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Conserved domains on  [gi|15231304|ref|NP_190184|]
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Histone superfamily protein [Arabidopsis thaliana]

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 ...
 61-148 1.60e-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: 173.86  E-value: 1.60e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304  61 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG 140
Cdd:cd22910   7 ESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEG 86


                ....*...
gi 15231304 141 TKAVTKFT 148
Cdd:cd22910  87 TKAVTKYT 94
valS super family cl36437
valyl-tRNA synthetase; Provisional
 2-47 2.45e-03

valyl-tRNA synthetase; Provisional


The actual alignment was detected with superfamily member PRK14900:

Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 37.28  E-value: 2.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15231304     2 APRAEKKPAEKKPAAEKPVEEKSKAEKAPAeKKPKAGKKLPKEAGA 47
Cdd:PRK14900  978 VRRSVKKAAATRAAMKKKVAKKAPAKKAAA-KKAAAKKAAAKKKVA 1022
 
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 ...
 61-148 1.60e-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: 173.86  E-value: 1.60e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304  61 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG 140
Cdd:cd22910   7 ESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEG 86


                ....*...
gi 15231304 141 TKAVTKFT 148
Cdd:cd22910  87 TKAVTKYT 94
H2B smart00427
Histone H2B;
59-149 2.11e-51

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 158.83  E-value: 2.11e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304     59 SVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVS 138
Cdd:smart00427   7 RKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVS 86

                           90
                   ....*....|.
gi 15231304    139 EGTKAVTKFTS 149
Cdd:smart00427  87 EGTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 28-150 9.05e-49

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 152.92  E-value: 9.05e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304   28 KAPAEKKPKAGKKLPKEAgaggdkkkkmkkkSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLA 107
Cdd:PLN00158   7 KKPAKKAAKGAKKKGSKS-------------KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLA 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 15231304  108 RYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 150
Cdd:PLN00158  74 RYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-127 1.71e-17

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 73.24  E-value: 1.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304     1 MAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKP-KAGKKLPKEagaggdKKKKMKKKSVETYKIYIFKVLKQVHP--- 76
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSSKKKTRRyRPGTVALKE------IRKYQSSTDLLIYKLPFARVVREVVQstk 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15231304    77 -DIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLV 127
Cdd:pfam00125  75 tDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
valS PRK14900
valyl-tRNA synthetase; Provisional
 2-47 2.45e-03

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 37.28  E-value: 2.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15231304     2 APRAEKKPAEKKPAAEKPVEEKSKAEKAPAeKKPKAGKKLPKEAGA 47
Cdd:PRK14900  978 VRRSVKKAAATRAAMKKKVAKKAPAKKAAA-KKAAAKKAAAKKKVA 1022
 
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 ...
 61-148 1.60e-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: 173.86  E-value: 1.60e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304  61 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG 140
Cdd:cd22910   7 ESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEG 86


                ....*...
gi 15231304 141 TKAVTKFT 148
Cdd:cd22910  87 TKAVTKYT 94
H2B smart00427
Histone H2B;
59-149 2.11e-51

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 158.83  E-value: 2.11e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304     59 SVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVS 138
Cdd:smart00427   7 RKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVS 86

                           90
                   ....*....|.
gi 15231304    139 EGTKAVTKFTS 149
Cdd:smart00427  87 EGTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 28-150 9.05e-49

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 152.92  E-value: 9.05e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304   28 KAPAEKKPKAGKKLPKEAgaggdkkkkmkkkSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLA 107
Cdd:PLN00158   7 KKPAKKAAKGAKKKGSKS-------------KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLA 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 15231304  108 RYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 150
Cdd:PLN00158  74 RYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
PTZ00463 PTZ00463
histone H2B; Provisional
 33-149 2.58e-37

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 123.75  E-value: 2.58e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304   33 KKPKAGKKlpkeAGAGGDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKK 112
Cdd:PTZ00463   4 KKPAKAKK----AATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRR 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 15231304  113 PTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 149
Cdd:PTZ00463  80 DTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-127 1.71e-17

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 73.24  E-value: 1.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15231304     1 MAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKP-KAGKKLPKEagaggdKKKKMKKKSVETYKIYIFKVLKQVHP--- 76
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSSKKKTRRyRPGTVALKE------IRKYQSSTDLLIYKLPFARVVREVVQstk 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15231304    77 -DIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLV 127
Cdd:pfam00125  75 tDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
valS PRK14900
valyl-tRNA synthetase; Provisional
 2-47 2.45e-03

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 37.28  E-value: 2.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15231304     2 APRAEKKPAEKKPAAEKPVEEKSKAEKAPAeKKPKAGKKLPKEAGA 47
Cdd:PRK14900  978 VRRSVKKAAATRAAMKKKVAKKAPAKKAAA-KKAAAKKAAAKKKVA 1022
valS PRK14900
valyl-tRNA synthetase; Provisional
 1-45 3.65e-03

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 36.51  E-value: 3.65e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15231304     1 MAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPK---AGKKLPKEA 45
Cdd:PRK14900  992 MKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAkkvARKPAAKKA 1039
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 69-125 5.37e-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: 33.73  E-value: 5.37e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15231304  69 KVLKQVHPDiGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVR 125
Cdd:cd00076   8 RILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
 
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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