NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|75180188|sp|Q9LQQ4|]
View 

RecName: Full=Histone H2B.1; Short=HTB1

Protein Classification

histone H2B family protein( domain architecture ID 19223400)

histone H2B is one of 4 core histone proteins, H2A, H2B, H3 and H4 to form the nucleosome core particle

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0005634|GO:0000786|GO:0046982|GO:0044877|GO:0030527

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 ...
 57-146 5.30e-58

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: 175.01  E-value: 5.30e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188  57 NVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVS 136
Cdd:cd22910   5 RKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVS 84

                        90
                ....*....|
gi 75180188 137 EGTKAVTKFT 146
Cdd:cd22910  85 EGTKAVTKYT 94
valS super family cl36437
valyl-tRNA synthetase; Provisional
 1-46 4.71e-04

valyl-tRNA synthetase; Provisional


The actual alignment was detected with superfamily member PRK14900:

Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 39.20  E-value: 4.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 75180188     1 MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKP--KAGKKLPPKEA 46
Cdd:PRK14900  992 MKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPakKVARKPAAKKA 1039
 
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 ...
 57-146 5.30e-58

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: 175.01  E-value: 5.30e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188  57 NVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVS 136
Cdd:cd22910   5 RKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVS 84

                        90
                ....*....|
gi 75180188 137 EGTKAVTKFT 146
Cdd:cd22910  85 EGTKAVTKYT 94
H2B smart00427
Histone H2B;
57-147 5.49e-52

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 159.99  E-value: 5.49e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188     57 NVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVS 136
Cdd:smart00427   7 RKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVS 86

                           90
                   ....*....|.
gi 75180188    137 EGTKAVTKFTS 147
Cdd:smart00427  87 EGTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 24-148 7.26e-51

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 157.93  E-value: 7.26e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188   24 KAAEKAPAEKKPKAGKKLPPKEagdkkkkrskkNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSK 103
Cdd:PLN00158   3 KTPSKKPAKKAAKGAKKKGSKS-----------KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGK 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 75180188  104 LARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 148
Cdd:PLN00158  72 LARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-125 3.40e-18

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 75.16  E-value: 3.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188     1 MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEagdKKKKRSKKNVETYKIYIFKVLKQVHP----DI 76
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKE---IRKYQSSTDLLIYKLPFARVVREVVQstktDL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 75180188    77 GISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLV 125
Cdd:pfam00125  78 RISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
valS PRK14900
valyl-tRNA synthetase; Provisional
 1-46 4.71e-04

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 39.20  E-value: 4.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 75180188     1 MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKP--KAGKKLPPKEA 46
Cdd:PRK14900  992 MKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPakKVARKPAAKKA 1039
 
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 ...
 57-146 5.30e-58

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: 175.01  E-value: 5.30e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188  57 NVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVS 136
Cdd:cd22910   5 RKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVS 84

                        90
                ....*....|
gi 75180188 137 EGTKAVTKFT 146
Cdd:cd22910  85 EGTKAVTKYT 94
H2B smart00427
Histone H2B;
57-147 5.49e-52

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 159.99  E-value: 5.49e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188     57 NVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVS 136
Cdd:smart00427   7 RKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVS 86

                           90
                   ....*....|.
gi 75180188    137 EGTKAVTKFTS 147
Cdd:smart00427  87 EGTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 24-148 7.26e-51

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 157.93  E-value: 7.26e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188   24 KAAEKAPAEKKPKAGKKLPPKEagdkkkkrskkNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSK 103
Cdd:PLN00158   3 KTPSKKPAKKAAKGAKKKGSKS-----------KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGK 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 75180188  104 LARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 148
Cdd:PLN00158  72 LARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
PTZ00463 PTZ00463
histone H2B; Provisional
 33-147 9.00e-37

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 122.21  E-value: 9.00e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188   33 KKPKAGKKlpPKEAGDKKKKRSKKNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPT 112
Cdd:PTZ00463   4 KKPAKAKK--AATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDT 81

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 75180188  113 ITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 147
Cdd:PTZ00463  82 LSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-125 3.40e-18

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 75.16  E-value: 3.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75180188     1 MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEagdKKKKRSKKNVETYKIYIFKVLKQVHP----DI 76
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKE---IRKYQSSTDLLIYKLPFARVVREVVQstktDL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 75180188    77 GISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLV 125
Cdd:pfam00125  78 RISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
valS PRK14900
valyl-tRNA synthetase; Provisional
 1-46 4.71e-04

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 39.20  E-value: 4.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 75180188     1 MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKP--KAGKKLPPKEA 46
Cdd:PRK14900  992 MKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPakKVARKPAAKKA 1039
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 67-123 5.97e-03

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: 33.35  E-value: 5.97e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 75180188  67 KVLKQVHPDiGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVR 123
Cdd:cd00076   8 RILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
valS PRK14900
valyl-tRNA synthetase; Provisional
 2-46 8.74e-03

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 35.35  E-value: 8.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 75180188     2 APRAEKKPAEKKTAAERPVEENKAAEKAPAEK---KPKAGKKLPPKEA 46
Cdd:PRK14900  978 VRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKaaaKKAAAKKKVAKKA 1025
 
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