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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYK 621
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 24762396 194 ASGESIAIFREIQILTPRGRYDIKIFSTFFQLHGKTFDYKIPMDSVLRLFMLPHKDSRQMFFVLSLDPPIKQGQTRYHYL 273
Cdd:cd13230   1 VTGDAIVTFEDILCLTPRGRYDIEMYPSFLRLHGKTYDYKIQYKSISRLFLLPKPDDRHVFFVISLDPPIRQGQTRYPFL 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 24762396 274 VLLFAPDEETTIELPFSEAELRDKYEGKLEKEISGPVYEVMGKVMKVLIGRKITGPG 330
Cdd:cd13230  81 VMQFDKDEEVELELNLTEEELEEKYKGKLEKEMSGPLYEVVSRVFKGLTGKKITVPG 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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYK 621
Cdd:cd21994   1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDeeDKEKWEQKAEKAKERYDKAMKEYK 67

high mobility group;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24762396    557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYK 621
Cdd:smart00398   4 RPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLseEEKAPYEEKAKKDKERYEEEMPEYK 70

high mobility group protein; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24762396  553 GKPKRATTAFMLWLNDTRESIKRENPGIK--VTEIAKKGGEMWKELKDKSK--WEDAAAKDKQRYHDEMRNY 620
Cdd:PTZ00199  21 NAPKRALSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKapYEKKAQEDKVRYEKEKAEY 92

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 24762396 194 ASGESIAIFREIQILTPRGRYDIKIFSTFFQLHGKTFDYKIPMDSVLRLFMLPHKDSRQMFFVLSLDPPIKQGQTRYHYL 273
Cdd:cd13230   1 VTGDAIVTFEDILCLTPRGRYDIEMYPSFLRLHGKTYDYKIQYKSISRLFLLPKPDDRHVFFVISLDPPIRQGQTRYPFL 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 24762396 274 VLLFAPDEETTIELPFSEAELRDKYEGKLEKEISGPVYEVMGKVMKVLIGRKITGPG 330
Cdd:cd13230  81 VMQFDKDEEVELELNLTEEELEEKYKGKLEKEMSGPLYEVVSRVFKGLTGKKITVPG 137

Histone chaperone Rttp106-like; This family includes Rttp106, a histone chaperone involved in heterochromatin-mediated silencing. This domain belongs to the Pleckstrin homology domain superfamily.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762396   340 AVGCSFKAAAGYLYPLERGFIY-IHKPPLHIRFEEISSVNFARSGGSTRSFDFEVTLKNGTVHIFSSIEKEEYAKLFDYI 418
Cdd:pfam08512   2 GVKCSRKAKEGYLYPLEKCLLFgFKKPPLVIPLSDIESVSFERVSFTLRTFDLVIVLKKDPEYEFSMIDQEELDGIKDFL 81

                  ...
gi 24762396   419 TQK 421
Cdd:pfam08512  82 KSK 84

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 24762396     5 LEYNDINAEVRGvlCSGRLKMTEQNIIFKNTKTGKVEQISAEDIDLINSQKFVGTWGLRVFTKGGVLHRFTGFRDSEHEK 84
Cdd:pfam17292   1 LEFDNIYLELSG--TPGRLRLADSGLGWKNSKGGKVVTLPKSDISSAQWSRVARGYELRIGLKNGGVVRFDGFKEEDFDK 78

                          90
                  ....*....|....*
gi 24762396    85 LGKFIKAAYSQEMVE 99
Cdd:pfam17292  79 LKKFFKNNYDVSLEE 93

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24762396   557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNY 620
Cdd:pfam00505   3 RPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALseEEKKPYEEKAEKEKARYEKEHPEY 68

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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRY 613
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELseEEKQPYEEKAKEDKERY 59

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNY 620
Cdd:cd01390  16 RGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELseEEKAPYEEKAAKDKKRYEEEKAAY 81

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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYK 621
Cdd:cd21979   5 RPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTsaKDKQPYEKKAAKLKEKYEKDIAAYR 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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK--WEDAAAKDKQRYHDEMRNY 620
Cdd:cd22007   3 RPQSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKkpYEEKAKKLKEAYLQEMEEY 68

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQRYHDEMRNYKP 622
Cdd:COG5648  73 RPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDeeKEPYYKEANSDRERYQREKEEYNK 140

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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSkwedaaakdKQRYHDEMRN 619
Cdd:cd22012   4 RPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESE---------KEPYQEEYEK 57

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 24762396 557 RATTAFMLWLNDTRESIKRENPG--IKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMR 618
Cdd:cd21978   4 GKMSSYAFFVQTCREEHKKKHPNesVNFSEFSKKCSERWKTMsaKEKKKFEDMAKKDKARYEREMK 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 24762396 561 AFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRyHDEMR-NYK 621
Cdd:cd01389   7 AFILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLseEEKEPYKELAEEEKEE-HKLKYpDYK 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMR 618
Cdd:cd21985   4 KPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLseEEKKKYEEKAAKDLERYNSQKK 67

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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWE--DAAAKDKQRYHDEMRNYK 621
Cdd:cd22028   4 RPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPfiDEAKRLRAQHMKEHPDYK 70

high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar proteins; 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'. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWE--DAAAKDKQRYHDEMRNYK 621
Cdd:cd22034   7 RPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPffQEAQKLQAMHREKYPNYK 73

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 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 have only one HMG-box domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 24762396 573 IKRENPGiKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNY 620
Cdd:cd22009  19 LKALYPG-KDREISKMIGEMWSNLteEEKEVYQDKGVEDKERYKREMEEY 67

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 24762396 557 RATTAFMLWLNDTRESIK----RENPGIKVTEIAKKGGEMWKELKDKSK--WEDAAAKDKQRYHDEMRNY 620
Cdd:cd22016  10 RPANAFFLFCQEQREKVReeykEEHQEIDHHDLTKALAQAWRNLDAEDKkpYYELYEKDKERYEKEMEEY 79

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and similar proteins; SOX-17 is a developmental transcription regulator involved in endoderm formation, angiogenesis, and carcinogenesis. It acts as a tumor suppressor and modulates WNT signaling. SOX-17 binds target promoter DNA and bends the DNA. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX-17 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYK 621
Cdd:cd22047   9 RPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTlaEKRPFVEEAERLRVQHMQDHPNYK 75

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar proteins; SOX-7 is an endothelial-associated transcription factor that acts as a tumor suppressor in a number of cancer types. It binds the DNA sequence 5'-AACAAT-3'. SOX-7 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYK 621
Cdd:cd22046  14 RPMNAFMVWAKDERKRLAVQNPDLHNAELSKMLGKSWKALTpsQKRPYVEEAERLRVQHMQDYPNYK 80

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 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK--WEDAAAKDKQRYHDEMRNYK 621
Cdd:cd01388   5 RPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSEAEKrpFIDEAKRLRALHMKEHPDYK 71

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYK 621
Cdd:cd22048   6 RPMNAFMVWAKDERKRLAQQNPDLHNAVLSKMLGQSWKSLSaaEKRPFVEEAERLRVQHLQDHPNYK 72

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and similar proteins; SOX-30 is a crucial transcription factor that controls the transition from a late meiotic to a post-meiotic gene expression program and subsequent round spermatid development. It specially prevents Wnt-signaling to suppress metastasis. SOX-30 binds to the DNA sequence 5'-ACAAT-3' and shows a preference for guanine residues surrounding this core motif. SOX-30 is the only member of the group H of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDkskwedaaaKDKQRYHDEMRNYK 621
Cdd:cd22033   4 RPMNAFMVWARIHRPALAKANPNANNADISVQLGEEWNKLTE---------EQKKPYYDEAQKLK 59

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 24762396 557 RATTAFMLWLNDTRESIKRENPgIKVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQRY 613
Cdd:cd21986   3 RPLSPYLRFYREQLPSFPAQNP-DATTDLSKRIGERWRELPDsqKKKYQDAYKAEWQKY 60

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 11 (SOX11) and similar proteins; SOX-11 is a neural transcriptional factor involved in precursor survival, neuronal fate determination, migration and morphogenesis. SOX-11 belongs to group C SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK 601
Cdd:cd22037  14 RPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLGKRWKMLKDSEK 58

high mobility group (HMG)-box found in group D SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxD transcription factors includes three members, Sox5, Sox6, and Sox13. They function as important transcriptional regulators of glial development in the central nervous system. SoxD proteins influence multiple stages of oligodendrocyte development and modulate SoxE protein function. This subfamily also contains SoxD transcription factor homolog EGL-13, which specifies distinct O2 and CO2 sensory neuron fates in Caenorhabditis elegans. SOX-5 plays important roles in various cancer types. It binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-6 plays a key role in cell proliferation, differentiation, and cell fate determination, as well as neurogenesis and skeleton formation. It is a tumor suppressor and downregulated in various cancers. SOX-6 binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-13, also called Islet cell antigen 12 (ICA12), or type 1 diabetes auto-antigen ICA12, modulates T cell specification and is an autoimmune antigen. It binds to the sequence 5'-AACAAT-3'.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK---WEDAAAKDKQ---RYHDemRNYKP 622
Cdd:cd22030   4 RPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKSMSNQEKqpyYEEQARLSKQhleKYPD--YKYKP 73

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
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 24762396 561 AFMLWLNDTRESIKRENPgikVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQRYHDEM 617
Cdd:cd22014   7 PFLLFMEEFRRNEDNGKN---LVELSRIAAEAWKNMSEdeKQPYIDRAKELLEEYKKQL 62

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 12 (SOX12) and similar proteins; SOX-12, also called SOX-22, is a transcription factor essential for embryonic development and cell fate determination. It binds to the sequence 5'-AACAAT-3'. SOX-12 belongs to the group C of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 24762396 557 RATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK 601
Cdd:cd22038  14 RPMNAFMVWSQIERRKIMEQWPDMHNAEISKRLGRRWKLLQDYEK 58