Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  422 RRISLSDMPRSPMSTNSSVHTGSDVEQD-AEK---KATSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 497
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDtAEKgqaKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  498 lsAPITTKTDKTSTTGSILNLNLDRSKAEMDLKELSESVQQ-QSTPVPLISPKRQIRSRFQLNLDKTIESCKAQLGINEI 576
Cdd:pfam12064   74 --APGTPKQEKTPTTGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGIDEI 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1392111426  577 SEDVYTAVEHSDSEDSEKSDSSDSEYISDDEQKSKNEPEDTEDK 620
Cdd:pfam12064  152 SVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar 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 plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  272 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 351
Cdd:cd20160      1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                           90
                   ....*....|.
gi 1392111426  352 NIRRKFGVFNY 362
Cdd:cd20160     81 KLREKFGKFNY 91

MYND finger;

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1392111426 1028 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 1062
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1392111426  957 IAEIRRLRIEIEKLQWLHQQELSEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 1024
Cdd:COG0711     40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118

Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  891 QSSPLVTSSGSMSTLVSSVNADLP-----------------IATASADVAADIAKYTSKMMDA--IKGTMTEIYNDLSK- 950
Cdd:COG4192     49 DSLPKLQASLKLEENSNELVAALPefaaatnttersqlrnqLNTQLADIEELLAELEQLTQDAgdLRAAVADLRNLLQQl 128

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1392111426  951 -NTTGSTIAEIRRLRIEIEKLQWLHQQELSEMKhnleltmaEMRQSLEQERDRLIAEVKKQLELEKQQA 1018
Cdd:COG4192    129 dSLLTQRIALRRRLQELLEQINWLHQDFNSELT--------PLLQEASWQQTRLLDSVETTESLRNLQN 189

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  422 RRISLSDMPRSPMSTNSSVHTGSDVEQD-AEK---KATSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 497
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDtAEKgqaKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  498 lsAPITTKTDKTSTTGSILNLNLDRSKAEMDLKELSESVQQ-QSTPVPLISPKRQIRSRFQLNLDKTIESCKAQLGINEI 576
Cdd:pfam12064   74 --APGTPKQEKTPTTGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGIDEI 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1392111426  577 SEDVYTAVEHSDSEDSEKSDSSDSEYISDDEQKSKNEPEDTEDK 620
Cdd:pfam12064  152 SVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar 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 plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  272 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 351
Cdd:cd20160      1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                           90
                   ....*....|.
gi 1392111426  352 NIRRKFGVFNY 362
Cdd:cd20160     81 KLREKFGKFNY 91

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426   152 EQLSYLLKFAI-QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 230
Cdd:smart00297    6 KKLQELLKAVLdKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGP 85

                            90       100
                    ....*....|....*....|..
gi 1392111426   231 NHKLTQIAKVVIKICEHEMNEI 252
Cdd:smart00297   86 DSEVYKDAKKLEKFFEKKLREL 107

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1392111426    90 YCWVCHR---EGQVLCCELCPRVYHAKCLRLT---SEPEGDWFCPEC 130
Cdd:smart00249    1 YCSVCGKpddGGELLQCDGCDRWYHQTCLGPPlleEEPDGKWYCPKC 47

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 1392111426  280 LVWAKLKGFPFWPAK---------ALRDKDGQVDA---RFFGQHDRAWVPINNCYLMSKEIPFSV------KKTKSIFNS 341
Cdd:pfam00855    3 LVWAKLKGYPWWPARvvdpeelpeNVLKPKKKDGEylvRFFGDSEFAWVKPKDLKPFDEGDEFEYlkkkkkKKKKKAFKK 82

                           90
                   ....*....|
gi 1392111426  342 AMQEMEVYVE 351
Cdd:pfam00855   83 ALEEAEEALK 92

MYND finger;

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1392111426 1028 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 1062
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426    4 STRSKDPGSAER-TAQKRKFPSPPHSSNGHSPQdTSTSPikkkkkpgLLNSNNKEQSELRhgpfyyMKQPLTTDPVDVVP 82
Cdd:COG5034    151 SQGSRHTKLKKRkNIHNLKRRSPELSSKREVSF-TLESP--------SVPDTATRVKEGN------NGGSTKSRGVSSED 215

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1392111426   83 QDGRNDFYCWvCHRE--GQVLCC--ELCPRV-YHAKCLRLTSEPEGDWFCPECEKI 133
Cdd:COG5034    216 NSEGEELYCF-CQQVsyGQMVACdnANCKREwFHLECVGLKEPPKGKWYCPECKKA 270

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  955 STIAEIRRLRIEIEKLQWLHQQEL-----------SEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETK 1023
Cdd:cd06503     37 ESLEEAEKAKEEAEELLAEYEEKLaearaeaqeiiEEARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELR 116

                   .
gi 1392111426 1024 K 1024
Cdd:cd06503    117 K 117

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  602 YISDDEQkSKNEPEDTEDkegcqmdkepsavKKKPKPTNPVEIkeelkstspasEKADPGAVKDKASPEPEKDFSEKAKP 681
Cdd:pfam05793  285 YISDSSA-SGNDPEERED-------------KLSPEEPAKGEI-----------EQSDDSEESEEEKNEEEGKLSKKGKK 339

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1392111426  682 SPHPiKDKLKGKDETDSptvhlglDSDSESELVIDLGEDHSGREGRKNKKEPKEPSPKQDVVGKTPPSttvGSHSPPET 760
Cdd:pfam05793  340 AKKL-KGKKNGKDKSES-------SDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPVDSGPSSPGNS---GPARPSPE 407

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  422 RRISLSDMPRSPMSTNSSVHTGSDVEQD-AEK---KATSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 497
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDtAEKgqaKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  498 lsAPITTKTDKTSTTGSILNLNLDRSKAEMDLKELSESVQQ-QSTPVPLISPKRQIRSRFQLNLDKTIESCKAQLGINEI 576
Cdd:pfam12064   74 --APGTPKQEKTPTTGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGIDEI 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1392111426  577 SEDVYTAVEHSDSEDSEKSDSSDSEYISDDEQKSKNEPEDTEDK 620
Cdd:pfam12064  152 SVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar 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 plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  272 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 351
Cdd:cd20160      1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                           90
                   ....*....|.
gi 1392111426  352 NIRRKFGVFNY 362
Cdd:cd20160     81 KLREKFGKFNY 91

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 1392111426  273 PCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFG-QHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 351
Cdd:cd20159      2 PCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGgHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQE 81

                   ....
gi 1392111426  352 NIRR 355
Cdd:cd20159     82 LLEE 85

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 1392111426  154 LSYLLKFAIQKMKQ-PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNH 232
Cdd:cd05511      1 LSFILDEIVNELKNlPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80

                           90       100
                   ....*....|....*....|.
gi 1392111426  233 KLTQIAKVVIKICEHEMNEIE 253
Cdd:cd05511     81 VYTKKAKEMLELAEELLAERE 101

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426   152 EQLSYLLKFAI-QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 230
Cdd:smart00297    6 KKLQELLKAVLdKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGP 85

                            90       100
                    ....*....|....*....|..
gi 1392111426   231 NHKLTQIAKVVIKICEHEMNEI 252
Cdd:smart00297   86 DSEVYKDAKKLEKFFEKKLREL 107

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        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1392111426  163 QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 239
Cdd:pfam00439    7 KLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83

Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. 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 1392111426  154 LSYLLKFAIQKMKQ--PGTDAFQKPVPLE-----QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCII 226
Cdd:cd05492      1 LNCLLKFIVSRMKSwlPPDTTNRAIVLNKrgkatKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAI 80

                           90       100
                   ....*....|....*....|....*....
gi 1392111426  227 YNGGNHKLTQIAKVVIKICEHEMNEIEVC 255
Cdd:cd05492     81 FHGADSEQYDAARWLYRDTCHDLRELRLC 109

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1392111426   90 YCWVCHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 130
Cdd:cd15567      1 WCFICSEGGSLICCESCPASFHPECLGLEPPPEGKFYCEDC 41

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  280 LVWAKLKGFPFWPAKALRDKDGQVDA-----------RFFGQHDRAWVPINNCYL----MSKEIPFSVKKTKSiFNSAMQ 344
Cdd:cd05162      3 LVWAKLKGYPWWPARVVDPEELPEEVgkkkkkggvlvQFFGDNDYAWVKSKNIKPfeegFKKEFKKKKKKSKK-FKKAVE 81

                   ....*
gi 1392111426  345 EMEVY 349
Cdd:cd05162     82 EAEEA 86

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 1392111426  280 LVWAKLKGFPFWPAKALR-DKDGQVDAR--------FFGQHDRAWVPINNC--YLMSKEIPFSVKKTKSiFNSAMQEMEV 348
Cdd:cd05836      6 LVWAKMKGFPPWPGKIVNpPPDLKKPPRkkkmhcvyFFGSENYAWIEDENIkpYEEFKEEMLKSKKSAG-FKDAVEAIEE 84

                   ..
gi 1392111426  349 YV 350
Cdd:cd05836     85 YI 86

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1392111426   90 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 130
Cdd:cd15559      1 HCRVCHKLGDLLCCETCSAVYHLECVDppLEEVPEEDWQCEVC 43

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). 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 1392111426  172 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG-NHKLTQIAKVVIKICEHEMN 250
Cdd:cd05510     28 PFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDpSHPLRRHANFMKKKAEHLLK 107

                   ..
gi 1392111426  251 EI 252
Cdd:cd05510    108 LI 109

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1392111426  172 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIkicEHEMNE 251
Cdd:cd05507     23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQ---REVMSQ 99

                   ...
gi 1392111426  252 IEV 254
Cdd:cd05507    100 IQQ 102

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 1392111426   90 YCWVCHREGQ----VLCCELCPRVYHAKCLRLTSE---PEGDWFCPEC 130
Cdd:cd15489      1 SCIVCGKGGDlggeLLQCDGCGKWFHADCLGPPLSsfvPNGKWICPVC 48

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        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1392111426  280 LVWAKLKGFPFWPAKALRDKDGQVDAR------FFGQHDRAWVPINNCYLMSKE-IPFSVKKTKSIFNSAMQEME 347
Cdd:cd05834      6 LVFAKVKGYPPWPARIDEIPEGAKIPKnkypvfFYGTHETAFLKPKDLFPYEENkEKYGKPRKRKGFNEGLWEIE 80

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1392111426   90 YCWVCHR---EGQVLCCELCPRVYHAKCLRLTSE----PEGDWFCPEC 130
Cdd:pfam00628    1 YCAVCGKsddGGELVQCDGCDDWFHLACLGPPLDpaeiPSGEWLCPEC 48

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1392111426   90 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 130
Cdd:cd15519      4 VCGLDDNEGEVLLCDGCDAEYHTSCLDppLGEIPPGTWFCPSC 46

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1392111426   90 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 130
Cdd:cd15523      1 FCSVCRKSGELLMCDTCSLVYHLDCLDppLKTIPKGMWICPKC 43

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 1392111426   90 YCWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 130
Cdd:cd15541      1 WCAVCQNGGELLCCDKCPRVFHLDCHipPIPEFPSGEWSCSLC 43

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. 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 1392111426  153 QLSYLLKFAIQKM-KQPGTDAFQKPVPLE--QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 229
Cdd:cd05497      5 QLQYLLKVVLKALwKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84

                           90
                   ....*....|....*
gi 1392111426  230 GNHKLTQIAKVVIKI 244
Cdd:cd05497     85 PGDDVVLMAQTLEKL 99

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. 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 1392111426  153 QLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYnggNH 232
Cdd:cd05504     13 NLSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLY---NP 89

                           90
                   ....*....|..
gi 1392111426  233 KLTQIAKVVIKI 244
Cdd:cd05504     90 EHTSVYKAGTRL 101

PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or 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, by 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 fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fourth PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1392111426   90 YCWVCHREGQVLCCELCPRVYHAKCLRLtSEPEGDWFCPEC 130
Cdd:cd15657      1 WCFVCSKGGSLLCCESCPAAFHPDCLNI-EMPDGSWFCNDC 40