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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1723428  147 PKKPSSAFILFYKELRNNPKLRQelgipeaisTLVEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFM 217
Cdd:cd22014   1 PKRPPSPFLLFMEEFRRNEDNGK---------NLVELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62

HMG (high mobility group) box;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1723428    147 PKKPSSAFILFYKELRnnPKLRQELgiPEAISTlvEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFMKE 219
Cdd:pfam00505   1 PKRPMSAFFLFSKEQR--AKLKAEN--PGLKNA--EISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPE 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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1723428  147 PKKPSSAFILFYKELRNNPKLRQelgipeaisTLVEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFM 217
Cdd:cd22014   1 PKRPPSPFLLFMEEFRRNEDNGK---------NLVELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62

high mobility group;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1723428     146 VPKKPSSAFILFYKELRNNPKLRQELGIPEAISTLVeetqnaSKAWKELAEDKKKPFIDKSKALKEQYDKFMKE 219
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKL------GERWKLLSEEEKAPYEEKAKKDKERYEEEMPE 68

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723428  140 RLRHPDVPKKPSSAFILFYKELRnnPKLRQELGIPEAISTLVEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFMKE 219
Cdd:cd22016   1 KEKDPNAPKRPANAFFLFCQEQR--EKVREEYKEEHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKERYEKEMEE 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        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1723428  149 KPSSAFILFYKELRnnPKLRQELgiPEAisTLVEETQNASKAWKELAEDKKKPFIDKSKALKEQY 213
Cdd:cd00084   1 RPLSAYLLFSKEKR--PKLKKEN--PDL--SFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

first 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 first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1723428  148 KKPSSAFILFYKELRNNPKLRQELGIPEAISTLVEETqnaskaWKELAEDKKKPFIDKSKALKEQYDKFMKE 219
Cdd:cd22006   1 KKPKTAYFLWCKDQREEVKKENPNADFSEVSKILGAK------WKNLSEEEKKPYEEKYKEEKEKYLKVVGE 66

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 1723428  145 DVPKKPSSAFILFYKELRnnPKLRQElgipEAISTLVEETQNASKAWKELAEDKKKPFIDKSKALKEQYDK 215
Cdd:cd21979   1 NAPKRPPSAFFLFCSEHR--PKIKGE----HPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEK 65

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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1723428  149 KPSSAFILFYKELRN-----NPKLRQelgipeaistlVEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFMKE 219
Cdd:cd21994   1 RPMSAYMLWLNENREkikkeNPGISV-----------TEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKE 65

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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1723428  147 PKKPSSAFILFYKELRNNPKLRQelgiPEAISTlvEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFMKE 219
Cdd:cd22010   1 PKRPLSAYFLYFQEHRSDFVKEN----PDAKMT--EISKIGGDKWKNLSADDKKKYEDDFQRELSEYQKAKAE 67

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 1723428  148 KKPSSAFILFYKELR-----NNPKLRqelgiPEAISTLVeetqnaSKAWKELAEDKKKPFIDKSKALKEQ 212
Cdd:cd22004   3 KRPMNAFMVWSQQERkkiakQNPKLH-----NSEISKIL------GKEWKKLTEEEKRPYVEEAERLREE 61

first 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 cells. 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 the HMGB family that 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 responses. 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. This 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, is a tumor suppressor that is a major constituent of 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 telomere 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, binds preferentially to 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 first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1723428  147 PKKPSSAFILFYKELRNNPKLRQelgiPEAISTLVEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFMK 218
Cdd:cd21978   2 PRGKMSSYAFFVQTCREEHKKKH----PNESVNFSEFSKKCSERWKTMSAKEKKKFEDMAKKDKARYEREMK 69

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1723428  148 KKPSSAFILFYKELRnnPKLRQElgIPEAisTLVEETQNASKAWKELAEDKKKPFIDKSKALKEQYDKFMKEA 220
Cdd:cd21985   3 RKPMSASALFEQETR--PQFLAE--NPKA--SLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERYNSQKKRA 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        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1723428  148 KKPSSAFILFYKELRNNPKLRQELGIPEAISTLveetqnASKAWKELAEDKKKPFIDKSKALKEQY 213
Cdd:cd22005   1 KRPPTAFFLFLADFRKTYKKKNPDKSVKAVGKA------AGEKWKSMSDEEKAPYVEKAEKEKAEY 60