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Conserved domains on  [gi|339639569|ref|NP_001229878|]
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histone cluster 2 family member [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_SF super family cl45933
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 50-94 1.84e-16

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.


The actual alignment was detected with superfamily member cd00074:

Pssm-ID: 480273  Cd Length: 89  Bit Score: 67.94  E-value: 1.84e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLFK 94
Cdd:cd00074   40 VLEYLTAEILELAGNAARDNKKKRITPRHIQLAIRNDEELNKLFK 84
 
Name Accession Description Interval E-value
HFD_H2A cd00074
histone-fold domain found in histone H2A and similar proteins; Histone H2A is the core ...
 50-94 1.84e-16

histone-fold domain found in histone H2A and similar proteins; Histone H2A is the 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 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: 467020  Cd Length: 89  Bit Score: 67.94  E-value: 1.84e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLFK 94
Cdd:cd00074   40 VLEYLTAEILELAGNAARDNKKKRITPRHIQLAIRNDEELNKLFK 84
H2A smart00414
Histone 2A;
50-94 1.89e-10

Histone 2A;


Pssm-ID: 197711  Cd Length: 106  Bit Score: 53.11  E-value: 1.89e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 339639569    50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLFK 94
Cdd:smart00414  39 VLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNKLLK 83
HTA1 COG5262
Histone H2A [Chromatin structure and dynamics];
22-92 3.53e-10

Histone H2A [Chromatin structure and dynamics];


Pssm-ID: 227587 [Multi-domain]  Cd Length: 132  Bit Score: 52.94  E-value: 3.53e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 339639569  22 PFSLVDRFLREEFHSSRLSSSALSFLTSVLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQL 92
Cdd:COG5262   28 PVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKL 98
PTZ00017 PTZ00017
histone H2A; Provisional
 50-92 5.19e-09

histone H2A; Provisional


Pssm-ID: 185399  Cd Length: 134  Bit Score: 50.13  E-value: 5.19e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQL 92
Cdd:PTZ00017  57 VLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKL 99
 
Name Accession Description Interval E-value
HFD_H2A cd00074
histone-fold domain found in histone H2A and similar proteins; Histone H2A is the core ...
 50-94 1.84e-16

histone-fold domain found in histone H2A and similar proteins; Histone H2A is the 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 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: 467020  Cd Length: 89  Bit Score: 67.94  E-value: 1.84e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLFK 94
Cdd:cd00074   40 VLEYLTAEILELAGNAARDNKKKRITPRHIQLAIRNDEELNKLFK 84
H2A smart00414
Histone 2A;
50-94 1.89e-10

Histone 2A;


Pssm-ID: 197711  Cd Length: 106  Bit Score: 53.11  E-value: 1.89e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 339639569    50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLFK 94
Cdd:smart00414  39 VLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNKLLK 83
HTA1 COG5262
Histone H2A [Chromatin structure and dynamics];
22-92 3.53e-10

Histone H2A [Chromatin structure and dynamics];


Pssm-ID: 227587 [Multi-domain]  Cd Length: 132  Bit Score: 52.94  E-value: 3.53e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 339639569  22 PFSLVDRFLREEFHSSRLSSSALSFLTSVLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQL 92
Cdd:COG5262   28 PVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKL 98
PTZ00017 PTZ00017
histone H2A; Provisional
 50-92 5.19e-09

histone H2A; Provisional


Pssm-ID: 185399  Cd Length: 134  Bit Score: 50.13  E-value: 5.19e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQL 92
Cdd:PTZ00017  57 VLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKL 99
PLN00153 PLN00153
histone H2A; Provisional
 20-93 1.20e-08

histone H2A; Provisional


Pssm-ID: 165721 [Multi-domain]  Cd Length: 129  Bit Score: 48.95  E-value: 1.20e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 339639569  20 ELPFSLVDRFLREEFHSSRLSSSALSFLTSVLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLF 93
Cdd:PLN00153  24 QFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLL 97
PLN00156 PLN00156
histone H2AX; Provisional
 20-93 2.10e-08

histone H2AX; Provisional


Pssm-ID: 215080  Cd Length: 139  Bit Score: 48.43  E-value: 2.10e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 339639569  20 ELPFSLVDRFLREEFHSSRLSSSALSFLTSVLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLF 93
Cdd:PLN00156  29 QFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL 102
PLN00157 PLN00157
histone H2A; Provisional
 50-92 2.12e-08

histone H2A; Provisional


Pssm-ID: 177758  Cd Length: 132  Bit Score: 48.31  E-value: 2.12e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQL 92
Cdd:PLN00157  56 VLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKL 98
PLN00154 PLN00154
histone H2A; Provisional
 50-94 5.31e-07

histone H2A; Provisional


Pssm-ID: 177756  Cd Length: 136  Bit Score: 44.94  E-value: 5.31e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLFK 94
Cdd:PLN00154  69 ILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 113
HFD_SOS1_rpt2 cd22915
second histone-fold domain found in son of sevenless homolog 1 (SOS-1) and similar proteins; ...
 50-93 1.78e-05

second histone-fold domain found in son of sevenless homolog 1 (SOS-1) and similar proteins; SOS-1 is a guanine nucleotide exchange factor for Ras that binds to GRB2. It promotes the exchange of Ras-bound GDP by GTP. It is a catalytic component of a trimeric complex that participates in transduction of signals from Ras to Rac, by promoting the Rac-specific guanine nucleotide exchange factor (GEF) activity. SOS-1 contains tandem histone folds at the N-terminal region. The model corresponds to the second repeat.


Pssm-ID: 467040  Cd Length: 75  Bit Score: 39.53  E-value: 1.78e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRKRIAPEDVRLVVQNNEQLRQLF 93
Cdd:cd22915   31 VLEYIAADILKLAGNYVRNIRHYEITSQDIKVAMCADKVLMDLF 74
PTZ00252 PTZ00252
histone H2A; Provisional
 50-94 8.66e-05

histone H2A; Provisional


Pssm-ID: 240330  Cd Length: 134  Bit Score: 38.79  E-value: 8.66e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 339639569  50 VLEYLTSNILELAGEVAQTTGRK--RIAPEDVRLVVQNNEQLRQLFK 94
Cdd:PTZ00252  55 VLEYLTAELLELSVKAAAQQAKKpkRLTPRTVTLAVRHDDDLGSLLK 101
 
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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