NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|578468|emb|CAA24380|]
View 

unnamed protein product, partial [Psammechinus miliaris]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PLN00035 super family cl29687
histone H4; Provisional
 10-66 1.52e-24

histone H4; Provisional


The actual alignment was detected with superfamily member PLN00035:

Pssm-ID: 177669 [Multi-domain]  Cd Length: 103  Bit Score: 87.20  E-value: 1.52e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 578468     10 GLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:PLN00035  10 GLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENV 66
 
Name Accession Description Interval E-value
PLN00035 PLN00035
histone H4; Provisional
 10-66 1.52e-24

histone H4; Provisional


Pssm-ID: 177669 [Multi-domain]  Cd Length: 103  Bit Score: 87.20  E-value: 1.52e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 578468     10 GLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:PLN00035  10 GLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENV 66
H4 smart00417
Histone H4;
17-66 2.25e-19

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 73.34  E-value: 2.25e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 578468      17 KRHRKVLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:smart00417  1 RRHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENV 50
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 22-66 1.07e-17

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: 69.17  E-value: 1.07e-17
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*
gi 578468   22 VLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:cd22912  1 VLRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENV 45
 
Name Accession Description Interval E-value
PLN00035 PLN00035
histone H4; Provisional
 10-66 1.52e-24

histone H4; Provisional


Pssm-ID: 177669 [Multi-domain]  Cd Length: 103  Bit Score: 87.20  E-value: 1.52e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 578468     10 GLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:PLN00035  10 GLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENV 66
PTZ00015 PTZ00015
histone H4; Provisional
 16-66 9.54e-23

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 82.86  E-value: 9.54e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 578468     16 AKRHRKVLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:PTZ00015  17 QKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENV 67
H4 smart00417
Histone H4;
17-66 2.25e-19

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 73.34  E-value: 2.25e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 578468      17 KRHRKVLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:smart00417  1 RRHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENV 50
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 22-66 1.07e-17

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: 69.17  E-value: 1.07e-17
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*
gi 578468   22 VLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVLKVFLENV 66
Cdd:cd22912  1 VLRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENV 45
PLN00163 PLN00163
histone H4; Provisional
 16-59 6.06e-13

histone H4; Provisional


Pssm-ID: 165730  Cd Length: 59  Bit Score: 56.62  E-value: 6.06e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 578468    16 AKRHRKVLRDNIQGITKPAIRRLARRGVVKRISGLIYEETRGVL 59
Cdd:PLN00163 16 AKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRTVL 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH