NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|254588087|ref|NP_081343|]
View 

histone variant H2bl2 [Mus musculus]

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
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 133-220 3.26e-39

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


:

Pssm-ID: 467035  Cd Length: 94  Bit Score: 130.33  E-value: 3.26e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087 133 KNSFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAE 212
Cdd:cd22910    6 KESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSE 85


                 ....*...
gi 254588087 213 GTMAMVRY 220
Cdd:cd22910   86 GTKAVTKY 93
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 133-220 3.26e-39

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 130.33  E-value: 3.26e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087 133 KNSFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAE 212
Cdd:cd22910    6 KESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSE 85


                 ....*...
gi 254588087 213 GTMAMVRY 220
Cdd:cd22910   86 GTKAVTKY 93
H2B smart00427
Histone H2B;
133-222 2.49e-30

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 107.99  E-value: 2.49e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087   133 KNSFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAE 212
Cdd:smart00427   8 KETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSE 87

                           90
                   ....*....|
gi 254588087   213 GTMAMVRYIS 222
Cdd:smart00427  88 GTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 135-223 9.86e-28

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 101.69  E-value: 9.86e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087 135 SFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAEGT 214
Cdd:PLN00158  28 TYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGT 107


                 ....*....
gi 254588087 215 MAMVRYISN 223
Cdd:PLN00158 108 KAVTKFTSA 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
100-200 1.71e-18

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 78.24  E-value: 1.71e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087  100 ETPEQEKPEVQRRRSLHQSIREDERRARLIRRRKNSFAIYFPKVLKNIH----VGLSLSQRSVNILDSFVKDMFERIASE 175
Cdd:pfam00125  22 SQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVqstkTDLRISADAVVALQEAVEDFLVELFEE 101

                          90       100
                  ....*....|....*....|....*
gi 254588087  176 ASFLARQARNSTINSREIQTAIRLL 200
Cdd:pfam00125 102 ANLLAIHAKRVTLTPKDIQLARRLR 126
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 133-220 3.26e-39

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 130.33  E-value: 3.26e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087 133 KNSFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAE 212
Cdd:cd22910    6 KESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSE 85


                 ....*...
gi 254588087 213 GTMAMVRY 220
Cdd:cd22910   86 GTKAVTKY 93
H2B smart00427
Histone H2B;
133-222 2.49e-30

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 107.99  E-value: 2.49e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087   133 KNSFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAE 212
Cdd:smart00427   8 KETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSE 87

                           90
                   ....*....|
gi 254588087   213 GTMAMVRYIS 222
Cdd:smart00427  88 GTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 135-223 9.86e-28

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 101.69  E-value: 9.86e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087 135 SFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAEGT 214
Cdd:PLN00158  28 TYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGT 107


                 ....*....
gi 254588087 215 MAMVRYISN 223
Cdd:PLN00158 108 KAVTKFTSA 116
PTZ00463 PTZ00463
histone H2B; Provisional
 134-222 3.85e-23

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 89.85  E-value: 3.85e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087 134 NSFAIYFPKVLKNIHVGLSLSQRSVNILDSFVKDMFERIASEASFLARQARNSTINSREIQTAIRLLLPGELCRRAVAEG 213
Cdd:PTZ00463  28 DSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEG 107


                 ....*....
gi 254588087 214 TMAMVRYIS 222
Cdd:PTZ00463 108 TKAVTKFTS 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
100-200 1.71e-18

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 78.24  E-value: 1.71e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254588087  100 ETPEQEKPEVQRRRSLHQSIREDERRARLIRRRKNSFAIYFPKVLKNIH----VGLSLSQRSVNILDSFVKDMFERIASE 175
Cdd:pfam00125  22 SQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVqstkTDLRISADAVVALQEAVEDFLVELFEE 101

                          90       100
                  ....*....|....*....|....*
gi 254588087  176 ASFLARQARNSTINSREIQTAIRLL 200
Cdd:pfam00125 102 ANLLAIHAKRVTLTPKDIQLARRLR 126
 
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