhgvNSDQTEIAR 250
Cdd:cd05503    31 PGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETF---NEDDSEVGR 84

PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called G/T mismatch-binding protein (GTBP or GTMBP), MutS protein homolog 6, or MutS-alpha 160 kDa subunit (p160), is a mismatch repair protein homologous to bacterial MutS. It is a component of the post-replicative DNA mismatch repair system (MMR). It heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, it forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. MSH6 contains a PWWP domain, but its role in MSH6 remains unclear. MSH6 orthologs found in Saccharomyces cerevisiae, Caenorhabditis elegans, and Arabidopsis thaliana lack the PWWP domain. PWWP domains typically recognize DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 290 ELVWARMKGFGYWPA----------KVMQREGNQVDVRFFGHQHQRAWIPSDNIQ----DITVSVQQLQVKRSS--GWKK 353
Cdd:cd05837     5 DLVWAKLEGYPWWPSlvcnhpttgfHKKFGKKGEVHVQFFDDPPSRAWVKAKNVKpftgSDDKEFQKGGMFFSKdpKWKK 84

                  ....
gi 1207165765 354 ACDE 357
Cdd:cd05837    85 AVKE 88

PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The HRP family includes hepatoma-derived growth factor (HDGF), and HDGF-related proteins (HRPs). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It is a prognostic factor in several types of cancer. HDGFL1 is also called PWWP domain-containing protein 1 (PWWP1). Its biological function remains unclear. HDGFL2, also called HDGF-related protein 2 (HRP-2), or hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. HDGFL3, also called HDGF-related protein 3 (HRP-3), enhances DNA synthesis and may play a role in cell proliferation. The family also includes PC4 and SFRS1-interacting protein (PSIP) and similar proteins. PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Members of the HRP family contains a PWWP domain, which is necessary for DNA binding.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1207165765 290 ELVWARMKGFGYWPAKVMQRE------GNQVDVRFFGhQHQRAWIPSDNI 333
Cdd:cd05834     5 DLVFAKVKGYPPWPARIDEIPegakipKNKYPVFFYG-THETAFLKPKDL 53

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. 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
                  ....*....|....*....|....*....|....*....|.
gi 1207165765 194 PIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHN 234
Cdd:cd05499    36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKN 76

PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ZCWPW2 is a histone H3K4me3 reader. In addition to the PWWP domain, ZCWPW2 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1207165765 290 ELVWARMKGFGYWPA-------------KVMQREGNQVDVRFFGHQHQRAWIPSDNI 333
Cdd:cd20146    13 SLVWAKMTGYPRWPAiltpdpicgeyvdYDEDGEVEKYHVEFLGKPHSHAWISAKSV 69

MYND finger;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1207165765 590 CYNCEEEA--MYHC--CWNTSYCSIKCQQEHWhADHKRTC 625
Cdd:pfam01753   1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADW-PYHKKEC 39

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1207165765 110 YCFECHLPGD----VMECDGCFRVYHLRCVSEDHRPRDTTSHWQCGIC 153
Cdd:cd15489     1 SCIVCGKGGDlggeLLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 157 KRKNLNKQEMTTYLK-FILGRMKERAVDLHKRG---------KEAKQPIYKRLIHTPLDVENIQENISDGKYKSFEEFRA 226
Cdd:COG5076   132 KRKTPKIEDELLYADnKAIAKFKKQLFLRDGRFlssiflglpSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVS 211

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1207165765 227 DAQLIVHNTAILHGVNSDQTEIARLLYNDTCHELNELMLC 266
Cdd:COG5076   212 DLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEE 251

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. 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
                  ....*....|....*....|....*....|....*....|.
gi 1207165765 194 PIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHN 234
Cdd:cd05509    32 PDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDN 72

PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 290 ELVWARMKGFGYWPAKVMQRE--GNQVD-----VRFFGHQhQRAWIPSDNIQDITVSVQQ------LQVKRSSGWKKACD 356
Cdd:cd20147     2 DLVLAKVKGFPAWPAQVSEPEdwGSAPDpkkvfVHFFGTQ-QIGFCNPGELSEFTEEIKQsllartLKKKKGSDFSRAVK 80

                  ...
gi 1207165765 357 ELE 359
Cdd:cd20147    81 EIC 83

PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins; ZCWPW1 is a histone H3K4me3 reader. It is associated with late-onset Alzheimer's disease (LOAD). In addition to the PWWP domain, ZCWPW1 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1207165765 291 LVWARMKGFGYWPAKV-----------MQREGNQVD---VRFFGHQHQRAWIPSDNIQ 334
Cdd:cd20145    11 LVWAKMPGYPWWPAMVeddpdteeffwLDEESDIPTkyhVTFFDKPVSRAWVRASSIK 68

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like proteins ATX1, ATX2, and similar proteins; This family includes A. thaliana ATX1 and ATX2, which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also called protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also called protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1207165765 290 ELVWARMKGFGYWPAKVMQRE--------------GNQVDVRFFG-HQHQR 325
Cdd:cd20142     4 DVVWAKVKGYPMWPALVIDEEhaercgleanrpgkKGTVPVQFFGtYEVAR 54

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. 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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1207165765 192 KQPIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHNTAILHGVNSD 244
Cdd:cd05525    37 KNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSP 89

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. 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. SP140 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 viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1207165765 110 YCFECHLPGDVMECDGCFRVYHLRCvsedHRP---RDTTSHWQCGIC 153
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDC----HIPpipEFPSGEWSCSLC 43

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. 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 1207165765 190 EAKQPIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHNTAILHGVNSDQTEIARLLYNDTCHELNELM 264
Cdd:cd05507    30 EDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQREVMSQIQQLL 104

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. 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
                  ....*....|....*....|....*....|....*....|.
gi 1207165765 194 PIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHN 234
Cdd:cd05512    32 PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINN 72

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. 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
                  ....*....|....*....|....*....|....*....|.
gi 1207165765 194 PIYKRLIHTPLDVENIQENISDGKYKSFEEFRADAQLIVHN 234
Cdd:cd05519    37 PDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFAN 77

recombination and DNA strand exchange inhibitor protein; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207165765 509 MKAENK-RETERVLKEAlDKLRGEMEEEK--------------RQAVNKAVSSTQAEMERKCKQVKEKC-------KEEL 566
Cdd:PRK00409  530 RELEQKaEEAEALLKEA-EKLKEELEEKKeklqeeedklleeaEKEAQQAIKEAKKEADEIIKELRQLQkggyasvKAHE 608

                          90       100
                  ....*....|....*....|..
gi 1207165765 567 MEEMKKMVSQHKQLLSQTKKKQ 588
Cdd:PRK00409  609 LIEARKRLNKANEKKEKKKKKQ 630

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1207165765 110 YCFECHLP-----GDVMECDG-CFRVYHLRCV-----SEDHRPRDTTshWQCGIC 153
Cdd:cd15504     1 FCAKCQSGeaspdNDILLCDGgCNRAYHQKCLeppllTEDIPPEDEG--WLCPLC 53

first PWWP domain found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2, also called histone-lysine N-methyltransferase NSD2, multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, through mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc finger motifs, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD domains mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1207165765 290 ELVWARMKGFGYWPAKV--------------MQREGNQVDVRFFGHQHQRAWI 328
Cdd:cd20162     5 DLVWSKVSGYPWWPCMVsadpllhshtklkgQKKSARQYHVQFFGDAPERAWI 57

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1207165765 110 YCFECHLPGDVMECDGCFRVYHLRCVSEDHRpRDTTSHWQCGIC 153
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELE-KAPEGKWSCPHC 43