B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998     266 QKVIIDTLITKLMEKTKYIKYTGNQIQNRIIEINQNQKQVEQDIKVAIFTLMVEINKKGKALLHQLESLAKDHRMKLMQQ 345
Cdd:smart00502    1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 94420998     346 QQEVAGLSKQLEHVMHFSKWAVSSGSSTALLYSKRLITYRLRHLLRA 392
Cdd:smart00502   81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127

RING finger, HC subclass, found in transcription inknown asiary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of RAR that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998   49 LDTCAVCHQNIQSRVPKLLPCLHSFCQRCLPAPQRYLMLTAPALGSAETpppapapapapgspaGGPSPFATQVGVIRCP 128
Cdd:cd16764    1 LDTCGVCKQHIQSREPRLLPCLHSFCQRCLPQPERYLMLPAPFSPSPGP---------------RATSSANRQVGVVRCP 65

                 ....*.
gi 94420998  129 VCSQEC 134
Cdd:cd16764   66 VCSQEC 71

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 94420998  829 WCAVCQNGGELLCCEKCPKVFHLTCHVPTLTNFPSGEWICTFCRDL 874
Cdd:cd15624    1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998     266 QKVIIDTLITKLMEKTKYIKYTGNQIQNRIIEINQNQKQVEQDIKVAIFTLMVEINKKGKALLHQLESLAKDHRMKLMQQ 345
Cdd:smart00502    1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 94420998     346 QQEVAGLSKQLEHVMHFSKWAVSSGSSTALLYSKRLITYRLRHLLRA 392
Cdd:smart00502   81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127

B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 94420998  218 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 274
Cdd:cd19828    1 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 57

B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoic X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 94420998  161 QVCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQK 205
Cdd:cd19845    1 QVCTSCEDNAEANGFCVECVEWLCKTCIEAHQRVKFTKDHTVRQK 45

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998    909 CERLLLFLYCHEMSLAFQDPVPLTV-PDYYKIIKNPMDLSTIKKRLQEDYcmYTKPEDFVADFRLIFQNCAEFNEPDSEV 987
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEyPDYYSVIKKPMDLSTIKKKLENGE--YKSLAEFLADVKLIFSNARTYNGPGSVI 78

                   ....*.
gi 94420998    988 ANAGIK 993
Cdd:pfam00439   79 YKAAEK 84

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 94420998     218 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFI 259
Cdd:smart00336    1 QRAPKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVLL 42

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 94420998     829 WCAVCQ---NGGELLCCEKCPKVFHLTCHVPTLTNF-PSGEWICTFC 871
Cdd:smart00249    1 YCSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 94420998     158 KSNQVCTSCEDnAEANGFCVECVEWLCKTCIRA----HQRV 194
Cdd:smart00336    1 QRAPKCDSHGD-EPAEFFCEECGALLCRTCDEAehrgHTVV 40

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 94420998     490 PVGLPNPRMQGPIQQPSISHQHPPPRLINFQNHSPKPNgPVLPPYPQQLRYSPSQNVPRQTTIKPNPLQMAFLAQ 564
Cdd:smart00818   66 PVVPQQPLMPVPGQHSMTPTQHHQPNLPQPAQQPFQPQ-PLQPPQPQQPMQPQPPVHPIPPLPPQPPLPPMFPMQ 139

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998    429 ESQPQMPKQNPVVEQSSQPPGGLPSNQLSKFPTQIslaqlrLQHiqqqvmaqrQQVQRRPAPVGLPNPRMQGPIQQPSIS 508
Cdd:pfam09770  231 QQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTI------LQR---------PQSPQPDPAQPSIQPQAQQFHQQPPPV 295

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 94420998    509 HQHP------PPRLINFQNHSPKPNGPVLPPYPQQLRYSPSQNVPRQTTIKPNPLQMAFLAQQ 565
Cdd:pfam09770  296 PVQPtqilqnPNRLSAARVGYPQNPQPGVQPAPAHQAHRQQGSFGRQAPIITHPQQLAQLSEE 358

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998     266 QKVIIDTLITKLMEKTKYIKYTGNQIQNRIIEINQNQKQVEQDIKVAIFTLMVEINKKGKALLHQLESLAKDHRMKLMQQ 345
Cdd:smart00502    1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 94420998     346 QQEVAGLSKQLEHVMHFSKWAVSSGSSTALLYSKRLITYRLRHLLRA 392
Cdd:smart00502   81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127

B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 94420998  218 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 274
Cdd:cd19828    1 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 57

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998  905 DKRKCERLLLFLYCHEMSLAFQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEDYcmYTKPEDFVADFRLIFQNCAEFNEP 983
Cdd:cd05509    2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEeAPDYYDVIKKPMDLSTMEEKLENGY--YVTLEEFVADLKLIFDNCRLYNGP 79

                         90       100
                 ....*....|....*....|..
gi 94420998  984 DSEVANAGIKLESYFEELLKNL 1005
Cdd:cd05509   80 DTEYYKCANKLEKFFWKKLKEL 101

B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoic X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 94420998  161 QVCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQK 205
Cdd:cd19845    1 QVCTSCEDNAEANGFCVECVEWLCKTCIEAHQRVKFTKDHTVRQK 45

B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-gamma is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling. It inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 94420998  215 VTSQRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQK 267
Cdd:cd19830    1 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53

Bromodomain, Brdt_like subfamily, repeat II. 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 94420998  927 DPVPLTVPDYYKIIKNPMDLSTIKKRLqeDYCMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLESYFEEL 1001
Cdd:cd05498   29 DPEALGLHDYHDIIKHPMDLSTIKKKL--DNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belong to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 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 and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. 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).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 94420998  220 PVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEA 262
Cdd:cd19775    1 PLFCPVHPQEPLKLFCETCDKLTCRDCQLLEHKDHKYQFAEEA 43

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 94420998  927 DPVPLTVPDYYKIIKNPMDLSTIKKRLQEDycMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLESYFE 999
Cdd:cd05500   30 DPVKLNIPHYPTIIKKPMDLGTIERKLKSN--VYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFE 100

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998    909 CERLLLFLYCHEMSLAFQDPVPLTV-PDYYKIIKNPMDLSTIKKRLQEDYcmYTKPEDFVADFRLIFQNCAEFNEPDSEV 987
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEyPDYYSVIKKPMDLSTIKKKLENGE--YKSLAEFLADVKLIFSNARTYNGPGSVI 78

                   ....*.
gi 94420998    988 ANAGIK 993
Cdd:pfam00439   79 YKAAEK 84

B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-gamma is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling. It inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1-gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 94420998  156 VEKSNQVCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQKEEVS 209
Cdd:cd19847    1 DEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54

B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-beta/KAP-1 acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 94420998  159 SNQVCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQK 205
Cdd:cd19846    2 TIQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRVK 48

RING finger, HC subclass, found in the transcriptional inknown asiary factor 1 (TIF1) subfamily and similar proteins; The TIF1 subfamily of transcriptional cofactors containing RING-HC fingers includes TIF1alpha (TRIM24), TIF1beta (TRIM28), and TIF1gamma (TRIM33), which belong to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. 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 and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. 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 heterochromatin proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs). TIF1delta (TRIM66) doesn't have a RING-HC finger and is not included in this model.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998   49 LDTCAVCHQNIQSRVPKLLPCLHSFCQRCLPAPQRYLMLTAPALGsaetpppapapapapgspaggpspFATQVGVIRCP 128
Cdd:cd16585    1 LDTCAVCKQSFQSREPKLLPCLHSFCKRCLPPADRAAANPSPSGG------------------------AAGQVGVIRCP 56

                 ....*.
gi 94420998  129 VCSQEC 134
Cdd:cd16585   57 VCKQEC 62

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 94420998  916 LYCHEMSLAFQ---DPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYcmYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGI 992
Cdd:cd05497   17 LWKHKFAWPFQqpvDAVKLNLPDYHKIIKTPMDLGTIKKRLENNY--YWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQ 94

                         90
                 ....*....|...
gi 94420998  993 KLESYFEELLKNL 1005
Cdd:cd05497   95 TLEKLFLQKLAQM 107

B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD) and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-beta acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 94420998  220 PVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEA 262
Cdd:cd19829    1 TVYCSIHKQEPLKLFCETCDTLTCRDCQLNAHKDHQYQFLEDA 43

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. 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 94420998  922 SLAFQ---DPVPLTVPDYYKIIKNPMDLSTIKKRLQEDycMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLESYF 998
Cdd:cd05495   22 SLPFRqpvDPKLLGIPDYFDIVKNPMDLSTIRRKLDTG--QYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVF 99

                 ....
gi 94420998  999 EELL 1002
Cdd:cd05495  100 EQEI 103

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 94420998  909 CERLLLFLYCH-EMSLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQEDYcmYTKPEDFVADFRLIFQNCAEFN-EPDS 985
Cdd:cd05510   12 LDKVLNELKTYtEHSTPFLTKVsKREAPDYYDIIKKPMDLGTMLKKLKNLQ--YKSKAEFVDDLNLIWKNCLLYNsDPSH 89

                         90       100
                 ....*....|....*....|
gi 94420998  986 EVANAGIKLESYFEELLKNL 1005
Cdd:cd05510   90 PLRRHANFMKKKAEHLLKLI 109

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998  919 HEMSLAFQD-PVPLTVPDYYKIIKNPMDLSTIKKRLQEDYcmYTKPEDFVADFRLIFQNCAEFNEPDSEV 987
Cdd:cd05515   21 RRLSLIFMRlPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQ--YQSLDDMVSDFVLMFDNACKYNEPDSQI 88

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 94420998  922 SLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQEDycMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLESYFEE 1000
Cdd:cd05511   18 SWPFHTPVnKKKVPDYYKIIKRPMDLQTIRKKISKH--KYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEE 95

                 ...
gi 94420998 1001 LLK 1003
Cdd:cd05511   96 LLA 98

B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins; TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 94420998  221 VFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEA 262
Cdd:cd19794    1 LMCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEHRFKHLDEA 42

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 94420998  905 DKRKCERLLLFLYCHEMSLAFQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEDycMYTKPEDFVADFRLIFQNCAEFNEP 983
Cdd:cd05505    1 ELQKCEEILSKILKYRFSWPFREPVTADeAEDYKKVITNPMDLQTMQTKCSCG--SYSSVQEFLDDMKLVFSNAEKYYEN 78

                         90
                 ....*....|....*....
gi 94420998  984 DSEVANAGIKLESYFEELL 1002
Cdd:cd05505   79 GSYVLSCMRKTEQCCVNLL 97

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 94420998  830 CAVCQNGGELLCCEKCPKVFHLTCHVPTL--TNFPSGEWICTFC 871
Cdd:cd15533    2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. 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 94420998  906 KRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDycMYTKPEDFVADFRLIFQNCAEFN-EP 983
Cdd:cd05496    7 KKQCKELVNLMWDCEDSEPFRQPVDLlKYPDYRDIIDTPMDLGTVKETLFGG--NYDDPMEFAKDVRLIFSNSKSYTpNK 84

                         90       100
                 ....*....|....*....|..
gi 94420998  984 DSEVANAGIKLESYFEELLKNL 1005
Cdd:cd05496   85 RSRIYSMTLRLSALFEEHIKKI 106

B-box-type 1 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif) family of proteins that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 94420998  163 CTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQ 204
Cdd:cd19812    2 CSSCDEGNAATSRCKDCNEYLCDNCVRAHQRVRLTKDHFIVR 43

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. 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 94420998  919 HEMSLAFQD-PVPLTVPDYYKIIKNPMDLSTIKKRLQEDycMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLESY 997
Cdd:cd05522   22 RLLTLHFEKlPDKAREPEYYQEISNPISLDDIKKKVKRR--KYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKE 99

                 ....
gi 94420998  998 FEEL 1001
Cdd:cd05522  100 ARLL 103

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. 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 94420998  934 PDYYKIIKNPMDLSTIKKRLQEdyCMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLESYFEE 1000
Cdd:cd05516   38 PEYYELIRKPVDFKKIKERIRN--HKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKS 102