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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6754850   52 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV 131
Cdd:cd22907   1 LREQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYV 80

                        90
                ....*....|.
gi 6754850  132 EPLKLYLQKFR 142
Cdd:cd22907  81 EPLKIYLQKYR 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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6754850   52 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV 131
Cdd:cd22907   1 LREQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYV 80

                        90
                ....*....|.
gi 6754850  132 EPLKLYLQKFR 142
Cdd:cd22907  81 EPLKIYLQKYR 91

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6754850   52 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV 131
Cdd:COG5150   5 KNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYI 84

                        90
                ....*....|....*
gi 6754850  132 EPLKLYLQKFREAMK 146
Cdd:COG5150  85 ESCMEEHENYKSYQK 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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6754850   52 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV 131
Cdd:cd22907   1 LREQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYV 80

                        90
                ....*....|.
gi 6754850  132 EPLKLYLQKFR 142
Cdd:cd22907  81 EPLKIYLQKYR 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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6754850   56 DIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLK 135
Cdd:cd22928   2 DLELPRAVITRIIKEALPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDVLKALEELEFDEFVPPLK 81

                ....*.
gi 6754850  136 LYLQKF 141
Cdd:cd22928  82 EELEAY 87

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6754850   52 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV 131
Cdd:COG5150   5 KNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYI 84

                        90
                ....*....|....*
gi 6754850  132 EPLKLYLQKFREAMK 146
Cdd:COG5150  85 ESCMEEHENYKSYQK 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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6754850   59 LPIANVARIMKNAIPQtgKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS 123
Cdd:cd00076   1 LLRSAVARILKSAGFD--SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63

histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) and similar proteins; Schizosaccharomyces pombe Dpb3 is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that is a heterotetramer consisting of cdc20/Pol2, Dpb2, Dpb3, and Dpb4, and participates in chromosomal DNA replication. 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. The Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation and H3K9 methylation in heterochromatin. The Dpb3-Dpb4 dimer is also required for the recruitment of sir2 to heterochromatin.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6754850   57 IYLPIANVARIMKnAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDI 118
Cdd:cd23645   1 TVLPLARVKRIIK-ADKDVKICSKDAVFLISKATELFIEYLAEQAYELAKLEKRKTVQYKDL 61

histone-fold domain found in histone H2B and similar proteins; Histone H2B is a 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 the 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6754850   49 KESFReqdIYlpianVARIMKNAIPQTGkIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAM 122
Cdd:cd22910   6 KESFS---IY-----IYKVLKQVHPDLG-ISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAV 70