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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716   1 MVTEKSKKPRSKTAVKRRKDPNAPKKPMSGYFIFGQEQRKKNEELSR-LPVADQGRAISEMWKKLSDEEREEYNKISNRE 79
Cdd:COG5648    48 LLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPkLTFGEVGKLLSEKWKELTDEEKEPYYKEANSD 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716  80 RELYQARIEEYKKSDEYHNHLEKVAADEAAAGKKKKGIKKVTGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSE 159
Cdd:COG5648   128 RERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSF 207

                  ....
gi 2416450716 160 DEKA 163
Cdd:COG5648   208 YPEA 211

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716   1 MVTEKSKKPRSKTAVKRRKDPNAPKKPMSGYFIFGQEQRKKNEELSR-LPVADQGRAISEMWKKLSDEEREEYNKISNRE 79
Cdd:COG5648    48 LLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPkLTFGEVGKLLSEKWKELTDEEKEPYYKEANSD 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716  80 RELYQARIEEYKKSDEYHNHLEKVAADEAAAGKKKKGIKKVTGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSE 159
Cdd:COG5648   128 RERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSF 207

                  ....
gi 2416450716 160 DEKA 163
Cdd:COG5648   208 YPEA 211

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2416450716  24 PKKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEY 90
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKlKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68

high mobility group;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716   23 APKKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYK 91
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKiKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716   1 MVTEKSKKPRSKTAVKRRKDPNAPKKPMSGYFIFGQEQRKKNEELSR-LPVADQGRAISEMWKKLSDEEREEYNKISNRE 79
Cdd:COG5648    48 LLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPkLTFGEVGKLLSEKWKELTDEEKEPYYKEANSD 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716  80 RELYQARIEEYKKSDEYHNHLEKVAADEAAAGKKKKGIKKVTGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSE 159
Cdd:COG5648   128 RERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSF 207

                  ....
gi 2416450716 160 DEKA 163
Cdd:COG5648   208 YPEA 211

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716  23 APKKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYKKSDEYHNHLE 101
Cdd:cd21980     1 APKAPLTGYVRFLNERREKlRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAYQQTEAYKAFLK 80

                  .
gi 2416450716 102 K 102
Cdd:cd21980    81 K 81

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 2416450716  26 KPMSGYFIFGQEQRKKN-EELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELY 83
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLkKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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 2416450716  22 NAPKKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYK 91
Cdd:cd21979     1 NAPKRPPSAFFLFCSEHRPKiKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71

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 2416450716  16 KRRKDPNAPKKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYKK 92
Cdd:cd22013     1 KKKKDPNAPKRALSGFMFFSLMERENlKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGYKN 78

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 2416450716 121 TGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNKIAEE 171
Cdd:cd00084     4 SAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKE 54

high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins; HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716   9 PRSKTAVKRRKDPNAPKKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARI 87
Cdd:cd22017     6 SKGRKRKKPLRDSNAPKAPLTGYVRFMNERREQlRAERPDVPFPEITRMLGNEWSKLPAEEKQRYLDEAEKDKERYMKEL 85

                          90
                  ....*....|....*.
gi 2416450716  88 EEYKKSDEYHNHLEKV 103
Cdd:cd22017    86 EQYQKTEAYKLFSRKA 101

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 2416450716  24 PKKP-MSGYFIFGQEQRKkNEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYKKS 93
Cdd:cd22003     3 PKKPpMSGYQLFSQEMLK-NGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKS 72

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 2416450716  26 KPMSGYFIFGQEQR-KKNEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYK 91
Cdd:cd21994     1 RPMSAYMLWLNENReKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67

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 2416450716  21 PNAPKKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQA 85
Cdd:pfam09011   1 PNKPKRARNAYAFFVQEMIPEhKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDR 66

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 2416450716  24 PKKPMSGYFIFGQEQRKKNEE--LSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYKK 92
Cdd:cd22011     1 PKRPSSAYFLFSQEIRKNLKSqgSPEEKVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEK 71

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
                  ....*....|....*....|....*....|....*....|....*..
gi 2416450716 121 TGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNK 167
Cdd:cd21998     9 TPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQ 55

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416450716  24 PKKPMSGYFIFGQEQRKKNEEL-SRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYKKSDEYHNHLEK 102
Cdd:cd22018     2 PKAPVTGYVRFLNERREQIRTQhPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREYQQSEAYKMCTEK 81

                  .
gi 2416450716 103 V 103
Cdd:cd22018    82 I 82

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
                  ....*....|....*....|....*....|....*....|....*.
gi 2416450716 126 FFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNKIAEE 171
Cdd:cd01389    11 FRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEE 56

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 2416450716  25 KKPMSGYFIFGQEQRKK-NEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYK 91
Cdd:cd22004     3 KRPMNAFMVWSQQERKKiAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKKEYPDYK 70

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2416450716 120 VTGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYN----KIAEEK 172
Cdd:cd21984     4 PSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEeraqKQAEQN 60

HMG (high mobility group) box;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2416450716 120 VTGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNKIAEE 171
Cdd:pfam00505   5 MSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEK 56

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
                  ....*....|....*....|....*....|....*....|....*..
gi 2416450716 126 FFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNKIAEEK 172
Cdd:cd22001    13 YSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALA 59

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 2416450716  25 KKPMSGYFIFGQ-EQRKKNEELSRLPVADQGRAISEMWKKLSDEEREEYNKISNRERELYQARIEEYK 91
Cdd:cd22029     3 KRPMNAFMVWSQiERRKIMEQQPDMHNAEISKRLGKRWKLLSDSEKIPFIEEAERLRLLHMQEYPDYK 70

high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain.

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gi 2416450716 120 VTGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNKIAE 170
Cdd:cd21995     4 VSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLDEEQKQVYKKKTE 54

high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins; SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain.

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gi 2416450716 123 YNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYN 166
Cdd:cd21983    12 YMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYI 55

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.

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gi 2416450716 121 TGYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNKIAEEKNVK 175
Cdd:cd22005     5 TAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEKEKAE 59

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.

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gi 2416450716 122 GYNEFFKAVRKAVSEENPSFTMMETTSAVAKRWKELSEDEKAVYNK 167
Cdd:cd22012     8 AYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQE 53