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 568916822   277 RRISLSDMPRSPTSTNSSVHTGSDVEQDP----EKKAPSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 352
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDTaekgQAKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822   353 APTPimTKPDKTSTstTGSILNLNLDRSKAEMDLKELSESVQQ-QSAPVPLISPKRQIRSRFQLNLDKTIESCKAQLGIN 431
Cdd:pfam12064   74 APGT--PKQEKTPT--TGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGID 149

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 568916822   432 EISEDVYTAVEHSDSEDSEKSESSDSEYVSDEEQKPKNEPEDPEDK 477
Cdd:pfam12064  150 EISVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 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 568916822  127 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20160     1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                          90
                  ....*....|.
gi 568916822  207 NIRRKFGVFNY 217
Cdd:cd20160    81 KLREKFGKFNY 91

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 568916822  824 IAEIRRLRIEIEKLQWLHQQELAEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 891
Cdd:COG0711    40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118

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 568916822   277 RRISLSDMPRSPTSTNSSVHTGSDVEQDP----EKKAPSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 352
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDTaekgQAKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822   353 APTPimTKPDKTSTstTGSILNLNLDRSKAEMDLKELSESVQQ-QSAPVPLISPKRQIRSRFQLNLDKTIESCKAQLGIN 431
Cdd:pfam12064   74 APGT--PKQEKTPT--TGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGID 149

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 568916822   432 EISEDVYTAVEHSDSEDSEKSESSDSEYVSDEEQKPKNEPEDPEDK 477
Cdd:pfam12064  150 EISVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 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 568916822  127 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20160     1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                          90
                  ....*....|.
gi 568916822  207 NIRRKFGVFNY 217
Cdd:cd20160    81 KLREKFGKFNY 91

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 568916822    18 QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 94
Cdd:pfam00439    7 KLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83

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 568916822   135 LVWAKLKGFPFWPAK---------ALRDKDGQVDA---RFFGQHDRAWVPVNNCYLMSKEIPFSV------KKTKSIFNS 196
Cdd:pfam00855    3 LVWAKLKGYPWWPARvvdpeelpeNVLKPKKKDGEylvRFFGDSEFAWVKPKDLKPFDEGDEFEYlkkkkkKKKKKAFKK 82

                           90
                   ....*....|
gi 568916822   197 AMQEMEVYVE 206
Cdd:pfam00855   83 ALEEAEEALK 92

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822    3 MLTIEQLSYLLKFAIQKMKQ---PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 79
Cdd:COG5076   141 ELLYADNKAIAKFKKQLFLRdgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 568916822   80 IIYNGGNHKLTQIAKVVIKICEHEMNEIevcPECYLAACQKRDNWFCEP 128
Cdd:COG5076   221 KLYNGPDSSVYVDAKELEKYFLKLIEEI---PEEMLELSIKPGREEREE 266

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 568916822  822 STIAEIRRLRIEIEKLQWLHQQELAE-----------MKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETK 890
Cdd:cd06503    37 ESLEEAEKAKEEAEELLAEYEEKLAEaraeaqeiieeARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELR 116

                  .
gi 568916822  891 K 891
Cdd:cd06503   117 K 117

104 kDa microneme/rhoptry antigen; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822  465 QKPKNePEDPEDKEGSR--VDKEAPAIKRKPKPTNQVEV-KEEAKSNSPVSEKPDPTPAKDKASPEPEKDFVEKAKPSPH 541
Cdd:PTZ00449  583 KDPKH-PKDPEEPKKPKrpRSAQRPTRPKSPKLPELLDIpKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPK 661

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822  542 PTK-------------DKLKGKDETDSPTVHLGLDSDSESELVIDLGEDPSGREGRKNK----------------KDPKV 592
Cdd:PTZ00449  662 SPKppfdpkfkekfydDYLDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTTPRPlppklprdeefpfepiGDPDA 741

                         170       180
                  ....*....|....*....|....*...
gi 568916822  593 PSPKQDAIGKPPPSSTSAGNQSPPETPV 620
Cdd:PTZ00449  742 EQPDDIEFFTPPEEERTFFHETPADTPL 769

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 568916822   277 RRISLSDMPRSPTSTNSSVHTGSDVEQDP----EKKAPSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 352
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDTaekgQAKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822   353 APTPimTKPDKTSTstTGSILNLNLDRSKAEMDLKELSESVQQ-QSAPVPLISPKRQIRSRFQLNLDKTIESCKAQLGIN 431
Cdd:pfam12064   74 APGT--PKQEKTPT--TGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGID 149

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 568916822   432 EISEDVYTAVEHSDSEDSEKSESSDSEYVSDEEQKPKNEPEDPEDK 477
Cdd:pfam12064  150 EISVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 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 568916822  127 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20160     1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                          90
                  ....*....|.
gi 568916822  207 NIRRKFGVFNY 217
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 568916822  128 PCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFG-QHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20159     2 PCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGgHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQE 81

                  ....
gi 568916822  207 NIRR 210
Cdd:cd20159    82 LLEE 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 568916822    5 TIEQLSYLLKfAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 84
Cdd:cd04369     1 LKKKLRSLLD-ALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNG 79

                          90       100
                  ....*....|....*....|
gi 568916822   85 GNHKLTQIAKVVIKICEHEM 104
Cdd:cd04369    80 PGSPIYKDAKKLEKLFEKLL 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        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568916822    18 QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 94
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 568916822    9 LSYLLKFAIQKMKQ--PGTDAFQKPVPLE-----QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCII 81
Cdd:cd05492     1 LNCLLKFIVSRMKSwlPPDTTNRAIVLNKrgkatKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAI 80

                          90       100
                  ....*....|....*....|....*....
gi 568916822   82 YNGGNHKLTQIAKVVIKICEHEMNEIEVC 110
Cdd:cd05492    81 FHGADSEQYDAARWLYRDTCHDLRELRLC 109

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 568916822  135 LVWAKLKGFPFWPAKALRDKDGQVDA-----------RFFGQHDRAWVPVNNCYL----MSKEIPFSVKKTKSiFNSAMQ 199
Cdd:cd05162     3 LVWAKLKGYPWWPARVVDPEELPEEVgkkkkkggvlvQFFGDNDYAWVKSKNIKPfeegFKKEFKKKKKKSKK-FKKAVE 81

                  ....*
gi 568916822  200 EMEVY 204
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 568916822  135 LVWAKLKGFPFWPAKALR-DKDGQVDAR--------FFGQHDRAWVPVNNC--YLMSKEIPFSVKKTKSiFNSAMQEMEV 203
Cdd:cd05836     6 LVWAKMKGFPPWPGKIVNpPPDLKKPPRkkkmhcvyFFGSENYAWIEDENIkpYEEFKEEMLKSKKSAG-FKDAVEAIEE 84

                  ..
gi 568916822  204 YV 205
Cdd:cd05836    85 YI 86

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 568916822   27 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIkicEHEMNE 106
Cdd:cd05507    23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQ---REVMSQ 99

                  ...
gi 568916822  107 IEV 109
Cdd:cd05507   100 IQQ 102

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

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 568916822    131 NPHPLVWAKLKGFPFWPA-----KALRD-------KDGQVDARFFGQHDRAWVPVNN 175
Cdd:smart00293    2 KPGDLVWAKMKGFPWWPAlvispKMTPDnimkrksDENLYPVLFFGDKDTAWIPSSK 58

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 568916822    8 QLSYLLKFAIQKM-KQPGTDAFQKPVPLE--QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 84
Cdd:cd05497     5 QLQYLLKVVLKALwKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84

                          90
                  ....*....|....*
gi 568916822   85 GNHKLTQIAKVVIKI 99
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 568916822    8 QLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYnggNH 87
Cdd:cd05504    13 NLSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLY---NP 89

                          90
                  ....*....|..
gi 568916822   88 KLTQIAKVVIKI 99
Cdd:cd05504    90 EHTSVYKAGTRL 101

second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein family consists 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 in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play nonredundant 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 the 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 (C5HCH). This model corresponds to the second PWWP domain. The family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822  136 VWAKLKGFPFWPAKAL------------RDKDGQVDARFFGQHDRAWVPVNNCYLMSKE----IPFSVKKTKSIFNSAMQ 199
Cdd:cd05838     6 VWVKLGNYRWWPAEILhprevpdniqslPHPPGEFPVRFFGSHDYYWVHRGRVFLFEEGdkgsKEKSKKSLDKSFKRALK 85

                  ....*...
gi 568916822  200 E-MEVYVE 206
Cdd:cd05838    86 EaNEAFRE 93

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its 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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568916822   28 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 83
Cdd:cd05513    22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822    3 MLTIEQLSYLLKFAIQKMKQ---PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 79
Cdd:COG5076   141 ELLYADNKAIAKFKKQLFLRdgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 568916822   80 IIYNGGNHKLTQIAKVVIKICEHEMNEIevcPECYLAACQKRDNWFCEP 128
Cdd:COG5076   221 KLYNGPDSSVYVDAKELEKYFLKLIEEI---PEEMLELSIKPGREEREE 266

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 568916822   28 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 83
Cdd:cd05503    21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFN 76

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822  135 LVWAKLKGFPFWPA--------------KALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEI--PFSVKKTKSIFNSAM 198
Cdd:cd20142     5 VVWAKVKGYPMWPAlvideehaercgleANRPGKKGTVPVQFFGTYEVARLNPKKVVGFSKGLdlKYHSKCKAPVFRQAL 84

                  ....*.
gi 568916822  199 QEMEVY 204
Cdd:cd20142    85 EEAERY 90

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. 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 568916822   28 FQKPVPLEQhPDYAEYIFHPMDLCTLEKNAKKK---MYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEM 104
Cdd:cd05502    25 FHEPVSPSV-PNYYKIIKTPMDLSLIRKKLQPKspqHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQL 103

                  ...
gi 568916822  105 NEI 107
Cdd:cd05502   104 KEI 106

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568916822   28 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN-GGNHKLTQIAK 94
Cdd:cd05505    21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYeNGSYVLSCMRK 88

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
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568916822  135 LVWAKLKGFPFWPA----------KALRDKDGQVDARFFGQ-HDRAWVPVNN 175
Cdd:cd05837     6 LVWAKLEGYPWWPSlvcnhpttgfHKKFGKKGEVHVQFFDDpPSRAWVKAKN 57

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 568916822  824 IAEIRRLRIEIEKLQWLHQQELAEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 891
Cdd:COG0711    40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118

PWWP domain found in PC4 and SFRS1-interacting protein (PSIP); 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. It contains a PWWP domain, which is necessary for DNA binding.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822  132 PHPLVWAKLKGFPFWPAKALRDKDGQVDAR-------FFGQHDRAwvpvnncYLMSKEI-PFSVKKTK-------SIFNS 196
Cdd:cd20151     3 PGDLIFAKMKGYPHWPARVDEVPDGAVKPPtnklpifFFGTHETA-------FLGPKDIfPYSENKEKygkpnkrKGFNE 75

                          90
                  ....*....|....*.
gi 568916822  197 AMQEMEvyvENIRRKF 212
Cdd:cd20151    76 GLWEID---NNPKVKF 88

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 568916822  822 STIAEIRRLRIEIEKLQWLHQQELAE-----------MKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETK 890
Cdd:cd06503    37 ESLEEAEKAKEEAEELLAEYEEKLAEaraeaqeiieeARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELR 116

                  .
gi 568916822  891 K 891
Cdd:cd06503   117 K 117

PWWP domain found in Hepatoma-derived growth factor (HDGF); 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 contains a PWWP domain, which is necessary for DNA binding.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568916822  132 PHPLVWAKLKGFPFWPAK-------ALRDKDGQVDARFFGQHDRAwvpvnncYLMSKEIpFSVKKTKSIF 194
Cdd:cd20148     3 CGDLVFAKMKGYPHWPARidempeaAVKSTANKYQVFFFGTHETA-------FLGPKDL-FPYEESKEKF 64