high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily have only one HMG-box domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1027096698 263 PKPNRSGYNFYFAEKHYKLKSLYPNREREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEY 329
Cdd:cd22009     1 PKPNRSGYNFFFAEQHARLKALYPGKDREISKMIGEMWSNLTEEEKEVYQDKGVEDKERYKREMEEY 67

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily have only one HMG-box domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1027096698 263 PKPNRSGYNFYFAEKHYKLKSLYPNREREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEY 329
Cdd:cd22009     1 PKPNRSGYNFFFAEQHARLKALYPGKDREISKMIGEMWSNLTEEEKEVYQDKGVEDKERYKREMEEY 67

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 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFEKvrlsipsfpkyqvffqVVAEKKWREVGAIFMFSPTT 113
Cdd:pfam01388   5 FLKSLRKFHEKRGTPLkQIPVIGGKPVDLYKLYKAVQKLGGYDK----------------VTEKNLWREVAEKLGFPPSA 68

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:pfam01388  69 ASAATQLKQIYEKYLLPYE 87

high mobility group protein; Provisional

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1027096698 259 DPNYPKPNRSGYNFYFAEKHYKLKSLYPNREREFT---KMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYKE 331
Cdd:PTZ00199   19 DPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAavgKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698 258 GDPNYPKPNRSGYNFYFAEKHYKLKSLYPN-REREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYKESMKLG 336
Cdd:COG5648    66 KDPNGPKRPLSAYFLYSAENRDEIRKENPKlTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNK 145

                          90
                  ....*....|...
gi 1027096698 337 SQAD--LGNEQKL 347
Cdd:COG5648   146 APIGpfIENEPKI 158

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily have only one HMG-box domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1027096698 263 PKPNRSGYNFYFAEKHYKLKSLYPNREREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEY 329
Cdd:cd22009     1 PKPNRSGYNFFFAEQHARLKALYPGKDREISKMIGEMWSNLTEEEKEVYQDKGVEDKERYKREMEEY 67

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 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFEKvrlsipsfpkyqvffqVVAEKKWREVGAIFMFSPTT 113
Cdd:pfam01388   5 FLKSLRKFHEKRGTPLkQIPVIGGKPVDLYKLYKAVQKLGGYDK----------------VTEKNLWREVAEKLGFPPSA 68

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:pfam01388  69 ASAATQLKQIYEKYLLPYE 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 1027096698  35 FWDTLRRFHLKMNTKFM-IPVIGGKELDLHILYVEVTRRGGFEKvrlsipsfpkyqvffqVVAEKKWREVGAIFMFSPTT 113
Cdd:cd16100     5 FLEQLRAFLESRGTPLLkPPTIGGKPLDLYKLYRAVVSRGGYEK----------------VTEKKLWKEVARKLGLPTSS 68

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:cd16100    69 TSAAQALKRIYEKYLLPFE 87

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1027096698 263 PKPNRSGYNFYFAEKHYKLKSLYPNRE-REFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYKES 332
Cdd:cd21980     2 PKAPLTGYVRFLNERREKLRAENPDLSfPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAYQQT 72

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1027096698  263 PKPNRSGYNFYFAEKHYKLKSLYPN-REREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYK 330
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDlSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1027096698 263 PKPNRSGYNFYFAEKHYKLKSLYPN-REREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEY 329
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGlKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ARID5B, and similar proteins; This subfamily contains ARID5A and its paralog ARID5B. 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 plays an important role in the promotion of inflammatory processes and autoimmune diseases. 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. 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. Both ARID5A and ARID5B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  31 DPVVFWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFEkvrlsipsfpkyqvffQVVAEKKWREVGAIFMF 109
Cdd:cd16869     1 EEQAFLKLLYKFMKDRGTPIeRIPHLGFKQIDLYTFFKLVQKLGGYE----------------QVTAKRLWKHVYDELGG 64

                          90       100
                  ....*....|....*....|...
gi 1027096698 110 SPTTTSASFVLRKHYSTLLYHYE 132
Cdd:cd16869    65 NPSSTSAATCTRRHYEKLLLPYE 87

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698 258 GDPNYPKPNRSGYNFYFAEKHYKLKSLYPN-REREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYKESMKLG 336
Cdd:COG5648    66 KDPNGPKRPLSAYFLYSAENRDEIRKENPKlTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNK 145

                          90
                  ....*....|...
gi 1027096698 337 SQAD--LGNEQKL 347
Cdd:COG5648   146 APIGpfIENEPKI 158

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) and similar proteins; NHP10, also called high mobility group protein 2, is probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1027096698 259 DPNYPKPNRSGYNFYFAEKHYKLKSLY-----PNREREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEY 329
Cdd:cd22016     4 DPNAPKRPANAFFLFCQEQREKVREEYkeehqEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKERYEKEMEEY 79

ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein family includes lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members of this subfamily contain the catalytic JmjC domain, JmjN, the AT-rich domain interacting domain (ARID)/BRIGHT domain, a C5HC2 zinc finger, as well as two or three plant homeodomain (PHD) fingers.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKFMIPVIGGKELDLHILYVEVTRRGGFEKvrlsipsfpkyqvffqVVAEKKWREVgAIFMFSPTTT 114
Cdd:cd16864     7 FLDQIAKFWELQGSSLKIPNVERKALDLFTLHKIVQEEGGFEE----------------VTKERKWSKV-ARRLGYPPGK 69

                          90
                  ....*....|....*...
gi 1027096698 115 SASFVLRKHYSTLLYHYE 132
Cdd:cd16864    70 GVGSLLRGHYERILYPYD 87

high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar proteins; HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2 (HMGXB2), HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1027096698 263 PKPNRSGYNFYFAEKHYKLKSLYPNRE-REFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYKES 332
Cdd:cd22018     2 PKAPVTGYVRFLNERREQIRTQHPDLPfPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREYQQS 72

ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and similar proteins; Saccharomyces cerevisiae Swi1p, also called SWI/SNF chromatin-remodeling complex subunit SWI1, regulatory protein GAM3, or transcription regulatory protein ADR6, is a transcription regulatory protein that is a subunit of the SWI/SNF complex, which plays critical roles in the regulation of gene transcription and expression. It can exist as a prion, [SWI(+)], which demonstrates a link between prionogenesis and global transcriptional regulation. Swi1p contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT) that binds DNA nonspecifically. This subfamily also includes Schizosaccharomyces pombe SWI/SNF chromatin-remodeling complex subunit sol1 (sol1p, also known as switch one-like protein). sol1p is a homolog of S. cerevisiae Swi1p and is also a part of SWI/SNF chromatin-remodeling complex.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFEkvrlsipsfpkyqvffQVVAEKKWREVGAIFMFSP-T 112
Cdd:cd16871     6 FMKSLREFMAKRGTPIeQQPVIGGRPVNLFRLYQLVQKLGGSR----------------QVTQNNQWPRVAQKLGFPPeQ 69

                          90       100
                  ....*....|....*....|.
gi 1027096698 113 TTSASFVLRKHYSTLLYHYEQ 133
Cdd:cd16871    70 NPQVAQQLAQIYQRYLLPYEE 90

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) and similar proteins; ARID3A, also called B-cell regulator of IgH transcription (Bright), dead ringer-like protein 1 (Dril1), or E2F-binding protein 1 (E2FBP1), is an ubiquitously expressed DNA-binding protein that has been implicated in embryonic patterning, cell lineage gene regulation, and cell cycle control, chromatin remodeling and transcriptional regulation. It was originally identified as a B cell-specific trans-activator of immunoglobulin heavy-chain (IgH) transcription, which increases immunoglobulin transcription in antigen-activated B cells and plays regulatory roles in hematopoiesis. It also functions as an E2F transcription regulator, inducing promyelocytic leukemia protein (PML) reduction and suppressing the formation of PML-nuclear bodies. It antagonizes the p16(INK4A)-Rb tumor suppressor machinery by regulating PML stability. ARID3A transcriptional activity can be modulated by SUMO (Small Ubiquitin-related Modifier) modification through the interaction with the SUMO-conjugating enzyme Ubc9. ARID3A also plays an important role in marginal zone B lymphocyte development and autoantibody production. Furthermore, ARID3A is a direct p53 target gene. It controls cell growth in a p53-dependent manner. ARID3A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFekvrlsipsfpkyqvfFQVVAEKKWREVGAIFMFSPTT 113
Cdd:cd16878    26 FLDDLFSFMQKRGTPVnRIPIMAKQVLDLYMLYVLVTEKGGL----------------VEVINKKLWREITKGLNLPTSI 89

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:cd16878    90 TSAAFTLRTQYMKYLYPYE 108

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) and similar proteins; ARID3C, also called Brightlike, is a new ARID3 family transcription factor that co-activates ARID3A-mediated immunoglobulin gene transcription. It also functions as a potential regulator of early events in B cell antigen receptor (BCR) signaling. ARID3C contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFekvrlsipsfpkyqvfFQVVAEKKWREVGAIFMFSPTT 113
Cdd:cd16880    19 FLDDLFSFMQKRGTPVnRIPIMAKQVLDLYTLYRLVTDKGGL----------------VEVINKKIWREITKGLSLPTSI 82

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:cd16880    83 TSAAFTLRTQYMKYLYPYE 101

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFekvrlsipsfpkyqvfFQVVAEKKWREVGAIFMFSPTT 113
Cdd:cd16867    16 FLDDLFSFMQKRGTPVnRIPIMAKQVLDLYELYRLVVEKGGL----------------VEVINKKIWREITKGLNLPSSI 79

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:cd16867    80 TSAAFTLRTQYMKYLYPYE 98

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner; its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKFMIPVIGGKELDLHILYVEVTRRGGFEkvrlsipsfpkyqvffQVVAEKKWREVGAIFMFSPTTT 114
Cdd:cd16873     7 FLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASEGGFE----------------MVTKEKKWSKVGSRMGYLPGKG 70

                          90
                  ....*....|....*...
gi 1027096698 115 SASfVLRKHYSTLLYHYE 132
Cdd:cd16873    71 TGS-LLKSHYERILYPYE 87

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1027096698 261 NYPKPNRSGYnFYFAEKHY-KLKSLYPNRE-REFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYK 330
Cdd:cd21979     1 NAPKRPPSAF-FLFCSEHRpKIKGEHPGLSiGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins; ARID1A, also called B120, BRG1-associated factor 250a (BAF250A), Osa homolog 1(OSA1), SWI-like protein, SWI/SNF complex protein p270, or SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 (SWI1), has been identified as a novel tumor suppressor in various tumor types. It interacts with BRG1 adenosine triphosphatase to form a SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complex, which plays a critical role in transcriptional control and gene expression. ARID1A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and Eld/Osa homology domains (EHD) 1 and 2 within the C-terminus. The ARID in ARID1A binds nonspecific DNA in general and plays an important role in targeting SWI/SNF to chromatin. The EHD1 may be capable of mediating an intramolecular association with EHD2, and/or an intermolecular association resulting in homo- or hetero-dimerization. The EHD2 binds Swi2/Brahma homologue Brahma-related gene 1 (BRG1, also known as Snf2b), a human homologue of yeast Swi2.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  52 IPVIGGKELDLHILYVEVTRRGGFEkvrlsipsfpkyqvffQVVAEKKWREVGAIFMFSpTTTSASFVLRKHYSTLLYHY 131
Cdd:cd16876    24 LPAVGRKPLDLYRLYVSVKEIGGLT----------------QVNKNKKWRELATNLNVG-TSSSAASSLKKQYIQCLYAF 86

                  .
gi 1027096698 132 E 132
Cdd:cd16876    87 E 87

ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar proteins; Dri, also termed retained (retn), is a nuclear protein with a sequence-specific DNA-binding domain termed AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is a founding member of the ARID family. Sequence comparison shows that DRI belongs to the "extended" or e-ARID subfamily, which exhibits an extended region of similarity either side of the ARID. Dri plays an important role in embryogenesis. It functions as an essential transcription factor involved in aspects of dorsal/ventral and anterior/posterior axis patterning, as well as myogenesis and hindgut development.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFekvrlsipsfpkyqvfFQVVAEKKWREVGAIFMFSPTT 113
Cdd:cd16881    23 FLDDLFSFMQKRGTPVnRIPIMAKQVLDLYELYNLVVARGGL----------------VEVINKKLWREITKGLHLPSSI 86

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:cd16881    87 TSAAFTLRTQYMKYLYPYE 105

second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698 263 PKPNRSGYNFYFAEKHYKLKSLYPNRE-REFTKMIGESWSNLTAEERLVYQniglqdkERYKKELKEYKE 331
Cdd:cd22012     2 PKRPASAYFLFAKEVRPKLKEENPNEKyTDITKLISEKWRSLDESEKEPYQ-------EEYEKALEEYEE 64

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins; ARID1B, also called BRG1-associated factor 250b (BAF250B), BRG1-binding protein ELD/OSA1, Osa homolog 2 (Osa2), or p250R, is the largest subunit of ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a critical role in transcriptional control and gene expression. ARID1B exhibits tumour-suppressor activities in pancreatic cancer cell lines. Mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Moreover, mutations in the ARID1B gene have been found in many cancers. ARID1B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner similar to ARID1A.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  52 IPVIGGKELDLHILYVEVTRRGGFEkvrlsipsfpkyqvffQVVAEKKWREVgAIFMFSPTTTSASFVLRKHYSTLLYHY 131
Cdd:cd16877    24 LPAVGKKPLDLFRLYVCVKEIGGLA----------------QVNKNKKWREL-ATNLNVGTSSSAASSLKKQYIQYLFAF 86

                  .
gi 1027096698 132 E 132
Cdd:cd16877    87 E 87

first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1027096698 264 KPnRSGYNFYFAEKHYKLKSLYPNRE-REFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYK 330
Cdd:cd22006     2 KP-KTAYFLWCKDQREEVKKENPNADfSEVSKILGAKWKNLSEEEKKPYEEKYKEEKEKYLKVVGEEK 68

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).

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027096698  35 FWDTLRRFHLKMNTKF-MIPVIGGKELDLHILYVEVTRRGGFEkvrlsipsfpkyqvffQVVAEKKWREVGAIFMFSPTT 113
Cdd:cd16884     5 FLVNLYKFMKERNTPIeRIPHLGFKQINLWKIYKAVEKLGGYE----------------LVTARRLWKNVYDELGGSPGS 68

                          90
                  ....*....|....*....
gi 1027096698 114 TSASFVLRKHYSTLLYHYE 132
Cdd:cd16884    69 TSAATCTRRHYERLVLPYV 87

high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar proteins; HBP2, also called HMG box transcription factor BBX, or Bobby sox homolog, is a transcription factor that is necessary for cell cycle progression from the G1 to S phase.

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                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1027096698 274 FAEKHYKL-KSLYPNRE-REFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYK 330
Cdd:cd21989    10 FCKRHRSLvRERHPRLDnRGITKILGDWWAVLDPDEKQKYTDLAKQYKEAFMKANPNFK 68

high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins; SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain.

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                  ....*....|....*....|....*....|....*....|
gi 1027096698 291 EFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKELKEYK 330
Cdd:cd21983    34 EIGKIIGQMWRELSDEEKQEYIEEYEAEKVEYEEQMKAYH 73

high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 and similar proteins; Cmb1 binds to cytosines in base mismatches and opposite chemically altered guanines. It contains only one HMG-box domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1027096698 263 PKPNRSGYNFYFAEkhykLKSLYPNRER--EFTKMIGESWSNLTAEERLVYQniglqdkERYKKELKEYKESM 333
Cdd:cd22014     1 PKRPPSPFLLFMEE----FRRNEDNGKNlvELSRIAAEAWKNMSEDEKQPYI-------DRAKELLEEYKKQL 62

ARID/BRIGHT DNA binding domain of Jumonji/ARID domain-containing protein 2 (JARID2) and similar proteins; JARID2, also called protein Jumonji, is a DNA-binding protein that contains both the Jumonji C (JmjC) domain and AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is an interacting component of Polycomb repressive complex-2 (PRC2) that catalyzes methylation of lysine 27 of histone H3 (H3K27) and regulates important gene expression patterns during development. It exhibits nucleosome-binding activity that contributes to PRC2 stimulation. However, unlike other JmjC domain-containing proteins, JARID2 is catalytically inactive due to the lack of conserved residues essential for histone demethylase activity. JARID2 is also involved in transforming growth factor-beta (TGF-beta)-induced epithelial-mesenchymal transition (EMT) of lung and colon cancer cell lines through the modulation of histone H3K27 methylation. Moreover, JARID2 is a part of GLP- and G9a-containing protein complex that promotes lysine 9 on histone H3 (H3K9) methylation on the cyclin D1 promoter and silences the expression of cyclin D1 and other cell cycle genes. It functions as a transcriptional repressor that plays critical roles in embryonic development including heart development in mice, and regulates cardiomyocyte proliferation via interaction with retinoblastoma protein (Rb), one of the master regulatory genes of the cell cycle. Furthermore, JARID2 acts as a transcriptional repressor of target genes, including Notch1. It directly binds to SETDB1 (SET domain, bifurcated 1) to form a complex that plays an important role in a novel process involving the modification of H3K9 methylation during heart development. Meanwhile, JARID2 is a key transcriptional repressor that plays a role in invariant natural killer T (iNKT) cell maturation. It regulates promyelocytic leukemia zinc finger (PLZF) expression by linking T-cell receptor (TCR) signaling to H3K9me3. JARID2 polymorphisms are associated with non-syndromic orofacial clefts (NSOC) susceptibility.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1027096698  31 DPVVFWDTLRRfHLKMNTKFM--IPVIGGKELDLHILYVEVTRRGGFEKV-----------RLSIPS 84
Cdd:cd16870     4 PNVQKLACIKK-HLESQGINLtpPPLIGGCELDLPRLYHLVQELGGMQQVtdkkkwnkvadHLNIPK 69

fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1027096698 262 YPKPNRSGYNFYFAEKHYKLKSLYPN-REREFTKMIGESWSNLTAEERLVYQNIGLQDKERYKKE 325
Cdd:cd22001     2 KPKRPISAMFIYSKEKRSKLKKKHPElSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEKK 66