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Conserved domains on  [gi|145526669|ref|XP_001449140|]
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uncharacterized protein GSPATT00016556001 [Paramecium tetraurelia]

Protein Classification

histone H4( domain architecture ID 11487839)

histone H4 is one of the four histones, along with H2A, H2B and H3, that form the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation

CATH:  1.10.20.10
Gene Ontology:  GO:0006334|GO:0006355|GO:0006325|GO:0046982|GO:0003677
PubMed:  32556547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 11-114 2.13e-40

histone H4; Provisional


:

Pssm-ID: 185397  Cd Length: 102  Bit Score: 129.47  E-value: 2.13e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145526669  11 TMKYRQNNQKLKGQGRNIDYKKFPqhTNKSRLISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYS 90
Cdd:PTZ00015   1 MSGMGKGKKSLGAKGGQKRQKKVL--RDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA 78

                         90       100
                 ....*....|....*....|....
gi 145526669  91 GRATILADDICRAAKRAGQTAIGF 114
Cdd:PTZ00015  79 RRKTVTAMDVVYALKRQGRTLYGF 102
 
Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 11-114 2.13e-40

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 129.47  E-value: 2.13e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145526669  11 TMKYRQNNQKLKGQGRNIDYKKFPqhTNKSRLISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYS 90
Cdd:PTZ00015   1 MSGMGKGKKSLGAKGGQKRQKKVL--RDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA 78

                         90       100
                 ....*....|....*....|....
gi 145526669  91 GRATILADDICRAAKRAGQTAIGF 114
Cdd:PTZ00015  79 RRKTVTAMDVVYALKRQGRTLYGF 102
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 36-113 3.23e-27

histone-fold domain found in histone H4 and similar proteins; Histone H4 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.


Pssm-ID: 467037 [Multi-domain]  Cd Length: 79  Bit Score: 95.36  E-value: 3.23e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 145526669  36 HTNKSRLISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYSGRATILADDICRAAKRAGQTAIG 113
Cdd:cd22912    2 LRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
H4 smart00417
Histone H4;
43-103 8.55e-12

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 56.01  E-value: 8.55e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 145526669    43 ISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYSGRATILADDICRA 103
Cdd:smart00417  14 ITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
48-106 1.38e-05

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 39.81  E-value: 1.38e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 145526669  48 IRRLARRGGVKRISSD-VYELSKlYMKLYISNILRDSMIYANYSGRATILADDICRAAKR 106
Cdd:COG2036    7 VDRIIKKAGAERVSEDaVEALAE-ILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
TFIID-31kDa pfam02291
Transcription initiation factor IID, 31kD subunit; This family represents the N-terminus of ...
 75-100 1.23e-03

Transcription initiation factor IID, 31kD subunit; This family represents the N-terminus of the 31kD subunit (42kD in drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated transcription activation.


Pssm-ID: 460525  Cd Length: 122  Bit Score: 35.95  E-value: 1.23e-03
                          10        20
                  ....*....|....*....|....*.
gi 145526669   75 YISNILRDSMIYANYSGRATILADDI 100
Cdd:pfam02291  38 YTTDVLEDALVYSEHAGKKQIDVDDV 63
 
Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 11-114 2.13e-40

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 129.47  E-value: 2.13e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145526669  11 TMKYRQNNQKLKGQGRNIDYKKFPqhTNKSRLISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYS 90
Cdd:PTZ00015   1 MSGMGKGKKSLGAKGGQKRQKKVL--RDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA 78

                         90       100
                 ....*....|....*....|....
gi 145526669  91 GRATILADDICRAAKRAGQTAIGF 114
Cdd:PTZ00015  79 RRKTVTAMDVVYALKRQGRTLYGF 102
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 36-113 3.23e-27

histone-fold domain found in histone H4 and similar proteins; Histone H4 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.


Pssm-ID: 467037 [Multi-domain]  Cd Length: 79  Bit Score: 95.36  E-value: 3.23e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 145526669  36 HTNKSRLISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYSGRATILADDICRAAKRAGQTAIG 113
Cdd:cd22912    2 LRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
PLN00035 PLN00035
histone H4; Provisional
 22-114 1.78e-16

histone H4; Provisional


Pssm-ID: 177669 [Multi-domain]  Cd Length: 103  Bit Score: 69.09  E-value: 1.78e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145526669  22 KGQGRNIDYKKFPQHTNKSRLISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYSGRATILADDIC 101
Cdd:PLN00035   9 KGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVV 88

                         90
                 ....*....|...
gi 145526669 102 RAAKRAGQTAIGF 114
Cdd:PLN00035  89 YALKRQGRTLYGF 101
H4 smart00417
Histone H4;
43-103 8.55e-12

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 56.01  E-value: 8.55e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 145526669    43 ISNGDIRRLARRGGVKRISSDVYELSKLYMKLYISNILRDSMIYANYSGRATILADDICRA 103
Cdd:smart00417  14 ITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 48-105 2.90e-06

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.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 41.43  E-value: 2.90e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 145526669  48 IRRLARRGGVKRISSDVYE-LSKLyMKLYISNILRDSMIYANYSGRATILADDICRAAK 105
Cdd:cd00076    6 VARILKSAGFDSVSKSALElLSDL-LERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 43-105 9.18e-06

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.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 40.22  E-value: 9.18e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 145526669  43 ISNGDIRRLARRGGVKRISSD-VYELSKLyMKLYISNILRDSMIYANYSGRATILADDICRAAK 105
Cdd:cd22909    2 LPKAPVKRIIKKAGAERVSEDaAEELAKL-LEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
48-106 1.38e-05

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 39.81  E-value: 1.38e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 145526669  48 IRRLARRGGVKRISSD-VYELSKlYMKLYISNILRDSMIYANYSGRATILADDICRAAKR 106
Cdd:COG2036    7 VDRIIKKAGAERVSEDaVEALAE-ILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
TFIID-31kDa pfam02291
Transcription initiation factor IID, 31kD subunit; This family represents the N-terminus of ...
 75-100 1.23e-03

Transcription initiation factor IID, 31kD subunit; This family represents the N-terminus of the 31kD subunit (42kD in drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated transcription activation.


Pssm-ID: 460525  Cd Length: 122  Bit Score: 35.95  E-value: 1.23e-03
                          10        20
                  ....*....|....*....|....*.
gi 145526669   75 YISNILRDSMIYANYSGRATILADDI 100
Cdd:pfam02291  38 YTTDVLEDALVYSEHAGKKQIDVDDV 63
HFD_TAF9 cd07979
histone-fold domain found in transcription initiation factor TFIID subunit 9 (TAF9) and ...
 75-100 1.63e-03

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.


Pssm-ID: 467024  Cd Length: 95  Bit Score: 34.89  E-value: 1.63e-03
                         10        20
                 ....*....|....*....|....*.
gi 145526669  75 YISNILRDSMIYANYSGRATILADDI 100
Cdd:cd07979   34 YTTEVLQDAKVYAEHAGRSQIDEEDV 59
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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