ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins; This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367  69 SPDLFWEKLKAFHQSFETKFMVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLS 148
Cdd:cd16872     1 DPDLFWETLRKFHESLGTKFRIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLS 80

                  ....*.
gi 2082461367 149 LLYHFE 154
Cdd:cd16872    81 LLHHYE 86

ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins; This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367  69 SPDLFWEKLKAFHQSFETKFMVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLS 148
Cdd:cd16872     1 DPDLFWETLRKFHESLGTKFRIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLS 80

                  ....*.
gi 2082461367 149 LLYHFE 154
Cdd:cd16872    81 LLHHYE 86

BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367   71 DLFWEKLKAFHQ-SFETKFMVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSL 149
Cdd:smart00501   4 VLFLDRLYKFMEeRGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERY 83

                           90
                   ....*....|
gi 2082461367  150 LYHFEQVYYF 159
Cdd:smart00501  84 LLPYERFLRG 93

high mobility group;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367  266 RPKSNRSGYNFFFAEHYARLKPLYYG-EEKAISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEYK 334
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDlSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

high mobility group protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367 246 SANPTRRDRKRSRLALRDPSRPKSNRSGYNFFFAEHYARL---KPLYYGEEKAISKKIGLLWSNLTEAEKQVYQEKGLRD 322
Cdd:PTZ00199    2 AKKQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIiaeNPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQED 81

                          90
                  ....*....|.
gi 2082461367 323 KERYRTEMLEY 333
Cdd:PTZ00199   82 KVRYEKEKAEY 92

ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins; This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367  69 SPDLFWEKLKAFHQSFETKFMVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLS 148
Cdd:cd16872     1 DPDLFWETLRKFHESLGTKFRIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLS 80

                  ....*.
gi 2082461367 149 LLYHFE 154
Cdd:cd16872    81 LLHHYE 86

BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367   71 DLFWEKLKAFHQ-SFETKFMVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSL 149
Cdd:smart00501   4 VLFLDRLYKFMEeRGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERY 83

                           90
                   ....*....|
gi 2082461367  150 LYHFEQVYYF 159
Cdd:smart00501  84 LLPYERFLRG 93

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 2082461367   68 QSPDLFWEKLKAFHQSFETKF-MVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYY 146
Cdd:smart01014   1 RERELFLDRLRKFMEKRGTPLdKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATSAGTSLRKHY 80

                   ....*...
gi 2082461367  147 LSLLYHFE 154
Cdd:smart01014  81 EKYLLPYE 88

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins; ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367  73 FWEKLKAFHQSFETKFM-VPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSLLY 151
Cdd:cd16866     5 FLNELRQFHASRGTPFKkIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFALKQIYLRYLE 84

                  ...
gi 2082461367 152 HFE 154
Cdd:cd16866    85 AYE 87

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 2082461367  73 FWEKLKAFHQSFETKF-MVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSLLY 151
Cdd:cd16867    16 FLDDLFSFMQKRGTPVnRIPIMAKQVLDLYELYRLVVEKGGLVEVINKKIWREITKGLNLPSSITSAAFTLRTQYMKYLY 95

                  ...
gi 2082461367 152 HFE 154
Cdd:cd16867    96 PYE 98

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 2082461367  73 FWEkLKAfhqsfeTKFMVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASfVLRKYYLSLLYH 152
Cdd:cd16864    14 FWE-LQG------SSLKIPNVERKALDLFTLHKIVQEEGGFEEVTKERKWSKVARRLGYPPGKGVGS-LLRGHYERILYP 85

                  ..
gi 2082461367 153 FE 154
Cdd:cd16864    86 YD 87

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal proteins NHP6A, NHP6B and similar proteins; This subfamily includes Saccharomyces cerevisiae high-mobility-group proteins NHP6A and its closely related paralog NHP6B. NHP6A and NHP6B seem to be functionally redundant. They are DNA-binding proteins that induce severe bending of DNA and are required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. They augment the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. They may also play essential roles in transcriptional initiation fidelity of some but not all tRNA genes.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367 249 PTRRDRKRsrlalRDPSRPKSNRSGYNFFFAEHYARLK---P-LYYGEekaISKKIGLLWSNLTEAEKQVYQEKGLRDKE 324
Cdd:cd01390     1 KKKKGRKK-----KDPNAPKRGLSAYMFFSQDNREKVKeenPdATFGE---VGKLLGEKWKELSEEEKAPYEEKAAKDKK 72

                  ....*....
gi 2082461367 325 RYRTEMLEY 333
Cdd:cd01390    73 RYEEEKAAY 81

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 2082461367  73 FWEKLKAFHQSFETKF-MVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSLLY 151
Cdd:cd16878    26 FLDDLFSFMQKRGTPVnRIPIMAKQVLDLYMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLY 105

                  ...
gi 2082461367 152 HFE 154
Cdd:cd16878   106 PYE 108

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367  73 FWEKLKAFHQSFETKF-MVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSLLY 151
Cdd:cd16881    23 FLDDLFSFMQKRGTPVnRIPIMAKQVLDLYELYNLVVARGGLVEVINKKLWREITKGLHLPSSITSAAFTLRTQYMKYLY 102

                  ...
gi 2082461367 152 HFE 154
Cdd:cd16881   103 PYE 105

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2082461367  90 VPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTiTSASFVLRKYYLSLLYHFE 154
Cdd:cd16876    24 LPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTS-SSAASSLKKQYIQCLYAFE 87

high mobility group protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367 246 SANPTRRDRKRSRLALRDPSRPKSNRSGYNFFFAEHYARL---KPLYYGEEKAISKKIGLLWSNLTEAEKQVYQEKGLRD 322
Cdd:PTZ00199    2 AKKQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIiaeNPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQED 81

                          90
                  ....*....|.
gi 2082461367 323 KERYRTEMLEY 333
Cdd:PTZ00199   82 KVRYEKEKAEY 92

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2082461367  90 VPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASfVLRKYYLSLLYHFE 154
Cdd:cd16877    24 LPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAAS-SLKKQYIQYLFAFE 87

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367 266 RPKSnrsGYNFFFAEHYARLKPLYYGEEKA-ISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEYK 334
Cdd:cd21994     1 RPMS---AYMLWLNENREKIKKENPGISVTeISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67

second high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and similar proteins; TFA, also called TFAM, mitochondrial transcription factor 1 (TF1), transcription factor 6 (TCF-6), or transcription factor 6-like 2, binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. It is a component of the mitochondrial transcription initiation complex, composed of at least TFB2M, TFAM and POLRMT that is required for basal transcription of mitochondrial DNA. TFA is required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. It can unwind DNA. It bends the mitochondrial light strand promoter DNA into a U-turn shape via its HMG boxes. TFA is required for maintenance of normal levels of mitochondrial DNA and may play a role in organizing and compacting mitochondrial DNA. TFA contains two HMG-box domains. This model corresponds to the second one.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367 250 TRRDRKRSRLALRDPSRPKSNRSGYNFFFAEHYARLKPLYYgeeKAISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTE 329
Cdd:cd21987     4 AKRKAMRKKKELTLLGKPKRPRSAFNIFVSEHFQEAKGDSP---QEKLKTLKEEWKNLSSSQKQLYIQLAEDDKIRYENE 80

                  .
gi 2082461367 330 M 330
Cdd:cd21987    81 M 81

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 2082461367 262 RDPSRPKSNRSGYNFFFAEHYARLKPLYYGEEKAIS-----KKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEY 333
Cdd:cd22016     3 KDPNAPKRPANAFFLFCQEQREKVREEYKEEHQEIDhhdltKALAQAWRNLDAEDKKPYYELYEKDKERYEKEMEEY 79

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 2082461367  69 SPDLFWEKLKAFHQSFETKF-MVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYL 147
Cdd:cd16869     1 EEQAFLKLLYKFMKDRGTPIeRIPHLGFKQIDLYTFFKLVQKLGGYEQVTAKRLWKHVYDELGGNPSSTSAATCTRRHYE 80

                  ....*..
gi 2082461367 148 SLLYHFE 154
Cdd:cd16869    81 KLLLPYE 87

high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins; HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367 252 RDRKRSRLaLRDPSRPKSNRSGYNFFFAEHYARLKP----LYYGEekaISKKIGLLWSNLTEAEKQVYQEKGLRDKERYR 327
Cdd:cd22017     7 KGRKRKKP-LRDSNAPKAPLTGYVRFMNERREQLRAerpdVPFPE---ITRMLGNEWSKLPAEEKQRYLDEAEKDKERYM 82

                  ....*....
gi 2082461367 328 TEMLEYKSS 336
Cdd:cd22017    83 KELEQYQKT 91

third 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 third one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2082461367 263 DPSRPKSNRSGYNFFFAEHYARLKPLYYGEEKA-ISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEYK 334
Cdd:cd22008     6 DPNKPKKPASSYLLFGKEYRKKLQEERPGANNAtVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKEVEEYN 78

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 2082461367 267 PKSNRSGYNFFFAEHYARLKPLY----YGEekaISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEYKSS 336
Cdd:cd22018     2 PKAPVTGYVRFLNERREQIRTQHpdlpFPE---ITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREYQQS 72

ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C, also called histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, protein SmcX, or protein Xe169, 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, also called histocompatibility Y antigen (H-Y), histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or protein SmcY, 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. Both KDM5C and KDM5D contain 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 two plant homeodomain (PHD) fingers.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2082461367  90 VPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASfVLRKYYLSLLYHFE 154
Cdd:cd16875    24 IPNVERRILDLYSLSKIVQEEGGYEAICKDRRWARVAQRLGYPPGKNIGS-LLRSHYERIIYPYE 87

second 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 second one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2082461367 267 PKSNRSGYNFFFAEHYARLKplyyGEEKA-----ISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEY 333
Cdd:cd22007     1 PKRPQSAYFLYANDRRAALK----EENKNvkiteIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEMEEY 68

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2082461367 294 KAISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEM 330
Cdd:cd21985    30 QDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQK 66

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367  71 DLFWEKLKAFHQSFETKFMVPSV-GGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSL 149
Cdd:cd16882     3 DNFLQQLYKFMEDRGTPINKPPVlGYKDLNLFKLFRLVYQQGGCDNIESGSVWKQIYMDLGIPILNSAASYNVKTAYRKY 82

                  ....*
gi 2082461367 150 LYHFE 154
Cdd:cd16882    83 LYGFE 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2082461367 294 KAISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEYK 334
Cdd:cd22006    28 SEVSKILGAKWKNLSEEEKKPYEEKYKEEKEKYLKVVGEEK 68

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082461367 264 PSRPksnRSGYNFFFAEH---YARLKPLyygeeKAISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEM 330
Cdd:cd22014     1 PKRP---PSPFLLFMEEFrrnEDNGKNL-----VELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2082461367 296 ISKKIGLLWSNLTEAEKQVYQEKGLRDKERYRTEMLEYK 334
Cdd:cd22004    32 ISKILGKEWKKLTEEEKRPYVEEAERLREEHKKEYPDYK 70

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called cancer/testis antigen 31 (CT31), histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It 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. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible earlygene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B 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 2082461367  73 FWEKLKAFHQSFETKFMVPSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFvLRKYYLSLLYH 152
Cdd:cd16874    10 FLDQIAKFWELQGCTLKIPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMGFAPGKAVGSH-IRAHYERILYP 88

                  .
gi 2082461367 153 F 153
Cdd:cd16874    89 Y 89

high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins; This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2082461367 277 FFAEHYARLKPLYYG-EEKAISKKIGLLWSNLTEAEKQVYQEKGLRDKER 325
Cdd:cd01389    11 FRKEKHKQLRAQNPGlTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEE 60

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 2082461367  91 PSVGGKPLDLHHLFVEVTSQGGLEKVIRDRKWKEVVLAFSFPTTITSASFVLRKYYLSLLYHFEQ 155
Cdd:cd16883    24 PVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYRKYLYGFEE 88