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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85702117  98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKRHP 173
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHP 76

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85702117  98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKRHP 173
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHP 76

high mobility group;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85702117    100 RPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFK 169
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 85702117    224 PRKPPMNAYHKFHQESWSSPELRH--LSFRKRWVEISRRWHQVPENEKEHYSNQVKRLQKQYRVKLDLW 290
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENpdLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85702117  98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKRHP 173
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHP 76

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85702117 101 PKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKK 170
Cdd:cd21980   2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAYQQ 71

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 85702117 103 RPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDF 161
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

high mobility group;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85702117    100 RPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFK 169
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85702117 101 PKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQK 163
Cdd:cd22012   2 PKRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEEYEKALEEYEE 64

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85702117  90 KNKilTEHPDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFK 169
Cdd:cd22008   1 KNK--NVDPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKEVEEYN 78

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85702117  98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKRHPVSGH 177
Cdd:COG5648  68 PNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAP 147

                ....
gi 85702117 178 PKKS 181
Cdd:COG5648 148 IGPF 151

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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85702117 100 RPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEdfqkkmrQFKKRHP 173
Cdd:cd22004   1 HIKRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLRE-------EHKKEYP 67

third 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 third one.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85702117 224 PRKPPMNAYHKFHQESWSspELRHLSFRKRWVEISRRWHQVPENEKEHYSNQVKRLQKQYRVKLDLWLKRLSPEEYAAYK 303
Cdd:cd22000   1 PTKPPPNGYSLFCAELMK--NMKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVL 78

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 85702117  98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKK 170
Cdd:cd22013   6 PNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGYKN 78

first 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 first one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85702117 101 PKRPLTAYLRFYKEQRAKYCQMYPKYSnAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKK 164
Cdd:cd21986   1 PKRPLSPYLRFYREQLPSFPAQNPDAT-TDLSKRIGERWRELPDSQKKKYQDAYKAEWQKYKEE 63

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85702117    98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKM 165
Cdd:pfam09011   1 PNKPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREM 68

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 85702117  98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQF 168
Cdd:cd01390  11 PNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAAY 81

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 85702117 101 PKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQF 168
Cdd:cd22007   1 PKRPQSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEMEEY 68

high mobility group (HMG)-box found in group A, group B and group G of SRY-related high-mobility group (HMG) box (Sox) transcription factors; This subfamily includes SoxA, SoxB, and SoxG proteins. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. 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'. 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-5 is the only member of group G Sox transcription factors. It is also called SOX-12, SOX-20, SOX-26, or SOX-27. SOX-5 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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 85702117 100 RPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKR 171
Cdd:cd22028   1 RVKRPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKRLRAQHMKEHPDYKYR 72

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        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85702117  98 PDRPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKR 171
Cdd:cd22035   5 LEKVKRPMNAFMVWSSAQRRQMAQEHPKMHNSEISKRLGAAWKLLPEAEKRPFVEEAKRLRARHMRDYPDYKYR 78

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
                ....*....|....*....|....*....|....*....|....*....
gi 85702117 102 KRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRY 150
Cdd:cd22042   4 KRPMNAFMVWAKDERRKILKACPDMHNSNISKILGAKWKAMSNAEKQPY 52

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        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 85702117 102 KRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYImdfkkekEDFQKKMRQFKKRHP 173
Cdd:cd22031   3 KRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLSESEKRPFI-------EEAERLRVQHKKDHP 67

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 85702117 101 PKRPLTAYLRFYKEQRAKYCQMYPkysNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKM 165
Cdd:cd22014   1 PKRPPSPFLLFMEEFRRNEDNGKN---LVELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62

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 85702117 227 PPMNAYHKFHQESWSSPELRH--LSFRKRWVEISRRWHQVPENEKEHYSNQVKRLQKQY 283
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKKENpdLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85702117 102 KRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKR 171
Cdd:cd22030   3 KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKSMSNQEKQPYYEEQARLSKQHLEKYPDYKYK 72

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        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 85702117 100 RPKRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKEDFQKKMRQFKKR 171
Cdd:cd22047   6 RIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYR 77

high mobility group (HMG)-box found in the transcription factor 7 (TCF-7)-like family; The TCF7-like family includes TCF-7, TCF7-like 1 (TF7L1), lymphoid enhancer-binding factor 1 (LEF-1), and similar proteins. TCF-7, also called T-cell-specific transcription factor 1, or T-cell factor 1 (TCF-1), is a T lymphocyte-specific transcriptional activator involved in T-cell lymphocyte differentiation. It is necessary for the survival of CD4(+) CD8(+) immature thymocytes. It binds to the T-lymphocyte-specific enhancer element (5'-WWCAAAG-3') found in the promoter of the CD3E gene. TF7L1, also called HMG box transcription factor 3 (TCF-3), participates in the Wnt signaling pathway. It binds to DNA and acts as a repressor in the absence of CTNNB1, and as an activator in its presence. TF7L2, also called HMG box transcription factor 4, or T-cell-specific transcription factor 4, or T-cell factor 4, or TCF-4, participates in the Wnt signaling pathway and modulates MYC expression by binding to its promoter in a sequence-specific manner. It acts as a repressor in the absence of CTNNB1, and it activates transcription from promoters with several copies of the TCF motif 5'-CCTTTGATC-3' in the presence of CTNNB1. LEF-1, also called T cell-specific transcription factor 1-alpha (TCF1-alpha), is a transcription factor that binds DNA in a sequence-specific manner. It may participate in the Wnt signaling pathway. All family members contain one HMG-box domain.

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gi 85702117 102 KRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQRYIMDFKKEKE 159
Cdd:cd21996   3 KKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQ 60

high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar proteins; HMGXB4, also called HMG box-containing protein 4, high mobility group protein 2-like 1 (HMG2L1), or protein HMGBCG, is a non-histone chromosomal protein that negatively regulates Wnt/beta-catenin signaling during development. It plays a role in the hematopoietic system.

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gi 85702117 102 KRPLTAYLRFYKEQRAKYCQMYPKYSNAQLTKILAEKYRQLPAEIKQ 148
Cdd:cd21982   2 KKNMSAYQVFCKEYRVSIVAEHPGIDFGELSKKLAEVWKQLPEKDKL 48