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Conserved domains on  [gi|2225702204|ref|NP_001391934|]
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histone H2B [Capsicum annuum]

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

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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 ...
 56-143 4.51e-57

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: 172.70  E-value: 4.51e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204  56 ETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKPTITSREIQTAVRLVLPGELAKHAVSEG 135
Cdd:cd22910     7 ESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEG 86


                  ....*...
gi 2225702204 136 TKAVTKFT 143
Cdd:cd22910    87 TKAVTKYT 94
 
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 ...
 56-143 4.51e-57

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: 172.70  E-value: 4.51e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204  56 ETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKPTITSREIQTAVRLVLPGELAKHAVSEG 135
Cdd:cd22910     7 ESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEG 86


                  ....*...
gi 2225702204 136 TKAVTKFT 143
Cdd:cd22910    87 TKAVTKYT 94
H2B smart00427
Histone H2B;
56-144 1.70e-50

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 156.14  E-value: 1.70e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204   56 ETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKPTITSREIQTAVRLVLPGELAKHAVSEG 135
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88


                   ....*....
gi 2225702204  136 TKAVTKFTS 144
Cdd:smart00427  89 TKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 30-145 1.39e-47

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 149.46  E-value: 1.39e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204  30 KPKAGKKLPKDASGAdkKKKKAKKSIETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKPT 109
Cdd:PLN00158    3 KTPSKKPAKKAAKGA--KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPT 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2225702204 110 ITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 145
Cdd:PLN00158   81 VTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
9-122 1.43e-15

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 68.23  E-value: 1.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204   9 KKPAEKKPVEEKKAEGVPAEKKPKAGKKLPKDASGADKKKKKAKKSIE--TYKIYIFKVLKQVHP----DIGISSKSMGI 82
Cdd:pfam00125   7 KANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDllIYKLPFARVVREVVQstktDLRISADAVVA 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2225702204  83 MNSFINDIFEKLAQESSRLARINKKPTITSREIQTAVRLV 122
Cdd:pfam00125  87 LQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 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 ...
 56-143 4.51e-57

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: 172.70  E-value: 4.51e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204  56 ETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKPTITSREIQTAVRLVLPGELAKHAVSEG 135
Cdd:cd22910     7 ESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEG 86


                  ....*...
gi 2225702204 136 TKAVTKFT 143
Cdd:cd22910    87 TKAVTKYT 94
H2B smart00427
Histone H2B;
56-144 1.70e-50

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 156.14  E-value: 1.70e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204   56 ETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKPTITSREIQTAVRLVLPGELAKHAVSEG 135
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88


                   ....*....
gi 2225702204  136 TKAVTKFTS 144
Cdd:smart00427  89 TKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 30-145 1.39e-47

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 149.46  E-value: 1.39e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204  30 KPKAGKKLPKDASGAdkKKKKAKKSIETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKPT 109
Cdd:PLN00158    3 KTPSKKPAKKAAKGA--KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPT 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2225702204 110 ITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 145
Cdd:PLN00158   81 VTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
PTZ00463 PTZ00463
histone H2B; Provisional
 29-144 4.29e-38

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 125.67  E-value: 4.29e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204  29 KKPKAGKKLpkdASGADKKKKKAKKSIETYKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARINKKP 108
Cdd:PTZ00463    4 KKPAKAKKA---ATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRD 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2225702204 109 TITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 144
Cdd:PTZ00463   81 TLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
9-122 1.43e-15

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 68.23  E-value: 1.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225702204   9 KKPAEKKPVEEKKAEGVPAEKKPKAGKKLPKDASGADKKKKKAKKSIE--TYKIYIFKVLKQVHP----DIGISSKSMGI 82
Cdd:pfam00125   7 KANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDllIYKLPFARVVREVVQstktDLRISADAVVA 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2225702204  83 MNSFINDIFEKLAQESSRLARINKKPTITSREIQTAVRLV 122
Cdd:pfam00125  87 LQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 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.
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