high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462565295  527 MKKKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQHNR 590
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEE 64

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 496 LLAAEKKATKGQVARapvkpkEKKKGPcppQMKKKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERR 575
Cdd:COG5648    48 LLTKPRKKTKSKRLV------RKKKDP---NGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKE 118

                  ....*...
gi 2462565295 576 PYCTKARR 583
Cdd:COG5648   119 PYYKEANS 126

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 2462565295 530 KCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462565295 518 KKKGPCPPqmkKKCVNGFIMFCRMNR----KQYIRSCPGTASTAATKELAQLWRVMTQQERRPY 577
Cdd:cd22016     1 KEKDPNAP---KRPANAFFLFCQEQRekvrEEYKEEHQEIDHHDLTKALAQAWRNLDAEDKKPY 61

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        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462565295 529 KKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQHNR 590
Cdd:cd22004     3 KRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKK 64

high mobility group (HMG)-box found in group D SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxD transcription factors includes three members, Sox5, Sox6, and Sox13. They function as important transcriptional regulators of glial development in the central nervous system. SoxD proteins influence multiple stages of oligodendrocyte development and modulate SoxE protein function. This subfamily also contains SoxD transcription factor homolog EGL-13, which specifies distinct O2 and CO2 sensory neuron fates in Caenorhabditis elegans. SOX-5 plays important roles in various cancer types. It binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-6 plays a key role in cell proliferation, differentiation, and cell fate determination, as well as neurogenesis and skeleton formation. It is a tumor suppressor and downregulated in various cancers. SOX-6 binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-13, also called Islet cell antigen 12 (ICA12), or type 1 diabetes auto-antigen ICA12, modulates T cell specification and is an autoimmune antigen. It binds to the sequence 5'-AACAAT-3'.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 529 KKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd22030     3 KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKSMSNQEKQPYYEEQARLSKQH 62

high mobility group (HMG)-box found in Caenorhabditis elegans protein egg laying defective 13 (EGL-13) and similar proteins; EGL-13 may act as a transcription factor that is required for uterine cell fate decisions in Caenorhabditis elegans. It controls genes required for the specification and differentiation of O(2) and CO(2)-sensing neurons and for maintaining URX sensory neuronal cell fate.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 529 KKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd22042     4 KRPMNAFMVWAKDERRKILKACPDMHNSNISKILGAKWKAMSNAEKQPYYEEQSRLSKLH 63

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 496 LLAAEKKATKGQVARapvkpkEKKKGPcppQMKKKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERR 575
Cdd:COG5648    48 LLTKPRKKTKSKRLV------RKKKDP---NGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKE 118

                  ....*...
gi 2462565295 576 PYCTKARR 583
Cdd:COG5648   119 PYYKEANS 126

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 2462565295 533 NGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd01389     6 NAFILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEH 61

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462565295 516 KEKKKGPCPPqmkKKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKA 581
Cdd:cd22008     1 KNKNVDPNKP---KKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKA 63

high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar proteins; SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 529 KKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd22034     6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and similar proteins; SOX-30 is a crucial transcription factor that controls the transition from a late meiotic to a post-meiotic gene expression program and subsequent round spermatid development. It specially prevents Wnt-signaling to suppress metastasis. SOX-30 binds to the DNA sequence 5'-ACAAT-3' and shows a preference for guanine residues surrounding this core motif. SOX-30 is the only member of the group H of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 529 KKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd22033     3 KRPMNAFMVWARIHRPALAKANPNANNADISVQLGEEWNKLTEEQKKPYYDEAQKLKEQH 62

high mobility group (HMG)-box found in group C SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxC transcription factors includes three members: SOX4, SOX11 and SOX12. They play key roles, often in redundancy, in multiple developmental pathways, including neurogenesis and skeletogenesis. SOX-4 is a transcriptional activator that promotes neuronal differentiation both in the adult and embryonic neural progenitors. It binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif. SOX-4 is abnormally expressed in various cancers. SOX-11 is a neural transcriptional factor involved in precursor survival, neuronal fate determination, migration and morphogenesis. SOX-12, also called SOX-22, is a transcription factor essential for embryonic development and cell fate determination. It binds to the sequence 5'-AACAAT-3'.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 529 KKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd22029     3 KRPMNAFMVWSQIERRKIMEQQPDMHNAEISKRLGKRWKLLSDSEKIPFIEEAERLRLLH 62

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 2462565295 529 KKCVNGFIMFcrMN--RKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKAR 582
Cdd:cd22005     1 KRPPTAFFLF--LAdfRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAE 54

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462565295 533 NGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRF 584
Cdd:cd21989     5 NAFLLFCKRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDLAKQY 56

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar proteins; SOX-7 is an endothelial-associated transcription factor that acts as a tumor suppressor in a number of cancer types. It binds the DNA sequence 5'-AACAAT-3'. SOX-7 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462565295 529 KKCVNGFIMFCRMNRKQYIRSCPGTASTAATKELAQLWRVMTQQERRPYCTKARRFSRQH 588
Cdd:cd22046    13 RRPMNAFMVWAKDERKRLAVQNPDLHNAELSKMLGKSWKALTPSQKRPYVEEAERLRVQH 72