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Conserved domains on  [gi|2067839569|gb|QXP00658|]
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histone H3, partial [Gryllidae gen. 2 sp. 6 JD-2021b]

Protein Classification

histone H3/H4 domain-containing protein( domain architecture ID 581047)

histone H3/H4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_SF super family cl45933
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 1-104 6.91e-69

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.


The actual alignment was detected with superfamily member PTZ00018:

Pssm-ID: 480273 [Multi-domain]  Cd Length: 136  Bit Score: 202.44  E-value: 6.91e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   1 GKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL 80
Cdd:PTZ00018   14 GKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLAL 93

                          90       100
                  ....*....|....*....|....
gi 2067839569  81 QEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:PTZ00018   94 QEAAEAYLVGLFEDTNLCAIHAKR 117
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-104 6.91e-69

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 202.44  E-value: 6.91e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   1 GKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL 80
Cdd:PTZ00018   14 GKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLAL 93

                          90       100
                  ....*....|....*....|....
gi 2067839569  81 QEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:PTZ00018   94 QEAAEAYLVGLFEDTNLCAIHAKR 117
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 27-104 2.62e-52

histone-fold domain found in histone H3 and similar proteins; Histone H3 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: 467036  Cd Length: 95  Bit Score: 158.86  E-value: 2.62e-52
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067839569  27 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:cd22911     1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKR 79
H3 smart00428
Histone H3;
21-104 8.65e-49

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 150.29  E-value: 8.65e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   21 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 98
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*.
gi 2067839569   99 AIHAKR 104
Cdd:smart00428  81 AIHAKR 86
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-104 9.40e-39

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 125.62  E-value: 9.40e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   1 GKAPRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL 80
Cdd:pfam00125  14 GTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVAL 87

                          90       100
                  ....*....|....*....|....
gi 2067839569  81 QEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:pfam00125  88 QEAVEDFLVELFEEANLLAIHAKR 111
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-104 6.91e-69

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 202.44  E-value: 6.91e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   1 GKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL 80
Cdd:PTZ00018   14 GKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLAL 93

                          90       100
                  ....*....|....*....|....
gi 2067839569  81 QEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:PTZ00018   94 QEAAEAYLVGLFEDTNLCAIHAKR 117
PLN00121 PLN00121
histone H3; Provisional
 1-104 1.22e-63

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 189.11  E-value: 1.22e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   1 GKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL 80
Cdd:PLN00121   14 GKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLAL 93

                          90       100
                  ....*....|....*....|....
gi 2067839569  81 QEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:PLN00121   94 QEAAEAYLVGLFEDTNLCAIHAKR 117
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 27-104 2.62e-52

histone-fold domain found in histone H3 and similar proteins; Histone H3 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: 467036  Cd Length: 95  Bit Score: 158.86  E-value: 2.62e-52
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067839569  27 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:cd22911     1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKR 79
H3 smart00428
Histone H3;
21-104 8.65e-49

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 150.29  E-value: 8.65e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   21 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 98
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*.
gi 2067839569   99 AIHAKR 104
Cdd:smart00428  81 AIHAKR 86
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-104 9.40e-39

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 125.62  E-value: 9.40e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   1 GKAPRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL 80
Cdd:pfam00125  14 GTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVAL 87

                          90       100
                  ....*....|....*....|....
gi 2067839569  81 QEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:pfam00125  88 QEAVEDFLVELFEEANLLAIHAKR 111
PLN00161 PLN00161
histone H3; Provisional
 1-104 1.94e-35

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 117.79  E-value: 1.94e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067839569   1 GKAPRKQLATKAARKSApatggvKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMA 79
Cdd:PLN00161   13 GKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREpFRWTAEALLA 86

                          90       100
                  ....*....|....*....|....*
gi 2067839569  80 LQEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:PLN00161   87 LQEATEDFLVHLFEDCNLCAIHAKR 111
PLN00160 PLN00160
histone H3; Provisional
 30-104 3.39e-29

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 100.51  E-value: 3.39e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2067839569  30 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 104
Cdd:PLN00160    2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMsREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKR 77
 
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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