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 1370511186  881 LTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQE-DYSMYSKPEDFVADFRLIFQNCAE 959
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPkSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1370511186  960 FNEPDSEVANAGIKLENYFEELLKNLYPE 988
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

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 1370511186  199 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 255
Cdd:cd19828      1 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 57

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. 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 vertebrate Kruppel-type (C2H2) zinc finger proteins that contain 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 plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha 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 1370511186  809 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFC 851
Cdd:cd15622      1 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43

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 1370511186  881 LTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQE-DYSMYSKPEDFVADFRLIFQNCAE 959
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPkSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1370511186  960 FNEPDSEVANAGIKLENYFEELLKNLYPE 988
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370511186   883 PIDKRKCERLLLFLYC----HEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYsmYSKPEDFVADFRLIFQNC 957
Cdd:smart00297    2 PKLQKKLQELLKAVLDkldsHPLSWPFLKPVSRkEAPDYYDIIKKPMDLKTIKKKLENGK--YSSVEEFVADFNLMFSNA 79

                            90       100
                    ....*....|....*....|....*...
gi 1370511186   958 AEFNEPDSEVANAGIKLENYFEELLKNL 985
Cdd:smart00297   80 RTYNGPDSEVYKDAKKLEKFFEKKLREL 107

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 1370511186  142 QVCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQK 186
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 1370511186  889 CERLLLFLYCHEMSLAFQDPVPLTV-PDYYKIIKNPMDLSTIKKRLQEDYsmYSKPEDFVADFRLIFQNCAEFNEPDSEV 967
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEyPDYYSVIKKPMDLSTIKKKLENGE--YKSLAEFLADVKLIFSNARTYNGPGSVI 78

                   ....*.
gi 1370511186  968 ANAGIK 973
Cdd:pfam00439   79 YKAAEK 84

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1370511186   199 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFI 240
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 1370511186   809 WCAVCQ---NGGELLCCEKCPKVFHLSCHVPTLTNF-PSGEWICTFC 851
Cdd:smart00249    1 YCSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 1370511186   139 KSNQVCTSCEDnAEANGFCVECVEWLCKTCIRA----HQRV 175
Cdd:smart00336    1 QRAPKCDSHGD-EPAEFFCEECGALLCRTCDEAehrgHTVV 40

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 1370511186  411 SQPQMPKQNPVVEQNSQPPSGLSSNQLSKFPTQislAQLRLQHMQQQVMAQRQQVQRRPAPVGLPNPRMQGPIQQPSISH 490
Cdd:pfam09770  220 QPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQ---PQQHPGQGHPVTILQRPQSPQPDPAQPSIQPQAQQFHQQPPPVP 296

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370511186  491 QQP------PPRLINFQNHSPKPNGPVLPPHPQQLRYPPNQNIPRQA-IKPNPLQMAFLAQQ 545
Cdd:pfam09770  297 VQPtqilqnPNRLSAARVGYPQNPQPGVQPAPAHQAHRQQGSFGRQApIITHPQQLAQLSEE 358

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 1370511186  881 LTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQE-DYSMYSKPEDFVADFRLIFQNCAE 959
Cdd:cd05502      1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPkSPQHYSSPEEFVADVRLMFKNCYK 80

                           90       100
                   ....*....|....*....|....*....
gi 1370511186  960 FNEPDSEVANAGIKLENYFEELLKNLYPE 988
Cdd:cd05502     81 FNEEDSEVAQAGKELELFFEEQLKEILPD 109

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370511186   883 PIDKRKCERLLLFLYC----HEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYsmYSKPEDFVADFRLIFQNC 957
Cdd:smart00297    2 PKLQKKLQELLKAVLDkldsHPLSWPFLKPVSRkEAPDYYDIIKKPMDLKTIKKKLENGK--YSSVEEFVADFNLMFSNA 79

                            90       100
                    ....*....|....*....|....*...
gi 1370511186   958 AEFNEPDSEVANAGIKLENYFEELLKNL 985
Cdd:smart00297   80 RTYNGPDSEVYKDAKKLEKFFEKKLREL 107

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 1370511186  885 DKRKCERLLLFLYCH--EMSLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQEDYsmYSKPEDFVADFRLIFQNCAEFN 961
Cdd:cd04369      1 LKKKLRSLLDALKKLkrDLSEPFLEPVdPKEAPDYYEVIKNPMDLSTIKKKLKNGE--YKSLEEFEADVRLIFSNAKTYN 78

                           90       100
                   ....*....|....*....|.
gi 1370511186  962 EPDSEVANAGIKLENYFEELL 982
Cdd:cd04369     79 GPGSPIYKDAKKLEKLFEKLL 99

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 1370511186  142 QVCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQK 186
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 1370511186  196 VTSQRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQK 248
Cdd:cd19830      1 ASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53

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 1370511186  809 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDL 854
Cdd:cd15624      1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI 46

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 1370511186  907 DPVPLTVPDYYKIIKNPMDLSTIKKRLqeDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEEL 981
Cdd:cd05498     29 DPEALGLHDYHDIIKHPMDLSTIKKKL--DNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101

B-box-type 1 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 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 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 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1-alpha and TIF1-beta 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. TIF1-gamma is structurally closely related to TIF1-alpha and TIF1-beta, 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 1370511186  143 VCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQK 186
Cdd:cd19805      1 VCTSCEDNAPATSFCVECSEWLCDTCVQAHQRVKVTKDHTIRSK 44

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 1370511186  907 DPVPLTVPDYYKIIKNPMDLSTIKKRLQEdySMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFE 979
Cdd:cd05500     30 DPVKLNIPHYPTIIKKPMDLGTIERKLKS--NVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFE 100

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 1370511186  140 SNQVCTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQK 186
Cdd:cd19846      2 TIQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRVK 48

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1370511186  809 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFC 851
Cdd:cd15541      1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43

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 1370511186  883 PIDKRKCERLLLFLYCHEMSLAFQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEDysMYSKPEDFVADFRLIFQNCAEFN 961
Cdd:cd05504     11 PLNLSALEQLLVEIVKHKDSWPFLRPVSKIeVPDYYDIIKKPMDLGTIKEKLNMG--EYKLAEEFLSDIQLVFSNCFLYN 88

                           90       100
                   ....*....|....*....|....*..
gi 1370511186  962 EPDSEVANAGIKLENYFEELLKNLYPE 988
Cdd:cd05504     89 PEHTSVYKAGTRLQRFFIKRCRKLGLP 115

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 1370511186  896 LYCHEMSLAFQ---DPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYsmYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGI 972
Cdd:cd05497     17 LWKHKFAWPFQqpvDAVKLNLPDYHKIIKTPMDLGTIKKRLENNY--YWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQ 94

                           90
                   ....*....|...
gi 1370511186  973 KLENYFEELLKNL 985
Cdd:cd05497     95 TLEKLFLQKLAQM 107

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370511186  866 PSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQ------------DPVPLTVPDYYKIIKNPMDLSTIKKRL 933
Cdd:COG5076    119 GSLLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKQLFLrdgrflssiflgLPSKREYPDYYEIIKSPMDLLTIQKKL 198

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370511186  934 QEDysMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPE--KRFPKPEFRNESEDN 1003
Cdd:COG5076    199 KNG--RYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEmlELSIKPGREEREERE 268

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 1370511186  889 CERLLLFLYCH-EMSLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQEdySMYSKPEDFVADFRLIFQNCAEFN-EPDS 965
Cdd:cd05510     12 LDKVLNELKTYtEHSTPFLTKVsKREAPDYYDIIKKPMDLGTMLKKLKN--LQYKSKAEFVDDLNLIWKNCLLYNsDPSH 89

                           90       100
                   ....*....|....*....|
gi 1370511186  966 EVANAGIKLENYFEELLKNL 985
Cdd:cd05510     90 PLRRHANFMKKKAEHLLKLI 109

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370511186  905 FQDPVPLT-VPDYYKIIKNPMDLSTIKKRLqEDYsMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKL 974
Cdd:cd05512     22 FSEPVDLSeVPDYLDHIKQPMDFSTMRKKL-ESQ-RYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRL 90

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 1370511186  885 DKRKCERLLLFLYCHEMSLAFQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEdySMYSKPEDFVADFRLIFQNCAEFNEP 963
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADeAEDYKKVITNPMDLQTMQTKCSC--GSYSSVQEFLDDMKLVFSNAEKYYEN 78

                           90
                   ....*....|....*....
gi 1370511186  964 DSEVANAGIKLENYFEELL 982
Cdd:cd05505     79 GSYVLSCMRKTEQCCVNLL 97

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 1370511186  202 VFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEA 243
Cdd:cd19794      1 LMCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEHRFKHLDEA 42

B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of TRIM (tripartite motif) family 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 region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1370511186  201 PVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEA 243
Cdd:cd19785      1 PVLCPFHPAEELRLFCETCDKPVCRDCVLVEHRGHQCDFTSDV 43

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 1370511186  810 CAVCQNGGELLCCEKCPKVFHLSCHVPTL--TNFPSGEWICTFC 851
Cdd:cd15533      2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45

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 1370511186  144 CTSCEDNAEANGFCVECVEWLCKTCIRAHQRVKFTKDHTVRQ 185
Cdd:cd19812      2 CSSCDEGNAATSRCKDCNEYLCDNCVRAHQRVRLTKDHFIVR 43

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1370511186  810 CAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFC 851
Cdd:cd15532      2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43

B-Box-type zinc finger;

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1370511186   199 QRPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFI 240
Cdd:smart00336    1 QRAPKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVLL 42

Bromodomain, polybromo repeat I. 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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370511186  914 PDYYKIIKNPMDLSTIKKRLQ-EDYSMYskpEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEE 980
Cdd:cd05524     39 PEYYEVVSNPIDLLKIQQKLKtEEYDDV---DDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLS 103

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1370511186  809 WCAVCQ---NGGELLCCEKCPKVFHLSCHVPTLT--NFPSGEWICTFCR 852
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECK 49

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370511186  903 LAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLqeDYSMYSKPEDFVADFRLIFQNCAEFNePDSEVANAGI 972
Cdd:cd05528     22 NAFTKPVdEEEVPDYYEIIKQPMDLQTILQKL--DTHQYLTAKDFLKDIDLIVTNALEYN-PDRDPADKLI 89

Bromodomain, polybromo repeat II. 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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370511186  901 MSLAFQD-PVPLTVPDYYKIIKNPMDLSTIKKRLQEDYsmYSKPEDFVADFRLIFQNCAEFNEPDSEV 967
Cdd:cd05517     23 ISELFQKlPSKVLYPDYYAVIKEPIDLKTIAQRIQSGY--YKSIEDMEKDLDLMVKNAKTFNEPGSQV 88