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 528881307  24 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 103
Cdd:cd20160    1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                         90
                 ....*....|.
gi 528881307 104 NIRRKFGVFNY 114
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 528881307 663 IAEIRRLRIEIEKLQWLHQQELSEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 730
Cdd:COG0711   40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118

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 528881307  354 YISDDEQkSKNEPEDTEDkegcqmdkepsavKKKPKPTNPVEIkeelkstspasEKADPGAVKDKASPEPEKDFSEKAKP 433
Cdd:pfam05793 285 YISDSSA-SGNDPEERED-------------KLSPEEPAKGEI-----------EQSDDSEESEEEKNEEEGKLSKKGKK 339

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881307  434 SPHPiKDKLKGKDETDSptvhlglDSDSESELVIDLGEDHSGREGRKNKKEPKEPSPKQDVVGKTPPSttvGSHSPPET 512
Cdd:pfam05793 340 AKKL-KGKKNGKDKSES-------SDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPVDSGPSSPGNS---GPARPSPE 407

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 528881307  24 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 103
Cdd:cd20160    1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                         90
                 ....*....|.
gi 528881307 104 NIRRKFGVFNY 114
Cdd:cd20160   81 KLREKFGKFNY 91

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 528881307    28 NPHPLVWAKLKGFPFWPA-----KALRD-------KDGQVDARFFGQHDRAWVPINN 72
Cdd:smart00293   2 KPGDLVWAKMKGFPWWPAlvispKMTPDnimkrksDENLYPVLFFGDKDTAWIPSSK 58

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 528881307 663 IAEIRRLRIEIEKLQWLHQQELSEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 730
Cdd:COG0711   40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118

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 528881307 661 STIAEIRRLRIEIEKLQWLHQQEL-----------SEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETK 729
Cdd:cd06503   37 ESLEEAEKAKEEAEELLAEYEEKLaearaeaqeiiEEARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELR 116

                 .
gi 528881307 730 K 730
Cdd:cd06503  117 K 117

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881307 597 QSSPLVTSSGSMSTLVSSVNADLP-----------------IATASADVAADIAKYTSKMMDA--IKGTMTEIYNDLSK- 656
Cdd:COG4192   49 DSLPKLQASLKLEENSNELVAALPefaaatnttersqlrnqLNTQLADIEELLAELEQLTQDAgdLRAAVADLRNLLQQl 128

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881307 657 -NTTGSTIAEIRRLRIEIEKLQWLHQQELSEMKhnleltmaEMRQSLEQERDRLIAEVKKQLELEKQQA 724
Cdd:COG4192  129 dSLLTQRIALRRRLQELLEQINWLHQDFNSELT--------PLLQEASWQQTRLLDSVETTESLRNLQN 189

Coiled-coil domain-containing protein 90-like; This entry includes coiled-coil domain-containing proteins 90 (CCDC90) and related proteins. CCDC90A is a key regulator of the mitochondrial calcium uniporter (MCU) and hence was renamed MCUR1. A study in mammals and in yeast homolog fmp32 has reported that MCUR1 is a cytochrome c oxidase assembly factor and that it has an indirect role as a regulator of MCU, however, subsequent publications confirmed the function of MCUR1 as a regulator of MCU. The role of CCDC90B proteins is still not known.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881307  639 MMDAIKGTMTEIYNDL-SK----NTTGSTIAEIRRLRIEIeklQWLHQQELSEMKHNLELTMAE---MRQSLEQERDRLI 710
Cdd:pfam07798  27 LRDLLNDSLENVSKDLvTKedleNETYLQKADLAELRSEL---QILEKSEFAALRSENEKLRRElekLKQRLREEITKLK 103

                          90       100
                  ....*....|....*....|
gi 528881307  711 AEVKKQLELEKQQAVDETKK 730
Cdd:pfam07798 104 ADVRLDLNLEKGRIREELKA 123

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 528881307  24 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 103
Cdd:cd20160    1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                         90
                 ....*....|.
gi 528881307 104 NIRRKFGVFNY 114
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 528881307  25 PCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFG-QHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 103
Cdd:cd20159    2 PCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGgHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQE 81

                 ....
gi 528881307 104 NIRR 107
Cdd:cd20159   82 LLEE 85

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 528881307  32 LVWAKLKGFPFWPAKALR-DKDGQVDAR--------FFGQHDRAWVPINNC--YLMSKEIPFSVKKTKSiFNSAMQEMEV 100
Cdd:cd05836    6 LVWAKMKGFPPWPGKIVNpPPDLKKPPRkkkmhcvyFFGSENYAWIEDENIkpYEEFKEEMLKSKKSAG-FKDAVEAIEE 84

                 ..
gi 528881307 101 YV 102
Cdd:cd05836   85 YI 86

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 528881307   32 LVWAKLKGFPFWPAK---------ALRDKDGQVDA---RFFGQHDRAWVPINNCYLMSKEIPFSV------KKTKSIFNS 93
Cdd:pfam00855   3 LVWAKLKGYPWWPARvvdpeelpeNVLKPKKKDGEylvRFFGDSEFAWVKPKDLKPFDEGDEFEYlkkkkkKKKKKAFKK 82

                          90
                  ....*....|
gi 528881307   94 AMQEMEVYVE 103
Cdd:pfam00855  83 ALEEAEEALK 92

MYND finger;

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 528881307  734 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 768
Cdd:pfam01753   1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881307  32 LVWAKLKGFPFWPA----------KALRDKDGQVD---ARFFGQ-HDRAWVPI-------NNCYLMSKEIPFSVKKTKSI 90
Cdd:cd20146   14 LVWAKMTGYPRWPAiltpdpicgeYVDYDEDGEVEkyhVEFLGKpHSHAWISAksvepynSNTKTPKCKTKKSKKRKKSY 93

                 ....*..
gi 528881307  91 fNSAMQE 97
Cdd:cd20146   94 -ESALEE 99

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 528881307  32 LVWAKLKGFPFWPA--------------KALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEI--PFSVKKTKSIFNSAM 95
Cdd:cd20142    5 VVWAKVKGYPMWPAlvideehaercgleANRPGKKGTVPVQFFGTYEVARLNPKKVVGFSKGLdlKYHSKCKAPVFRQAL 84

                 ....*.
gi 528881307  96 QEMEVY 101
Cdd:cd20142   85 EEAERY 90

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 528881307  32 LVWAKLKGFPFWPAKALRDKD-------GQVDARFFGQHDRAWVPINNCYLMSKEIPFSV------KKTKSIFNSAMQEM 98
Cdd:cd20147    3 LVLAKVKGFPAWPAQVSEPEDwgsapdpKKVFVHFFGTQQIGFCNPGELSEFTEEIKQSLlartlkKKKGSDFSRAVKEI 82

                 .
gi 528881307  99 E 99
Cdd:cd20147   83 C 83

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 528881307 663 IAEIRRLRIEIEKLQWLHQQELSEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 730
Cdd:COG0711   40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118

first 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 the 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 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, through 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 first PWWP domain. This 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528881307  32 LVWAKLKGFPFWPA------------KALRDKDG---QVDARFFGqhD---RAWVPINNCylmskeIPFSVKK 86
Cdd:cd20144    4 LVWAKVSGHPWWPCmvtydpesglytKIKGSGGRtyrQYHVQFFG--DngeRGWVSEKSL------MPFEGKE 68

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 528881307  29 PHPLVWAKLKGFPFWPAK-------ALRDKDGQVDARFFGQHDRAwvpinncYLMSKEIpFSVKKTKSIF 91
Cdd:cd20148    3 CGDLVFAKMKGYPHWPARidempeaAVKSTANKYQVFFFGTHETA-------FLGPKDL-FPYEESKEKF 64

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 528881307 661 STIAEIRRLRIEIEKLQWLHQQEL-----------SEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETK 729
Cdd:cd06503   37 ESLEEAEKAKEEAEELLAEYEEKLaearaeaqeiiEEARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELR 116

                 .
gi 528881307 730 K 730
Cdd:cd06503  117 K 117

PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is a methyl-CpG-binding protein that binds to heterochromatin. It does not interact with either methylated or unmethylated DNA. MBD5 acts as a transcriptional regulator responsible for 2q23.1 deletion syndrome. It belongs to the MBD family proteins, which play central roles in transcriptional regulation and development. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 528881307  32 LVWAKLKGFPFWPAKALR------DKDGQVDARFFGQHDRAWVPIN 71
Cdd:cd20141    6 LVWGQIRGFPSWPGKLVSendvgkTNEGKVWVSWFGDHSFGQVEPD 51

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881307 597 QSSPLVTSSGSMSTLVSSVNADLP-----------------IATASADVAADIAKYTSKMMDA--IKGTMTEIYNDLSK- 656
Cdd:COG4192   49 DSLPKLQASLKLEENSNELVAALPefaaatnttersqlrnqLNTQLADIEELLAELEQLTQDAgdLRAAVADLRNLLQQl 128

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881307 657 -NTTGSTIAEIRRLRIEIEKLQWLHQQELSEMKhnleltmaEMRQSLEQERDRLIAEVKKQLELEKQQA 724
Cdd:COG4192  129 dSLLTQRIALRRRLQELLEQINWLHQDFNSELT--------PLLQEASWQQTRLLDSVETTESLRNLQN 189

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 528881307  354 YISDDEQkSKNEPEDTEDkegcqmdkepsavKKKPKPTNPVEIkeelkstspasEKADPGAVKDKASPEPEKDFSEKAKP 433
Cdd:pfam05793 285 YISDSSA-SGNDPEERED-------------KLSPEEPAKGEI-----------EQSDDSEESEEEKNEEEGKLSKKGKK 339

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881307  434 SPHPiKDKLKGKDETDSptvhlglDSDSESELVIDLGEDHSGREGRKNKKEPKEPSPKQDVVGKTPPSttvGSHSPPET 512
Cdd:pfam05793 340 AKKL-KGKKNGKDKSES-------SDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPVDSGPSSPGNS---GPARPSPE 407