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
                 ....*....|....*....|....*....|....*....|.
gi 1208991285 56 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 96
Cdd:cd22034    1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 41

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
                 ....*....|....*....|....*....|....*....|.
gi 1208991285 56 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 96
Cdd:cd22034    1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 41

high mobility group;

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1208991285  59 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:smart00398  1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLG 37

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
                 ....*....|....*....|....*....|....*....|.
gi 1208991285 56 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 96
Cdd:cd22034    1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 41

high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-1 is involved in the regulation of embryonic development and cell fate determination. It also acts as a tumor suppressor that plays an anti-tumorigenicity role in different cells and its expression is inhibited in a variety of cancers. SOX-2 plays an important role in various phases of embryonic development, including cell fate and differentiation. Its overexpression and gene amplification may be associated with tumor aggression and metastasis in various cancer types, including breast, prostate, lung, ovarian and colon cancer. SOX-3 is required during the formation of the hypothalamic-pituitary axis. It plays a role in both normal neural development and carcinogenesis. SOX-14, also called SOX-28, acts as a negative regulator of transcription. It is mainly involved in the regulation of neural development. It can also promote proliferation and invasion capacity of cervical cancer cells by activating the Wnt/beta-catenin pathway. SOX-21, also called SOX-A, or SOX-25, promotes the progression of vertebrate neurogenesis.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1208991285 58 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd01388    1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 38

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and similar proteins; SOX-15, also called SOX-12, SOX-20, SOX-26, or SOX-27, is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types. SOX-5 is the only member of group G SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1208991285 58 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22035    6 EKVKRPMNAFMVWSSAQRRQMAQEHPKMHNSEISKRLG 43

high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxF transcription factors includes three members: Sox7, Sox17, and Sox18. They regulate endothelial cell fate as well as development and differentiation of the developing heart, blood cells, and lymphatic vessels.

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 1208991285 59 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22032    1 RIRRPMNAFMVWAKDERKRLADENPDLHNAELSKMLG 37

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
                 ....*....|....*....|....*....|....*....
gi 1208991285 57 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22046    9 EPRIRRPMNAFMVWAKDERKRLAVQNPDLHNAELSKMLG 47

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and similar proteins; SOX-17 is a developmental transcription regulator involved in endoderm formation, angiogenesis, and carcinogenesis. It acts as a tumor suppressor and modulates WNT signaling. SOX-17 binds target promoter DNA and bends the DNA. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX-17 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1208991285 54 GNVQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22047    1 GKGESRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLG 42

high mobility group (HMG)-box found in group E SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxE transcription factors includes three members: Sox8, Sox9, and Sox10. They function as important transcriptional regulators of neural differentiation and nervous system development. They regulate mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. SOX-8 is specifically expressed by M cells in the intestinal epithelium. It acts as a transcription factor necessary for the maintenance of spermatogenesis. It may play a role in central nervous system, limb and facial development. SOX-9 is involved in cell differentiation, sex determination, and tumorigenesis. It plays a role in chondrocyte differentiation and skeletal development. SOX-10 plays a central role in the development of melanocytes and glial cells from neural crest precursors.

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 1208991285 59 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22031    1 HVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLG 37

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
                 ....*....|....*....|....*....|....*.
gi 1208991285 60 VKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22030    2 IKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILG 37

high mobility group;

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1208991285  59 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:smart00398  1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLG 37

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 4 (SOX4) and similar proteins; 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-4 belongs to group C SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 1208991285 60 VKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22036    3 IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLG 38

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
                 ....*....|....*....|....*....|....
gi 1208991285 62 RPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLG 34

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
                 ....*....|....*....|....*....|....*
gi 1208991285 61 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22005    1 KRPPTAFFLFLADFRKTYKKKNPDKSVKAVGKAAG 35

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
                 ....*....|....*....|....*....|....
gi 1208991285 62 RPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd21994    1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAG 34

first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. ABF2 contains two HMG-box domains. This model corresponds to the first one.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 1208991285 61 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd22010    2 KRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGG 36

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
                 ....*....|....*....|....*....|....*
gi 1208991285 61 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd21989    1 RRPMNAFLLFCKRHRSLVRERHPRLDNRGITKILG 35

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
                 ....*....|....*....|....*....|....*
gi 1208991285 61 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 95
Cdd:cd21979    4 KRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLG 38