histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 943463929   1 MKTQMDPQAKLAKDAKECAQECVSEFISFIASEAAEICNITKRKTITADDLLTAMEATGFDNYAEPMRIFLQKYR 75
Cdd:cd22907   17 MKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYVEPLKIYLQKYR 91

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 943463929   1 MKTQMDPQAKLAKDAKECAQECVSEFISFIASEAAEICNITKRKTITADDLLTAMEATGFDNYAEPMRIFLQKYR 75
Cdd:cd22907   17 MKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYVEPLKIYLQKYR 91

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 943463929   1 MKTQMDPQ-AKLAKDAKECAQECVSEFISFIASEAAEICNITKRKTITADDLLTAMEATGFDNYAEPMRIFLQKYRQAHK 79
Cdd:COG5150   20 MVSSILPKdLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESCMEEHENYKSYQK 99

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 943463929   1 MKTQMDPQAKLAKDAKECAQECVSEFISFIASEAAEICNITKRKTITADDLLTAMEATGFDNYAEPMRIFLQKYR 75
Cdd:cd22907   17 MKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYVEPLKIYLQKYR 91

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 943463929   1 MKTQMDPQAKLAKDAKECAQECVSEFISFIASEAAEICNITKRKTITADDLLTAMEATGFDNYAEPMRIFLQKY 74
Cdd:cd22928   14 IKEALPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDVLKALEELEFDEFVPPLKEELEAY 87

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 943463929   1 MKTQMDPQ-AKLAKDAKECAQECVSEFISFIASEAAEICNITKRKTITADDLLTAMEATGFDNYAEPMRIFLQKYRQAHK 79
Cdd:COG5150   20 MVSSILPKdLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESCMEEHENYKSYQK 99

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 943463929  13 KDAKECAQECVSEFISFIASEAAEICNITKRKTITADDLLTAME 56
Cdd:cd00076   20 KSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 943463929   9 AKLAKDAKECAQECVS-------EFISFIASEAAEICNITKRKTITADDLLTAMEATgfDNYA 64
Cdd:cd22929   13 MKLDPDVTLVSQEAVVaiakateLFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSD--DRFA 73