HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115529449  442 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 521
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 80

                  ....
gi 115529449  522 KKMK 525
Cdd:pfam14887  81 KKMK 84

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 115529449 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPD 185
Cdd:cd21998    1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHPD 77

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115529449 368 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 433
Cdd:cd22001    1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEKK 66

HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115529449  442 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 521
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 80

                  ....
gi 115529449  522 KKMK 525
Cdd:pfam14887  81 KKMK 84

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 115529449 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPD 185
Cdd:cd21998    1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHPD 77

fifth 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 fifth one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 115529449 443 KLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP 514
Cdd:cd22002    1 KLPELPKTAEEIWQQSVIEDYLARFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYERELSEMRKP 72

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 115529449  112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARF 179
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115529449   112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFR 180
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115529449 311 DQKKKDYEVELLRF---LESLPEEEQQRVLGEEKMLNINKKQATSPASKKPAQEGGKGGSEKPKRPVSAMFIFSEEKRRQ 387
Cdd:COG5648    9 PYLTLQAPLSLIIFhkmVFMSGIRQLHTTLVELEKPLQQLLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDE 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115529449 388 LQEERPELSESELTRLLARMWNDLSEKKKAKY--KAREAALKAQSERKPGGEREERGKLPESPKRAEEIWQQSVIGDYLa 465
Cdd:COG5648   89 IRKENPKLTFGEVGKLLSEKWKELTDEEKEPYykEANSDRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSP- 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 115529449 466 rfKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSE 510
Cdd:COG5648  168 --DKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYPE 210

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115529449   260 PTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVEL 321
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKaenpDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEM 66

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115529449   445 PESPKRAEEIWQQSVIGDYLARFKNDRVKAL-KAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMR 512
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEIsKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

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 115529449  262 KPPPNSYSLYCAELMANMKD----VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRF 324
Cdd:pfam09011   5 KRARNAYAFFVQEMIPEHKRqnpvIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71

HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115529449  442 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 521
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 80

                  ....
gi 115529449  522 KKMK 525
Cdd:pfam14887  81 KKMK 84

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 115529449 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPD 185
Cdd:cd21998    1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHPD 77

fifth 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 fifth one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 115529449 443 KLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP 514
Cdd:cd22002    1 KLPELPKTAEEIWQQSVIEDYLARFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYERELSEMRKP 72

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 115529449  112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARF 179
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 115529449 110 DFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFER 174
Cdd:cd22001    1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEK 65

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 115529449 109 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARF 179
Cdd:cd21983    2 PKPPEKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYIEEYEAEKVEYEEQMKAY 72

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        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 115529449 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARF 179
Cdd:cd22010    1 PKRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQRELSEYQKAKAEF 68

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115529449  370 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 432
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEK 63

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115529449 370 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 432
Cdd:cd21979    3 PKRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEK 65

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 115529449 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFER 174
Cdd:cd22012    2 PKRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEEYEKALEEYEE 64

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115529449 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFR 180
Cdd:cd21980    2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAYQ 70

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115529449 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE 181
Cdd:cd22018    2 PKAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREYQQ 71

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
                 ....*....|....*....|....*....|....*....|....*....|
gi 115529449 370 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 419
Cdd:cd21980    2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKY 51

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) and similar proteins; NHP10, also called high mobility group protein 2, is probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 115529449 106 KKHPDFPKKPLTPYFRFFMEKR----AKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNL 176
Cdd:cd22016    2 EKDPNAPKRPANAFFLFCQEQRekvrEEYKEEHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKERYEKEM 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 115529449 368 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPGGEREE 440
Cdd:cd21998    2 DFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREE 74

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 115529449 263 PPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDY 317
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKkenpDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 115529449 103 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFR 180
Cdd:cd22008    1 KNKNVDPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKEVEEYN 78

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 115529449 101 KGKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARF 179
Cdd:cd01390    3 KKGRKKKDPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAAY 81

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115529449   530 PKKPPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLW 596
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENpdLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69

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 115529449 371 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKA 428
Cdd:cd22005    1 KRPPTAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEKEKA 58

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 115529449 533 PPMNGYQKFSQELLSN--GELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQY 589
Cdd:cd00084    1 RPLSAYLLFSKEKRPKlkKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 115529449 371 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 429
Cdd:cd22028    3 KRPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKRLRAQ 61

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115529449 113 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEfernlarFREDHPD 185
Cdd:cd22004    3 KRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREE-------HKKEYPD 68

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 115529449 103 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFER 174
Cdd:COG5648   62 VRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQR 133

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 115529449 372 RPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 433
Cdd:cd21994    1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKA 62

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 115529449 113 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKqefernlARFREDHPD 185
Cdd:cd22028    3 KRPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKRLR-------AQHMKEHPD 68

high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 (HMO1) and similar proteins; HMO1, also called high spontaneous mutagenesis protein 2 (HSM2), is a DNA-binding protein that is probably part of the rDNA transcription apparatus. It acts synergetically with the RPA49 subunit of RNA polymerase I during rDNA transcription. It may participate in mutagenesis control.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 115529449 112 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARF 179
Cdd:cd22015    1 PKKPLTPYFAFSNHVRPQLKAERPKASPTEIAEEISERWANLSDEEKQLWEDKYEEEMKEYQKALEAY 68

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 115529449 370 PKRPVSAMFIFSEEKRRQLQEE-RPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 433
Cdd:cd22011    1 PKRPSSAYFLFSQEIRKNLKSQgSPEEKVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVE 65