histone H4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 361126736  54 GAKRHRKVLKDNIDGVTKGDIRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQ 133
Cdd:PTZ00015  16 GQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95

                 ....*..
gi 361126736 134 GRPIYGF 140
Cdd:PTZ00015  96 GRTLYGF 102

histone H4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 361126736  54 GAKRHRKVLKDNIDGVTKGDIRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQ 133
Cdd:PTZ00015  16 GQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95

                 ....*..
gi 361126736 134 GRPIYGF 140
Cdd:PTZ00015  96 GRTLYGF 102

Histone H4;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 361126736    56 KRHRKVLKDNIDGVTKGDIRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFA 129
Cdd:smart00417   1 RRHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74

Centromere kinetochore component CENP-T histone fold; CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 361126736   68 GVTKGDIRRMARRGGVK-RISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQG 134
Cdd:pfam15511  11 AVVKRLAQRFARTSGSKgKLSKEALAALEQASDWFFEQMGEDLAAYAKHAGRKTIDESDVILLMKRQR 78

histone H4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 361126736  54 GAKRHRKVLKDNIDGVTKGDIRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQ 133
Cdd:PTZ00015  16 GQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95

                 ....*..
gi 361126736 134 GRPIYGF 140
Cdd:PTZ00015  96 GRTLYGF 102

histone H4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 361126736  54 GAKRHRKVLKDNIDGVTKGDIRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQ 133
Cdd:PLN00035  15 GAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94

                 ....*..
gi 361126736 134 GRPIYGF 140
Cdd:PLN00035  95 GRTLYGF 101

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 361126736  71 KGDIRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALR 131
Cdd:cd22909    4 KAPVKRIIKKAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64

histone-fold domain found in histone H3 and similar proteins; Histone H3 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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 361126736  85 RISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQG 134
Cdd:cd22911   46 RFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRVTLMPKDMQLARRIRG 95

histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 361126736  74 IRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQG 134
Cdd:cd22920    8 VKKLFKHFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVELLMKRQR 68

histone-fold domain found in transcription initiation factor TFIID subunit 6 (TAF6) and similar proteins; This subfamily includes TAF6 and TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (TAF6L). TAF6, also called TATA Binding Protein (TBP) associated factor 6, RNA polymerase II TBP-associated factor subunit E, transcription initiation factor TFIID 70 kDa subunit (TAF(II)70, TAFII-70, TAFII70), or transcription initiation factor TFIID 80 kDa subunit, (TAF(II)80, TAFII-80, TAFII80), is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. TAF6L, also called PCAF-associated factor 65-alpha (PAF65-alpha), is a component of the PCAF complex, which can efficiently acetylate histones in a nucleosomal context. The PCAF complex is composed of several TAFs and PCAF-associated factors (PAFs). It might be the human version of the yeast SAGA complex. With TAF5L, TAF6L acts as an epigenetic regulator essential for somatic reprogramming. It also regulates target genes through H3K9ac deposition and MYC recruitment, which trigger the MYC regulatory network to orchestrate gene expression programs to control embryonic stem cell state.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 361126736  74 IRRMARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALR 131
Cdd:cd22917    6 VKLIAESLGIVNLSEEVAQLLAEDAEYRILEVIQNAKKFAHHSKRKKLTADDINNALR 63

Core histone H2A/H2B/H3/H4;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 361126736   77 MARRGGVKRISADIYSSMKTALKDYLTKVLNDAVQITSHCNRKTVTVPDVIFALR 131
Cdd:pfam00125  70 VQSTKTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARR 124

histone-fold domain found in transcription initiation factor TFIID subunit 9 (TAF9) and similar proteins; The family includes TAF9 (also called TATA Binding Protein (TBP) associated factor 9, RNA polymerase II TBP-associated factor subunit G, STAF31/32, transcription initiation factor TFIID 31 kDa subunit, TAFII-31, TAFII31, transcription initiation factor TFIID 32 kDa subunit, TAFII-32, or TAFII32) and TAF9-like (also called transcription initiation factor TFIID subunit 9B, neuronal cell death-related protein 7, DN-7, or transcription-associated factor TAFII31L), which are essential for cell viability. They are involved in transcriptional activation as well as the repression of distinct but overlapping sets of genes. They may have roles in gene regulation associated with apoptosis. Both TAF9 and TAF9-like are TAFs that are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription. TAF9 interacts directly with different transcription factors such as p53, herpes simplex virus activator vp16, and the basal transcription factor TFIIB.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 361126736 101 YLTKVLNDAVQITSHCNRKTVTVPDVIFALRRQGR 135
Cdd:cd07979   34 YTTEVLQDAKVYAEHAGRSQIDEEDVRLAIQSRAD 68

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 361126736  88 ADIYSSMKTALKDYlTKVLNDA---VQ---------ITS----HC---NRKTVTVPDVIFALRRqgrpiYGFDNYED 145
Cdd:cd22907   11 ANIARIMKKALPPN-AKISKDAketMQecvsefisfVTSeaseRCqreKRKTITGDDILWAMST-----LGFDNYVE 81