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Conserved domains on  [gi|1387703672|gb|AUG98059|]
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histone H3, partial [Taeniopoda varipennis]

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 4.91e-70

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: 205.14  E-value: 4.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   1 PRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA 80
Cdd:PTZ00018   17 PRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEA 96

                          90       100
                  ....*....|....*....|....
gi 1387703672  81 SEAYLVGLFEDTNLCAIHAKRVTI 104
Cdd:PTZ00018   97 AEAYLVGLFEDTNLCAIHAKRVTI 120
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-104 4.91e-70

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 205.14  E-value: 4.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   1 PRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA 80
Cdd:PTZ00018   17 PRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEA 96

                          90       100
                  ....*....|....*....|....
gi 1387703672  81 SEAYLVGLFEDTNLCAIHAKRVTI 104
Cdd:PTZ00018   97 AEAYLVGLFEDTNLCAIHAKRVTI 120
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 24-104 1.10e-54

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: 165.02  E-value: 1.10e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672  24 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 102
Cdd:cd22911     1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80


                  ..
gi 1387703672 103 TI 104
Cdd:cd22911    81 TL 82
H3 smart00428
Histone H3;
18-104 4.83e-51

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 156.07  E-value: 4.83e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   18 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 95
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*....
gi 1387703672   96 AIHAKRVTI 104
Cdd:smart00428  81 AIHAKRVTI 89
Histone pfam00125
Core histone H2A/H2B/H3/H4;
2-104 9.37e-41

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 130.63  E-value: 9.37e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   2 RKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS 81
Cdd:pfam00125  12 RGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVALQEAV 91

                          90       100
                  ....*....|....*....|...
gi 1387703672  82 EAYLVGLFEDTNLCAIHAKRVTI 104
Cdd:pfam00125  92 EDFLVELFEEANLLAIHAKRVTL 114
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-104 4.91e-70

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 205.14  E-value: 4.91e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   1 PRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA 80
Cdd:PTZ00018   17 PRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEA 96

                          90       100
                  ....*....|....*....|....
gi 1387703672  81 SEAYLVGLFEDTNLCAIHAKRVTI 104
Cdd:PTZ00018   97 AEAYLVGLFEDTNLCAIHAKRVTI 120
PLN00121 PLN00121
histone H3; Provisional
 1-104 1.68e-64

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 191.42  E-value: 1.68e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   1 PRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA 80
Cdd:PLN00121   17 PRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEA 96

                          90       100
                  ....*....|....*....|....
gi 1387703672  81 SEAYLVGLFEDTNLCAIHAKRVTI 104
Cdd:PLN00121   97 AEAYLVGLFEDTNLCAIHAKRVTI 120
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 24-104 1.10e-54

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: 165.02  E-value: 1.10e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672  24 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 102
Cdd:cd22911     1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80


                  ..
gi 1387703672 103 TI 104
Cdd:cd22911    81 TL 82
H3 smart00428
Histone H3;
18-104 4.83e-51

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 156.07  E-value: 4.83e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   18 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 95
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*....
gi 1387703672   96 AIHAKRVTI 104
Cdd:smart00428  81 AIHAKRVTI 89
Histone pfam00125
Core histone H2A/H2B/H3/H4;
2-104 9.37e-41

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 130.63  E-value: 9.37e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   2 RKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS 81
Cdd:pfam00125  12 RGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVALQEAV 91

                          90       100
                  ....*....|....*....|...
gi 1387703672  82 EAYLVGLFEDTNLCAIHAKRVTI 104
Cdd:pfam00125  92 EDFLVELFEEANLLAIHAKRVTL 114
PLN00161 PLN00161
histone H3; Provisional
 6-104 2.12e-37

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 122.80  E-value: 2.12e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387703672   6 ATKAARKSAPATGGV--KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASE 82
Cdd:PLN00161   13 GKKPQKEASGVTRQEldKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREpFRWTAEALLALQEATE 92

                          90       100
                  ....*....|....*....|..
gi 1387703672  83 AYLVGLFEDTNLCAIHAKRVTI 104
Cdd:PLN00161   93 DFLVHLFEDCNLCAIHAKRVTI 114
PLN00160 PLN00160
histone H3; Provisional
 27-104 2.81e-31

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 105.90  E-value: 2.81e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1387703672  27 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 104
Cdd:PLN00160    2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMsREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTI 80
 
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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