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 15222957  40 DSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLN 119
Cdd:cd16872   1 DPDLFWETLRKFHESLGTKFRIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLS 80

                ....*.
gi 15222957 120 LLFHYE 125
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 15222957  40 DSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLN 119
Cdd:cd16872   1 DPDLFWETLRKFHESLGTKFRIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLS 80

                ....*.
gi 15222957 120 LLFHYE 125
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 15222957     39 KDSSVFWDTLRRFHSIM-STKFMIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHY 117
Cdd:smart00501   1 RERVLFLDRLYKFMEERgSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY 80

                           90
                   ....*....|.
gi 15222957    118 LNLLFHYEQVH 128
Cdd:smart00501  81 ERYLLPYERFL 91

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15222957   255 PKPNRSGYNFFFAEKHCKLKSLYPN-KEREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEY 321
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGlKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68

high mobility group protein; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15222957  250 EDPNYPKPNRSGYNFFFAEKHCKLKSLYPNKEREFT---KLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRE 323
Cdd:PTZ00199  18 KDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAavgKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

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 15222957  40 DSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLN 119
Cdd:cd16872   1 DPDLFWETLRKFHESLGTKFRIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLS 80

                ....*.
gi 15222957 120 LLFHYE 125
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 15222957     39 KDSSVFWDTLRRFHSIM-STKFMIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHY 117
Cdd:smart00501   1 RERVLFLDRLYKFMEERgSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY 80

                           90
                   ....*....|.
gi 15222957    118 LNLLFHYEQVH 128
Cdd:smart00501  81 ERYLLPYERFL 91

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 15222957     44 FWDTLRRFHSIMSTKF-MIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLF 122
Cdd:smart01014   6 FLDRLRKFMEKRGTPLdKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATSAGTSLRKHYEKYLL 85

                   ...
gi 15222957    123 HYE 125
Cdd:smart01014  86 PYE 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 15222957  44 FWDTLRRFHSIMSTKFM-IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLF 122
Cdd:cd16866   5 FLNELRQFHASRGTPFKkIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFALKQIYLRYLE 84

                ...
gi 15222957 123 HYE 125
Cdd:cd16866  85 AYE 87

ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins; This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15222957  44 FWDTLRRFHSIMSTKF-MIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSaTTTSASFVLRKHYLNLLF 122
Cdd:cd16865   6 FLDRLLRFMEERGSPItNCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIG-ASSSAAFTLRKNYIKYLL 84

                ...
gi 15222957 123 HYE 125
Cdd:cd16865  85 AYE 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15222957 251 DPNYPKPNRSGYNFFFAEKHCKLKSLYPNKE-REFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEY 321
Cdd:cd01390  10 DPNAPKRGLSAYMFFSQDNREKVKEENPDATfGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAAY 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 15222957 251 DPNYPKPNRSGYNFFFAEKHCKLKSLY--PNKE---REFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEY 321
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 15222957  44 FWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFsATTTSASFVLRKHYLNLLFH 123
Cdd:cd16864   7 FLDQIAKFWELQGSSLKIPNVERKALDLFTLHKIVQEEGGFEEVTKERKWSKVARRLGY-PPGKGVGSLLRGHYERILYP 85

                ..
gi 15222957 124 YE 125
Cdd:cd16864  86 YD 87

high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins; SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, 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. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15222957 250 EDPNYPKPNRSGYNFFFAEKHCKLKSLYPNKE-REFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRET 324
Cdd:cd22013   4 KDPNAPKRALSGFMFFSLMERENLKKEKPGISfGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGYKNG 79

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15222957 259 RSGYNFFFAEKHCKLKSLYPN-KEREFTKLIGESWSNLSTEERMVYQDIGLKDKERY 314
Cdd:cd00084   3 LSAYLLFSKEKRPKLKKENPDlSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15222957 251 DPNYPKPNRSGYNFFFAEKHCKLKSLYPN-KEREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRETL 325
Cdd:COG5648  67 DPNGPKRPLSAYFLYSAENRDEIRKENPKlTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKL 142

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15222957  61 IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYE 125
Cdd:cd16878  44 IPIMAKQVLDLYMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLYPYE 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15222957  61 IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYE 125
Cdd:cd16880  37 IPIMAKQVLDLYTLYRLVTDKGGLVEVINKKIWREITKGLSLPTSITSAAFTLRTQYMKYLYPYE 101

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        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15222957  50 RFHSIMSTKFM----IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFsATTTSASFVLRKHYLNLLFHYE 125
Cdd:cd16876   9 RYLAFTEEKAMgmtnLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNV-GTSSSAASSLKKQYIQCLYAFE 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 15222957 255 PKPNRSGYNFFFAEKHCKLKSLYPNKE-REFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRET 324
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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15222957  61 IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRF-SATTTSASFVLRKHYLNLLFHYEQ 126
Cdd:cd16871  24 QPVIGGRPVNLFRLYQLVQKLGGSRQVTQNNQWPRVAQKLGFpPEQNPQVAQQLAQIYQRYLLPYEE 90

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15222957 255 PKPNRSGYNFFFAEKHCKLKSLYPNKER-EFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEY 321
Cdd:cd22007   1 PKRPQSAYFLYANDRRAALKEENKNVKItEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEMEEY 68

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15222957 255 PKPNRSGYNFFFAEKHCKLKSLYPnkeREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRE 323
Cdd:cd21987  21 PKRPRSAFNIFVSEHFQEAKGDSP---QEKLKTLKEEWKNLSSSQKQLYIQLAEDDKIRYENEMKSWEE 86

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; 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. Ixr1 contains two HMG-box domains. This model corresponds to the first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15222957 255 PKPNRSGYNFFFAEKHCKLKSLYPNKER--EFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRETL 325
Cdd:cd22011   1 PKRPSSAYFLFSQEIRKNLKSQGSPEEKvpELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKEL 73

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 15222957 253 NYPKPNRSGYNFFFAEKHCKLKSLYPNKE-REFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYR 322
Cdd:cd21979   1 NAPKRPPSAFFLFCSEHRPKIKGEHPGLSiGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15222957  61 IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYE 125
Cdd:cd16884  23 IPHLGFKQINLWKIYKAVEKLGGYELVTARRLWKNVYDELGGSPGSTSAATCTRRHYERLVLPYV 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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15222957  61 IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYEQ 126
Cdd:cd16885  23 IPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERLILPYER 88

first 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 first one. This model also includes the first HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15222957 252 PNYPKPNRSGYNFFFAEKHCKLKSLYPN-KEREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRE 323
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEmSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFRE 73

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15222957 259 RSGYNFFFAEKHCKLKSLYPNKE-REFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYR 322
Cdd:cd21994   3 MSAYMLWLNENREKIKKENPGISvTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67

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 15222957  44 FWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREVGGVFRFSATTTSASFvLRKHYLNLLFH 123
Cdd:cd16874  10 FLDQIAKFWELQGCTLKIPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMGFAPGKAVGSH-IRAHYERILYP 88

                .
gi 15222957 124 Y 124
Cdd:cd16874  89 Y 89

sixth 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 sixth one. This model also includes the second HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15222957 256 KPNRSGYNFFFAE--KHCKLKSLyPNKERefTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYRETL 325
Cdd:cd22003   5 KPPMSGYQLFSQEmlKNGELVHL-SLKER--MVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSL 73

fifth 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 fifth one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15222957 277 YPNKEREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYR 322
Cdd:cd22002  25 FKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYERELSEMR 70

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 15222957 265 FFAEKHCKLKSLYPN-KEREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNEYR 322
Cdd:cd01389  11 FRKEKHKQLRAQNPGlTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDYK 69

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.

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 15222957  61 IPVIGGKELDLHVLYVEVTRRGGYEKVVVEKKWREV 96
Cdd:cd16870  26 PPLIGGCELDLPRLYHLVQELGGMQQVTDKKKWNKV 61

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15222957 254 YPKPNRSGYNFFFAEKHCKLKSLYPN-KEREFTKLIGESWSNLSTEERMVYqdiglkdKERYQRELNEYRE 323
Cdd:cd22001   2 KPKRPISAMFIYSKEKRSKLKKKHPElSEQELTRLLAKKYNELPDKKKAKY-------KKKEALAKAEYEK 65

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 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 contain only one HMG-box domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15222957 260 SGYNFFFAEKHCKLKSLYPNKE-REFTKLIGESWSNLSTEERMVYQDIGLKDKERY 314
Cdd:cd22005   5 TAFFLFLADFRKTYKKKNPDKSvKAVGKAAGEKWKSMSDEEKAPYVEKAEKEKAEY 60