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 17507971 563 RATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
Cdd:cd21994   1 RPMSAYMLWLNENREKIKKENPGIsvTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67

Structure Specific Recognition protein 1 (SSRP1) Pleckstrin homology (PH) domain, repeat 1; SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. In yeast FACT (yFACT) is composed of three proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in human and mouse, respectively. The middle domain of the Pob3 subunit (Pob3-M) has an unusual double pleckstrin homology (PH) architecture. yFACT interacts in a physiologically important way with the central single-strand DNA binding factor RPA to promote a step in DNA Replication. Coordinated function by yFACT and RPA is important during nucleosome deposition. These results support the model that the FACT family has an essential role in constructing nucleosomes during DNA replication, and suggest that RPA contributes to this process. Members of this cd are composed of the first PH-like repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507971 196 TEQPICLLTDILCTTPRGRYDIKVYPTSIALHGKTYDYKIPVKTINRLFLVPHKDGRQVYFVLSLNPPIRQGQTHYSYLI 275
Cdd:cd13230   2 TGDAIVTFEDILCLTPRGRYDIEMYPSFLRLHGKTYDYKIQYKSISRLFLLPKPDDRHVFFVISLDPPIRQGQTRYPFLV 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 17507971 276 FEFGKDEEEDLELSLTDEQL-DYFNGNLQREMTGPIYETISILFKSICNLKVTVPG 330
Cdd:cd13230  82 MQFDKDEEVELELNLTEEELeEKYKGKLEKEMSGPLYEVVSRVFKGLTGKKITVPG 137

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 17507971 563 RATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
Cdd:cd21994   1 RPMSAYMLWLNENREKIKKENPGIsvTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17507971    561 PKRATTAYIIWFNANRNSMKED--GDTLGDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAEnpDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

high mobility group protein; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17507971  557 DPNEPKRATTAYIIWFNANRNSM-KEDGDTLGDVA---KKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYKK 628
Cdd:PTZ00199  19 DPNAPKRALSAYMFFAKEKRAEIiAENPELAKDVAavgKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Structure Specific Recognition protein 1 (SSRP1) Pleckstrin homology (PH) domain, repeat 1; SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. In yeast FACT (yFACT) is composed of three proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in human and mouse, respectively. The middle domain of the Pob3 subunit (Pob3-M) has an unusual double pleckstrin homology (PH) architecture. yFACT interacts in a physiologically important way with the central single-strand DNA binding factor RPA to promote a step in DNA Replication. Coordinated function by yFACT and RPA is important during nucleosome deposition. These results support the model that the FACT family has an essential role in constructing nucleosomes during DNA replication, and suggest that RPA contributes to this process. Members of this cd are composed of the first PH-like repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507971 196 TEQPICLLTDILCTTPRGRYDIKVYPTSIALHGKTYDYKIPVKTINRLFLVPHKDGRQVYFVLSLNPPIRQGQTHYSYLI 275
Cdd:cd13230   2 TGDAIVTFEDILCLTPRGRYDIEMYPSFLRLHGKTYDYKIQYKSISRLFLLPKPDDRHVFFVISLDPPIRQGQTRYPFLV 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 17507971 276 FEFGKDEEEDLELSLTDEQL-DYFNGNLQREMTGPIYETISILFKSICNLKVTVPG 330
Cdd:cd13230  82 MQFDKDEEVELELNLTEEELeEKYKGKLEKEMSGPLYEVVSRVFKGLTGKKITVPG 137

Structure-specific recognition protein (SSRP1); SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair. This domain belongs to the Pleckstrin homology fold superfamily.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17507971   105 GWNYGQADVKGKNIEFSWENEPIFEIPCTNVSNV-IANKNEAILEFHQNEQSKV---QLMEMRFHMP 167
Cdd:pfam03531   1 GWNWGKADFEGSELSFNVDNKPAFEIPLSDVSNSnLPGKNEVALEFHQDDDADVngdELVEMRFYVP 67

POB3-like N-terminal PH domain; This domain is found at the N-terminus of POB3 and related proteins.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507971     4 LKFKGVYVEDIGhlTCGTLTLTENSINFIGDKGGKSVYITGTDVDKLKWQKLGNKPGLRVGLSDGGAHRFGGFLDDDLQK 83
Cdd:pfam17292   1 LEFDNIYLELSG--TPGRLRLADSGLGWKNSKGGKVVTLPKSDISSAQWSRVARGYELRIGLKNGGVVRFDGFKEEDFDK 78

                          90
                  ....*....|....*
gi 17507971    84 IQSFTSSNWSKSINQ 98
Cdd:pfam17292  79 LKKFFKNNYDVSLEE 93

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 17507971 557 DPNEPKRATTAYIIWFNANRNSMKED--GDTLGDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEY 626
Cdd:cd01390  10 DPNAPKRGLSAYMFFSQDNREKVKEEnpDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAAY 81

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17507971   561 PKRATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEY 626
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLknAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17507971 557 DPNEPKRATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYKK 628
Cdd:COG5648  67 DPNGPKRPLSAYFLYSAENRDEIRKENPKLtfGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNK 140

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 17507971 563 RATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARY 619
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKKENPDLsfTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17507971   558 PNEPKRATTAYIIWFNANRNSMKEDGDT--LGDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEY 626
Cdd:pfam09011   1 PNKPKRARNAYAFFVQEMIPEHKRQNPVigFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71

second 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 second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17507971 561 PKRATTAYIIWFNANRNSMKEDGD--TLGDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEY 626
Cdd:cd22007   1 PKRPQSAYFLYANDRRAALKEENKnvKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEMEEY 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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17507971 561 PKRATTAYIIWFNANRNSMKEDGDT---LGDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYKKN 629
Cdd:cd22011   1 PKRPSSAYFLFSQEIRKNLKSQGSPeekVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKE 72

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17507971 561 PKRATTAYIIWFNANRNSMKEDGDTLG----DVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMK 624
Cdd:cd21978   2 PRGKMSSYAFFVQTCREEHKKKHPNESvnfsEFSKKCSERWKTMSAKEKKKFEDMAKKDKARYEREMK 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 17507971 562 KRATTAYIIWFNANRNSMKEDGDTLG--DVAKKAGAKWKSMSADDKKEWNDKAAQDKARY 619
Cdd:cd22005   1 KRPPTAFFLFLADFRKTYKKKNPDKSvkAVGKAAGEKWKSMSDEEKAPYVEKAEKEKAEY 60

second 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 second one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17507971 561 PKRATTAYIIWFNANRNSMKEDGDTLGDVAKKAGAKWKSMSadDKKE--WNDKAAQDKARYEAEMKEYKKN 629
Cdd:cd21999   1 PKKPKTPFQLFYNKELKKLEPGTPDKKELKEKLREKWKQMS--DKKKlkWINKALEDEKRYEEELKEYKKE 69

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17507971 561 PKRATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
Cdd:cd01389   1 IPRPPNAFILFRKEKHKQLRAQNPGLtnSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDYK 69

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17507971 557 DPNEPKRATTAYIIWFNANRNSMK-EDGDT-LGDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYKK 628
Cdd:cd22017  17 DSNAPKAPLTGYVRFMNERREQLRaERPDVpFPEITRMLGNEWSKLPAEEKQRYLDEAEKDKERYMKELEQYQK 90

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17507971 558 PNEPKRATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
Cdd:cd22035   5 LEKVKRPMNAFMVWSSAQRRQMAQEHPKMhnSEISKRLGAAWKLLPEAEKRPFVEEAKRLRARHMRDYPDYK 76

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 17507971 561 PKRATTAYIIWFNANRNSMKEDGDTLG--DVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYKKN 629
Cdd:cd22018   2 PKAPVTGYVRFLNERREQIRTQHPDLPfpEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREYQQS 72

high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) transcription factors; 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-1 is involved in the regulation of embryonic development and cell fate determination. It also acts as a tumor suppressor that plays an anti-tumorigenicity role in different cells and its expression is inhibited in a variety of cancers. SOX-2 plays an important role in various phases of embryonic development, including cell fate and differentiation. Its overexpression and gene amplification may be associated with tumor aggression and metastasis in various cancer types, including breast, prostate, lung, ovarian and colon cancer. SOX-3 is required during the formation of the hypothalamic-pituitary axis. It plays a role in both normal neural development and carcinogenesis. SOX-14, also called SOX-28, acts as a negative regulator of transcription. It is mainly involved in the regulation of neural development. It can also promote proliferation and invasion capacity of cervical cancer cells by activating the Wnt/beta-catenin pathway. SOX-21, also called SOX-A, or SOX-25, promotes the progression of vertebrate neurogenesis.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17507971 562 KRATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
Cdd:cd01388   4 KRPMNAFMVWSRGQRRKMAQENPKMhnSEISKRLGAEWKLLSEAEKRPFIDEAKRLRALHMKEHPDYK 71

first high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and similar proteins; TFA, also called TFAM, mitochondrial transcription factor 1 (TF1), transcription factor 6 (TCF-6), or transcription factor 6-like 2, binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. It is a component of the mitochondrial transcription initiation complex, composed of at least TFB2M, TFAM and POLRMT that is required for basal transcription of mitochondrial DNA. TFA is required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. It can unwind DNA. It bends the mitochondrial light strand promoter DNA into a U-turn shape via its HMG boxes. TFA is required for maintenance of normal levels of mitochondrial DNA and may play a role in organizing and compacting mitochondrial DNA. TFA contains two HMG-box domains. This model corresponds to the first one.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17507971 561 PKRATTAYIIWFNANRNSMKEDG-DTLGDVAKKAGAKWKSMSADDKKEWNDKaaqdkarYEAEMKEYKK 628
Cdd:cd21986   1 PKRPLSPYLRFYREQLPSFPAQNpDATTDLSKRIGERWRELPDSQKKKYQDA-------YKAEWQKYKE 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17507971 562 KRATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
Cdd:cd22028   3 KRPMNAFMVWSREQRRKIAQENPKMhnSEISKRLGAEWKQLSEDEKRPFIDEAKRLRAQHMKEHPDYK 70

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17507971 558 PNEPKRATTAYII-----WFNANRNSMKEDGDTLGDVakkagakWKSMSADDKKEWNDKAAQDKARYEAEMKEYKK 628
Cdd:cd22002   3 PELPKTAEEIWQQsviedYLARFKNDRGKALKAMEAT-------WNNMEKKEKLPWIKKAAEDQKRYERELSEMRK 71

U3 small nucleolar RNA-associated protein 14 [Function unknown];

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507971 394 EIDLKTGSSLTFSAMDKEENNKLFDYLN-KKEIKIR------NSHRIDNKsAGYGSSDEDDIDPYKSTVKAEGREQddds 466
Cdd:COG5644  64 EEDEKRFADWSFNASKSGKSNKDHKNLNnTKEISLNdsddsvNSDKLENE-GSVSSIDENELVDLDTLLDNDQPEK---- 138

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 17507971 467 dDESTDEDYDLDKDMKKQKNDKdSSEGSGSEpddEYDSGSEKDASgtgESDPDEEN 522
Cdd:COG5644 139 -NESGNNDHATDKENLLESDAS-SSNDSESE---ESDSESEIESS---DSDHDDEN 186

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 17507971 562 KRATTAYIIWFNANRNSMKEDGDTL--GDVAKKAGAKWKSMSADDKKEWNDKAAQDKARYEAEMKEYK 627
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 17507971 562 KRATTAYIIWFNANRNS-MKEDGD-TLGDVAKKAGAKWKSMSADDKKEWNDKAAQ 614
Cdd:cd21984   1 KRNPSGYILFSSEVRKSiKAENPDySFGEISRLVGTEWRNLPAEKKAEYEERAQK 55