histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar proteins; NF-YC, also called CAAT box DNA-binding protein subunit C, or nuclear transcription factor Y subunit C, or transactivator HSM-1/2, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. The family also includes NF-YC homologs such as Aspergillus fumigatus CCAAT-binding complex (CBC) subunit HapE and Saccharomyces cerevisiae transcriptional activator Hap5. HapE is a component of CBC, which is composed of the histone-like subunits HapC and HapE as well as the DNA specificity conferring subunit HapB. In yeast, Hap5 is a component of the CCAT-binding factor (CBF or HAP complex II), which is a transcriptional activator and binds to the upstream activation site (UAS2) of the CYC1 gene and other genes involved in mitochondrial electron transport and activates their expression. It recognizes the sequence 5'-CCAAT-3'. Hap5 is essential for DNA-binding activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462509555  37 DFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLID 116
Cdd:cd22908     2 DFKNHELPLARIKKIMKSDEDVKMISAEAPVLFAKACELFILELTLRAWIHTEENKRRTLQRSDIAAAITSSDMFDFLID 81

                  ...
gi 2462509555 117 IVP 119
Cdd:cd22908    82 IVP 84

histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar proteins; NF-YC, also called CAAT box DNA-binding protein subunit C, or nuclear transcription factor Y subunit C, or transactivator HSM-1/2, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. The family also includes NF-YC homologs such as Aspergillus fumigatus CCAAT-binding complex (CBC) subunit HapE and Saccharomyces cerevisiae transcriptional activator Hap5. HapE is a component of CBC, which is composed of the histone-like subunits HapC and HapE as well as the DNA specificity conferring subunit HapB. In yeast, Hap5 is a component of the CCAT-binding factor (CBF or HAP complex II), which is a transcriptional activator and binds to the upstream activation site (UAS2) of the CYC1 gene and other genes involved in mitochondrial electron transport and activates their expression. It recognizes the sequence 5'-CCAAT-3'. Hap5 is essential for DNA-binding activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462509555  37 DFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLID 116
Cdd:cd22908     2 DFKNHELPLARIKKIMKSDEDVKMISAEAPVLFAKACELFILELTLRAWIHTEENKRRTLQRSDIAAAITSSDMFDFLID 81

                  ...
gi 2462509555 117 IVP 119
Cdd:cd22908    82 IVP 84

Core histone H2A/H2B/H3/H4;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462509555  27 MEEIRNLTVKDFRVQELPLARI-KKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAI 105
Cdd:pfam00125  44 KEIRKYQSSTDLLIYKLPFARVvREVVQSTKTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLAR 123

histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar proteins; NF-YC, also called CAAT box DNA-binding protein subunit C, or nuclear transcription factor Y subunit C, or transactivator HSM-1/2, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. The family also includes NF-YC homologs such as Aspergillus fumigatus CCAAT-binding complex (CBC) subunit HapE and Saccharomyces cerevisiae transcriptional activator Hap5. HapE is a component of CBC, which is composed of the histone-like subunits HapC and HapE as well as the DNA specificity conferring subunit HapB. In yeast, Hap5 is a component of the CCAT-binding factor (CBF or HAP complex II), which is a transcriptional activator and binds to the upstream activation site (UAS2) of the CYC1 gene and other genes involved in mitochondrial electron transport and activates their expression. It recognizes the sequence 5'-CCAAT-3'. Hap5 is essential for DNA-binding activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462509555  37 DFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLID 116
Cdd:cd22908     2 DFKNHELPLARIKKIMKSDEDVKMISAEAPVLFAKACELFILELTLRAWIHTEENKRRTLQRSDIAAAITSSDMFDFLID 81

                  ...
gi 2462509555 117 IVP 119
Cdd:cd22908    82 IVP 84

histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; POLE4, also called DNA polymerase II subunit 4, or DNA polymerase epsilon subunit p12, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex that consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. POLE4 forms a complex with POLE3. The POLE3-POLE4 is a histone chaperone that promotes tetrasome formation and DNA supercoiling in vitro. Interaction with POLE3 is a prerequisite for further binding with POLE and POLE2. In fungi, POLE4 has been named as DNA polymerase epsilon subunit C (DPB3, also known as DNA polymerase II subunit C). It is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that participates in chromosomal DNA replication. DNA polymerase epsilon is a heterotetramer consisting of POL2, DPB2, DPB3 and DPB4. DPB3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. This subfamily also includes protein DLS1 (DPB3-like subunit of ISW2 complex 1). It functions as a component of the ISW2 complex, which at least consists of ISW2, ITC1, DLS1 and DPB4, and acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW2 complex is involved in coordinating transcriptional repression and in inheritance of telomeric silencing. It is involved in repression of MAT a-specific genes, INO1, and early meiotic genes during mitotic growth dependent upon transcription factor UME6 and in a parallel pathway to the RPD3-SIN3 histone deacetylase complex. DLS1 is partially required for the ISW2 complex chromatin remodeling activity and is not required for its interaction with chromatin.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462509555  43 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIV 118
Cdd:cd22929     4 LPLSRVKRIMKLDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRFAFLEDVL 79

histone-fold domain found in Dr1-associated protein 1 (DRAP1) and similar proteins; DRAP1, also called Dr1-associated corepressor or negative cofactor 2-alpha (NC2-alpha), acts as a corepressor for Dr1 (down-regulator of transcription 1)-mediated repression of transcription. It forms a heterodimer with Dr1. The association of the Dr1/DRAP1 heterodimer with TBP results in a functional repression of both activated and basal transcription of class II genes. DRAP1 can bind to DNA on its own. It also binds TATA-binding protein-associated factor 172 (BTAF1).

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462509555  44 PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFL 114
Cdd:cd22906     5 PAARIKKIMQSDEEVGKVAAAVPVLISKALELFLEDLLTKAAEVAKERNAKTITPSHLKQCVESEEKFDFL 75

histone-fold domain found in chromatin accessibility complex protein 1 (CHRAC-1) and similar proteins; CHRAC-1, also called chromatin accessibility complex 15 kDa protein, or CHRAC-15, or DNA polymerase epsilon subunit p15, forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1. Together with POLE3, ACF1 and ISWI/SNF2H proteins, CHRAC-1 forms the ISWI chromatin-remodeling complex, CHRAC. This subfamily also includes Drosophila melanogaster chromatin accessibility complex 16kD protein (CHRAC-16), which is a histone-like protein that promotes nucleosome sliding of ATP-dependent nucleosome remodeling complexes. It is part of the CHRAC, composed of CHRAC-14, CHRAC-16, ACF and ISWI, which uses energy/ATP to increase the general accessibility of DNA in chromatin. It forms a heterodimer with CHRAC-14, binds DNA, and facilitates nucleosome sliding by ACF. It is required for oogenesis.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462509555  43 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAwiHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIV 118
Cdd:cd22924     1 LPLSRVRTIMKSSPDVSSISQDAVFLITKATELFVEYLAKEA--YKKSKDKKKLTYKDLADVVNDDENLEFLLDIV 74

Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462509555  44 PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDEL 123
Cdd:COG5247    25 PIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNMEQFKNR 104

                  ....*..
gi 2462509555 124 KPPKRQE 130
Cdd:COG5247   105 ETQPEEE 111

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462509555  42 ELPLARIKKIMKlDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAI 105
Cdd:cd22909     1 ELPKAPVKRIIK-KAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAV 63

Archaeal histone H3/H4 [Chromatin structure and dynamics];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462509555  42 ELPLARIKKIMKlDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFD 109
Cdd:COG2036     1 ELPVAPVDRIIK-KAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKLLN 67

histone-fold domain found in histone H2A and similar proteins; Histone H2A is the core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462509555  44 PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAI 105
Cdd:cd00074    12 PVGRIHRLLKKGTYAKRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKKRITPRHIQLAI 73