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 30688969  68 TDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:cd22005   5 TAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAE 54

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 30688969  68 TDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:cd22005   5 TAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAE 54

HMG (high mobility group) box;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 30688969    67 LTDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:pfam00505   5 MSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAE 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30688969  68 TDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:cd22005   5 TAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAE 54

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
                ....*....|....*....|....*....|....*....|....*..
gi 30688969  70 FAVFMNHFRKSFRTDYNgalVKEGSKIGWEMWKSMTEDEKKDYLDKA 116
Cdd:cd22014   8 FLLFMEEFRRNEDNGKN---LVELSRIAAEAWKNMSEDEKQPYIDRA 51

HMG (high mobility group) box;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 30688969    67 LTDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:pfam00505   5 MSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAE 55

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
                ....*....|....*....|....*....|....*....|....*....|..
gi 30688969  66 SLTDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:cd21994   2 PMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAE 53

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
                ....*....|....*....|....*....|....*....|....*....|..
gi 30688969  66 SLTDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:cd21985   5 PMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAA 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
                ....*....|....*....|....*....|....*....|....*....|
gi 30688969  74 MNHF-------RKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKA 116
Cdd:cd22004   6 MNAFmvwsqqeRKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEA 55

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
                ....*....|....*....|....*....|....*....|....*....|...
gi 30688969  67 LTDFAVFMNHFRKSFRTDYNGALV--KEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:cd21978   6 MSSYAFFVQTCREEHKKKHPNESVnfSEFSKKCSERWKTMSAKEKKKFEDMAK 58

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
                ....*....|....*....|....*....|....*....|....*.
gi 30688969  70 FAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDK 115
Cdd:cd22012   9 YFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEE 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
                ....*....|....*....|....*....|....*....|....*....|
gi 30688969  67 LTDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKA 116
Cdd:cd22017  25 LTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEKQRYLDEA 74

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
                ....*....|....*....|....*....|....*....|....*....|.
gi 30688969  67 LTDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKAA 117
Cdd:cd01390  18 LSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAA 68