ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of transcription factors, found in a broad array of organisms from fungi to mammals, is characterized by a highly conserved, helix-turn-helix DNA binding domain that binds to the major groove of DNA. The ARID domain, also called BRIGHT, was first identified in the mouse B-cell-specific transcription factor Bright and in the product of the dead ringer (dri) gene of Drosophila melanogaster. ARID family members are implicated in normal development, differentiation, cell cycle regulation, transcriptional activation and chromatin remodeling. Different family members exhibit different DNA-binding properties. Drosophila Dri, mammalian ARID3A/3B/3C and ARID5A/5B, selectively bind AT-rich sites. However, ARID1A/1B, Drosophila Osa, yeast SWI1, ARID2, ARID4A/4B, JARID1A/1B/1C/1D, and JARID2, bind DNA without sequence specificity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYELqsmalgerigwpllepqsscqtavlrvparaagaar 140
Cdd:cd16884    5 FLVNLYKFMKERNTPIERIPHLGFKQINLWKIYKAVEKLGGYEL------------------------------------ 48

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 977376791 141 tpppggarrprphevplqVTGRRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYV 197
Cdd:cd16884   49 ------------------VTARRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYV 87

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) and similar proteins; ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also associates with thyroid receptor alpha (TR alpha) and retinoid X receptor alpha (RXR alpha) in a ligand-dependent manner, and with ER beta, androgen receptor (AR), and the retinoic acid receptor (RAR) in a ligand-independent manner. ARID5A functions as a negative regulator of RORgamma-induced Th17 cell differentiation and may be involved in the pathogenesis of rheumatoid arthritis (RA). Moreover, it is an important transcriptional partner of the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) in stimulation of chondrocyte-specific transcription. Meanwhile, ARID5A plays an important role in promotion of inflammatory processes and autoimmune diseases. It works as a unique RNA binding protein, which stabilizes interleukin-6 (IL-6) but not tumor necrosis factor-alpha (TNF-alpha) mRNA through binding to the 3' untranslated region (UTR) of IL-6 mRNA, and inhibits the destabilizing effect of regnase-1 on IL-6 mRNA. ARID5A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYELqsmalgerigwpllepqsscqtavlrvparaagaar 140
Cdd:cd16884    5 FLVNLYKFMKERNTPIERIPHLGFKQINLWKIYKAVEKLGGYEL------------------------------------ 48

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 977376791 141 tpppggarrprphevplqVTGRRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYV 197
Cdd:cd16884   49 ------------------VTARRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYV 87

ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791   61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYElqsmalgerigwpllepqsscqtavlrvparaagaar 140
Cdd:pfam01388   5 FLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYD------------------------------------- 47

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 977376791  141 tpppggarrprphevplQVTGRRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPY 196
Cdd:pfam01388  48 -----------------KVTEKNLWREVAEKLGFPPSAASAATQLKQIYEKYLLPY 86

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) and similar proteins; ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also associates with thyroid receptor alpha (TR alpha) and retinoid X receptor alpha (RXR alpha) in a ligand-dependent manner, and with ER beta, androgen receptor (AR), and the retinoic acid receptor (RAR) in a ligand-independent manner. ARID5A functions as a negative regulator of RORgamma-induced Th17 cell differentiation and may be involved in the pathogenesis of rheumatoid arthritis (RA). Moreover, it is an important transcriptional partner of the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) in stimulation of chondrocyte-specific transcription. Meanwhile, ARID5A plays an important role in promotion of inflammatory processes and autoimmune diseases. It works as a unique RNA binding protein, which stabilizes interleukin-6 (IL-6) but not tumor necrosis factor-alpha (TNF-alpha) mRNA through binding to the 3' untranslated region (UTR) of IL-6 mRNA, and inhibits the destabilizing effect of regnase-1 on IL-6 mRNA. ARID5A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYELqsmalgerigwpllepqsscqtavlrvparaagaar 140
Cdd:cd16884    5 FLVNLYKFMKERNTPIERIPHLGFKQINLWKIYKAVEKLGGYEL------------------------------------ 48

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 977376791 141 tpppggarrprphevplqVTGRRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYV 197
Cdd:cd16884   49 ------------------VTARRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYV 87

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins; ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex, which is a signal-sensing modulator of histone methylation and gene transcription. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Its polymorphism has been associated with risk for pediatric acute lymphoblastic leukemia (ALL). ARID5B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which can bind both the major and minor grooves of its target sequences.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYELqsmalgerigwpllepqsscqtavlrvparaagaar 140
Cdd:cd16885    5 FLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYET------------------------------------ 48

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 977376791 141 tpppggarrprphevplqVTGRRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYVRHLKGEDD 205
Cdd:cd16885   49 ------------------ITARRQWKHIYDELGGNPGSTSAATCTRRHYERLILPYERFIKGEED 95

ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791    61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYElqsmalgerigwpllepqsscqtavlrvparaagaar 140
Cdd:smart01014   6 FLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFD------------------------------------- 48

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 977376791   141 tpppggarrprphevplQVTGRRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPY 196
Cdd:smart01014  49 -----------------KVTKKKKWKQVARELGIPPSATSAGTSLRKHYEKYLLPY 87

ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of transcription factors, found in a broad array of organisms from fungi to mammals, is characterized by a highly conserved, helix-turn-helix DNA binding domain that binds to the major groove of DNA. The ARID domain, also called BRIGHT, was first identified in the mouse B-cell-specific transcription factor Bright and in the product of the dead ringer (dri) gene of Drosophila melanogaster. ARID family members are implicated in normal development, differentiation, cell cycle regulation, transcriptional activation and chromatin remodeling. Different family members exhibit different DNA-binding properties. Drosophila Dri, mammalian ARID3A/3B/3C and ARID5A/5B, selectively bind AT-rich sites. However, ARID1A/1B, Drosophila Osa, yeast SWI1, ARID2, ARID4A/4B, JARID1A/1B/1C/1D, and JARID2, bind DNA without sequence specificity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYElqsmalgerigwpllepqsscqtavlrvparaagaar 140
Cdd:cd16100    5 FLEQLRAFLESRGTPLLKPPTIGGKPLDLYKLYRAVVSRGGYE------------------------------------- 47

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 977376791 141 tpppggarrprphevplQVTGRRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPY 196
Cdd:cd16100   48 -----------------KVTEKKLWKEVARKLGLPTSSTSAAQALKRIYEKYLLPF 86

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1, or RBBP1L1), is a tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating cell cycle. ARID4B contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYE-LQSMALGERI----GWPLL 118
Cdd:cd16883    5 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDnIESGAVWKQVyqdlGIPVL 67

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1, or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B (also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities. It is also involved in the pocket domain of pRb-mediated repression of E2F-dependent transcription and cellular proliferation. Moreover, it acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYKAVEKLGAYE-LQSMALGERI----GWPLLEPQSS 123
Cdd:cd16882    5 FLQQLYKFMEDRGTPINKPPVLGYKDLNLFKLFRLVYQQGGCDnIESGSVWKQIymdlGIPILNSAAS 72

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  132 PARAAGAARTPPPGGARRPRPHEVPLQVTGRRLWKNVYDELGGSPGSTSAATctRRHYERLVLPYVRHLKGEDDKPLPTS 211
Cdd:PHA03247 2629 PSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPP--QRPRRRAARPTVGSLTSLADPPPPPP 2706

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  212 KPRKQYKMAKENRGDDGATERPKKAKEERRMDQMMPGKTKADAADPAPLPSQEPPRNSTeqqglASGSSVSFVGASGCPE 291
Cdd:PHA03247 2707 TPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAG-----PPAPAPPAAPAAGPPR 2781

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 977376791  292 AYKRLLSSFYCKGTHGIMSPLAKKKLLAQVSKVEAlqcQEEGCRHGAEPQASPAVHLPESPQSPKGLTENSrhrlTPQEG 371
Cdd:PHA03247 2782 RLTRPAVASLSESRESLPSPWDPADPPAAVLAPAA---ALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPS----LPLGG 2854

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 977376791  372 LQAPGGSLREEAQAGPCPAAPIFKgcfyTHPtevlkPVSQHPRDFFSRLKDGVLLGPPGKEGLSVKEPQ 440
Cdd:PHA03247 2855 SVAPGGDVRRRPPSRSPAAKPAAP----ARP-----PVRRLARPAVSRSTESFALPPDQPERPPQPQAP 2914

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ARID3B, ARID3C, dead ringer (Dri) from Drosophila melanogaster, and similar proteins; The ARID3 subfamily includes AT-rich interactive domain (ARID, also known as BRIGHT)-containing proteins ARID3A, ARID3B and ARID3C, which are the most direct mammalian counterparts of the Drosophila "dead ringer" protein Dri. They consist of an acidic N-terminal region of unknown function, the central ARID matrix association (or attachment) region (MAR)-DNA binding domain, a SUMO-I conjugation (SUMO) motif, and a multifunctional homomerization/nuclear export REKLES domain in the C-terminal third of the molecule. The ARID domain in this subfamily has been described as the "extended" or e-ARID due to additional conserved sequences at both the N and C termini of the core ARID region. The REKLES domain is found only in the ARID3 subfamily. It has co-evolved with and regulates functional properties of the ARID DNA-binding domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 977376791  61 FLVSLYKFMKERHTPIERVPHLGFKQINLWKIYK-AVEKLGAYEL 104
Cdd:cd16867   16 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYRlVVEKGGLVEV 60