Core component of nucleosome. Nucleosomes wrap and compact 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. Solanum lycopersicum (taxid: 4081)
Score = 112 bits (281), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 74/118 (62%), Positives = 82/118 (69%), Gaps = 18/118 (15%)
Query: 2 EKKPKAGKKLPKKAASSDKEMKCAKKSIKTYKIYIFKVL----------NKSILILESRA 51
EKKPKAGKKLPK A DK+ K AKKSI+TYKIYIFKVL +KS+ I+ S
Sbjct: 28 EKKPKAGKKLPKDAGRPDKKKKRAKKSIETYKIYIFKVLKQVHPDIGISSKSMGIMNSFI 87
Query: 52 RHNIFEEFA-------RYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
++IFE+ A RY KKP ITS EIQT RLVLPGEL KH VSEGTKAVTKFTS
Sbjct: 88 -NDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 144
Core component of nucleosome. Nucleosomes wrap and compact 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.
Core component of nucleosome. Nucleosomes wrap and compact 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.
Core component of nucleosome. Nucleosomes wrap and compact 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.
Score = 109 bits (272), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 72/119 (60%), Positives = 83/119 (69%), Gaps = 19/119 (15%)
Query: 2 EKKPKAGKKLPKKA-ASSDKEMKCAKKSIKTYKIYIFKVL----------NKSILILESR 50
EKKPKAGKKLPK+A A DK+ K KKS++TYKIYIFKVL +K++ I+ S
Sbjct: 32 EKKPKAGKKLPKEAGAGGDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSF 91
Query: 51 ARHNIFEEFA-------RYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
++IFE+ A RY KKP ITS EIQT RLVLPGEL KH VSEGTKAVTKFTS
Sbjct: 92 I-NDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 149
Core component of nucleosome. Nucleosomes wrap and compact 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.
Score = 109 bits (272), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 72/119 (60%), Positives = 83/119 (69%), Gaps = 19/119 (15%)
Query: 2 EKKPKAGKKLPKKA-ASSDKEMKCAKKSIKTYKIYIFKVL----------NKSILILESR 50
EKKPKAGKKLPK+A A DK+ K KKS++TYKIYIFKVL +K++ I+ S
Sbjct: 27 EKKPKAGKKLPKEAGAGGDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSF 86
Query: 51 ARHNIFEEFA-------RYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
++IFE+ A RY KKP ITS EIQT RLVLPGEL KH VSEGTKAVTKFTS
Sbjct: 87 I-NDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 144
Core component of nucleosome. Nucleosomes wrap and compact 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.
Score = 109 bits (272), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 72/119 (60%), Positives = 83/119 (69%), Gaps = 19/119 (15%)
Query: 2 EKKPKAGKKLPKKA-ASSDKEMKCAKKSIKTYKIYIFKVL----------NKSILILESR 50
EKKPKAGKKLPK+A A DK+ K KKS++TYKIYIFKVL +K++ I+ S
Sbjct: 32 EKKPKAGKKLPKEAGAGGDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSF 91
Query: 51 ARHNIFEEFA-------RYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
++IFE+ A RY KKP ITS EIQT RLVLPGEL KH VSEGTKAVTKFTS
Sbjct: 92 I-NDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 149
Core component of nucleosome. Nucleosomes wrap and compact 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.
Score = 105 bits (262), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 70/118 (59%), Positives = 82/118 (69%), Gaps = 19/118 (16%)
Query: 2 EKKPKAGKKLPKKAASSDKEMKCAKKSIKTYKIYIFKVL----------NKSILILESRA 51
EKKPKAGKKLP K A DK+ K +KK+++TYKIYIFKVL +K++ I+ S
Sbjct: 32 EKKPKAGKKLPPKEAG-DKKKKRSKKNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFI 90
Query: 52 RHNIFEEFA-------RYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
++IFE+ A RY KKP ITS EIQT RLVLPGEL KH VSEGTKAVTKFTS
Sbjct: 91 -NDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 147
Core component of nucleosome. Nucleosomes wrap and compact 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.
Score = 104 bits (260), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 67/120 (55%), Positives = 79/120 (65%), Gaps = 20/120 (16%)
Query: 2 EKKPKAGKKLPKKAASSDKEMKCAKKS--IKTYKIYIFKVL----------NKSILILES 49
EKKPKAGKKLPK+ S+ E K + ++TYKIYIFKVL +K++ I+ S
Sbjct: 29 EKKPKAGKKLPKEGGSAAGEKKKKRSKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNS 88
Query: 50 RARHNIFEEFA-------RYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
++IFE+ A RY KKP ITS EIQT RLVLPGEL KH VSEGTKAVTKFTS
Sbjct: 89 FI-NDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 147
Core component of nucleosome. Nucleosomes wrap and compact 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.
Score = 104 bits (259), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 68/120 (56%), Positives = 79/120 (65%), Gaps = 20/120 (16%)
Query: 2 EKKPKAGKKLPKKAASSDKEMKCAKK--SIKTYKIYIFKVL----------NKSILILES 49
EKKPKAGKKLPK+A + E K + S +TYKIYIFKVL +K++ I+ S
Sbjct: 32 EKKPKAGKKLPKEAVTGGVEKKKKRVKKSTETYKIYIFKVLKQVHPDIGISSKAMGIMNS 91
Query: 50 RARHNIFEEFA-------RYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
++IFE+ A RY KKP ITS EIQT RLVLPGEL KH VSEGTKAVTKFTS
Sbjct: 92 FI-NDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 150
Core component of nucleosome. Nucleosomes wrap and compact 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.
Arabidopsis thaliana (taxid: 3702)
Close Homologs in the Non-Redundant Database Detected by BLAST
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]
Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex
The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome
The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin
The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex
The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
>pdb|1ID3|D Chain D, Crystal Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Differences In Inter-Nucleosome Interactions Length = 130
class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Histone domain of Son of sevenless protein
species: Human (Homo sapiens) [TaxId: 9606]
Probab=99.45 E-value=7e-14 Score=102.84 Aligned_cols=68 Identities=10% Similarity=0.106 Sum_probs=62.9
Q ss_pred CchhHHHHHHHHHH----------HHHHHHHHhhhhhHHHHhHhhcCCCCcchHHHHHHHHhhcchhHHHHHHhhhhhhh
Q 041086 28 SIKTYKIYIFKVLN----------KSILILESRARHNIFEEFARYKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAV 97 (102)
Q Consensus 28 r~esy~~YI~KVLK----------kAm~ImnSfv~nDiFerLa~~~kr~TltsreIQtAvrLlLPGELaKhAvseGtkAv 97 (102)
-+..|..||+|||+ .|+.+||+|+ +|+|++|+ .+++.|.+|||.+|+++|||+|++||++++..++
T Consensus 14 w~g~f~~~i~KVl~qvhP~l~i~~~Al~~i~~~i-~~ll~~L~---~~~p~sv~dVe~~v~~~fp~~i~~~ai~~a~~~~ 89 (172)
T d1q9ca_ 14 WRGLLVPALKKVQGQVHPTLESNDDALQYVEELI-LQLLNMLC---QAQPRSASDVEERVQKSFPHPIDKWAIADAQSAI 89 (172)
T ss_dssp HTTSSHHHHHHHHHHHCSSSBCCHHHHHHHHHHH-HHHHHHHH---TTCCCSTTHHHHHHHHSSCTTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHH-HHHHHHHH---ccCCccHHHHHHHHHHhCCchHHHHHHHHHHHHH
Confidence 35689999999999 9999999999 99999998 5889999999999999999999999999999887
Q ss_pred hc
Q 041086 98 TK 99 (102)
Q Consensus 98 ~k 99 (102)
..
T Consensus 90 ~s 91 (172)
T d1q9ca_ 90 EK 91 (172)
T ss_dssp C-
T ss_pred hc
Confidence 54
class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Histone domain of Son of sevenless protein
species: Human (Homo sapiens) [TaxId: 9606]
