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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 217 IPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYIP 296
Cdd:cd01389    1 IPRPPNAFILFRKEKHKQLRAQNPGL--------TNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDYKYQP 72

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 217 IPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYIP 296
Cdd:cd01389    1 IPRPPNAFILFRKEKHKQLRAQNPGL--------TNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDYKYQP 72

high mobility group;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 367000011   216 HIPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERW 274
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDL--------SNAEISKKLGERWKLLSEEEKAPY 51

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 217 IPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYIP 296
Cdd:cd01389    1 IPRPPNAFILFRKEKHKQLRAQNPGL--------TNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDYKYQP 72

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 367000011 219 RPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERW 274
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDL--------SFTEISKLLGERWKELSEEEKQPY 48

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 216 HIPRPRNAFILFRQQMHGEMFGKYKNLlvsHgsfktNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYI 295
Cdd:cd22004    1 HIKRPMNAFMVWSQQERKKIAKQNPKL---H-----NSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKKEYPDYKYR 72

                 ...
gi 367000011 296 PRR 298
Cdd:cd22004   73 PRR 75

high mobility group;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 367000011   216 HIPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERW 274
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDL--------SNAEISKKLGERWKLLSEEEKAPY 51

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 12 (SOX12) and similar proteins; 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'. SOX-12 belongs to the group C of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 216 HIPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYI 295
Cdd:cd22038   11 HIKRPMNAFMVWSQIERRKIMEQWPDM--------HNAEISKRLGRRWKLLQDYEKIPFIKEAERLRLKHMADYPDYKYR 82

                 ...
gi 367000011 296 PRR 298
Cdd:cd22038   83 PRK 85

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
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 367000011 218 PRPRNAFILFRQQMHGEMFGKYKNLLVSHgsfktnsiISKEIGQKWRALSDKEKER 273
Cdd:cd22012    3 KRPASAYFLFAKEVRPKLKEENPNEKYTD--------ITKLISEKWRSLDESEKEP 50

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 217 IPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYIP 296
Cdd:cd22035    8 VKRPMNAFMVWSSAQRRQMAQEHPKM--------HNSEISKRLGAAWKLLPEAEKRPFVEEAKRLRARHMRDYPDYKYRP 79

                 ..
gi 367000011 297 RR 298
Cdd:cd22035   80 RR 81

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        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 216 HIPRPRNAFILFRQQMHGEMFGKYKNLlvsHgsfktNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYI 295
Cdd:cd22032    1 RIRRPMNAFMVWAKDERKRLADENPDL---H-----NAELSKMLGKKWKSLSLAEKRPFVEEAERLRVQHMQDYPNYKYR 72

                 ...
gi 367000011 296 PRR 298
Cdd:cd22032   73 PRR 75

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and similar proteins; SOX-18 is a transcription factor involved in the development of cardiovascular and lymphatic vessels during embryonic development. It binds to the consensus sequence 5'-AACAAAG-3' and is able to trans-activate transcription via this site. SOX-18 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 214 GKHIPRPRNAFILFRQQMHGEMFGKYKNLlvshgsfkTNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYK 293
Cdd:cd22048    1 ESRIRRPMNAFMVWAKDERKRLAQQNPDL--------HNAVLSKMLGQSWKSLSAAEKRPFVEEAERLRVQHLQDHPNYK 72

                 ....*...
gi 367000011 294 YIPRRTET 301
Cdd:cd22048   73 YRPRRKKQ 80

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 367000011 216 HIPRPRNAFILFRQQMHGEMFGKYKNllvshgsfKTNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKY 294
Cdd:cd21990    1 HIRRPMNAFMIFSKRHRALVHQRHPN--------QDNRTVSKILGEWWYALGPEEKQKYHDLAFQVKEAHFKAHPDWKW 71

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367000011 217 IPRPRNAFILFRQQmhgemfgKYKNLLVSHGSFKtNSIISKEIGQKWRALSDKEKERWHELAKKEKEEHKLKYTDYKYIP 296
Cdd:cd22046   12 IRRPMNAFMVWAKD-------ERKRLAVQNPDLH-NAELSKMLGKSWKALTPSQKRPYVEEAERLRVQHMQDYPNYKYRP 83

                 ..
gi 367000011 297 RR 298
Cdd:cd22046   84 RR 85

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 367000011 219 RPRNAFILF----RQQMHGEmfgkyknllvshGSFKTNSIISKEIGQKWRALSDKEKE 272
Cdd:cd22005    2 RPPTAFFLFladfRKTYKKK------------NPDKSVKAVGKAAGEKWKSMSDEEKA 47

high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar proteins; HBP1, also called HMG box transcription factor 1, or high mobility group box transcription factor 1, is a transcriptional repressor that binds to the promoter region of target genes. It plays a role in the regulation of the cell cycle and the Wnt pathway. HBP1 binds preferentially to the sequence 5'-TTCATTCATTCA-3'.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 367000011 219 RPRNAFILFRQQMHGEMFGKYKNllvshgsfKTNSIISKEIGQKWRALSDKEKE 272
Cdd:cd21988    2 RPMNAFMLFAKKYRVEYTQMHPG--------KDNRAISVILGDRWKKMKNEERR 47