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Conserved domains on  [gi|37788229|gb|AAP45030|]
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histone H3, partial [Pomphorhynchus laevis]

Protein Classification

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 ...
 1-109 5.11e-72

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: 210.53  E-value: 5.11e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229    1 RKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 80
Cdd:PTZ00018   9 RKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 88

                         90       100
                 ....*....|....*....|....*....
gi 37788229   81 AVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:PTZ00018  89 AVLALQEAAEAYLVGLFEDTNLCAIHAKR 117
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-109 5.11e-72

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 210.53  E-value: 5.11e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229    1 RKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 80
Cdd:PTZ00018   9 RKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 88

                         90       100
                 ....*....|....*....|....*....
gi 37788229   81 AVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:PTZ00018  89 AVLALQEAAEAYLVGLFEDTNLCAIHAKR 117
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 32-109 2.24e-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: 159.24  E-value: 2.24e-52
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 37788229  32 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:cd22911   1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKR 79
H3 smart00428
Histone H3;
26-109 1.07e-48

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 150.29  E-value: 1.07e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229     26 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 103
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*.
gi 37788229    104 AIHAKR 109
Cdd:smart00428  81 AIHAKR 86
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-109 1.25e-39

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 128.32  E-value: 1.25e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229     1 RKSTGGKAPRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 80
Cdd:pfam00125   9 NPRRGGTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISAD 82

                          90       100
                  ....*....|....*....|....*....
gi 37788229    81 AVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:pfam00125  83 AVVALQEAVEDFLVELFEEANLLAIHAKR 111
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-109 5.11e-72

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 210.53  E-value: 5.11e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229    1 RKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 80
Cdd:PTZ00018   9 RKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 88

                         90       100
                 ....*....|....*....|....*....
gi 37788229   81 AVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:PTZ00018  89 AVLALQEAAEAYLVGLFEDTNLCAIHAKR 117
PLN00121 PLN00121
histone H3; Provisional
 1-109 2.27e-66

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 196.04  E-value: 2.27e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229    1 RKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 80
Cdd:PLN00121   9 RKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 88

                         90       100
                 ....*....|....*....|....*....
gi 37788229   81 AVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:PLN00121  89 AVLALQEAAEAYLVGLFEDTNLCAIHAKR 117
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 32-109 2.24e-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: 159.24  E-value: 2.24e-52
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 37788229  32 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:cd22911   1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKR 79
H3 smart00428
Histone H3;
26-109 1.07e-48

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 150.29  E-value: 1.07e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229     26 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 103
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*.
gi 37788229    104 AIHAKR 109
Cdd:smart00428  81 AIHAKR 86
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-109 1.25e-39

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 128.32  E-value: 1.25e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229     1 RKSTGGKAPRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS 80
Cdd:pfam00125   9 NPRRGGTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISAD 82

                          90       100
                  ....*....|....*....|....*....
gi 37788229    81 AVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:pfam00125  83 AVVALQEAVEDFLVELFEEANLLAIHAKR 111
PLN00161 PLN00161
histone H3; Provisional
 1-109 3.03e-35

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 117.41  E-value: 3.03e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37788229    1 RKSTGGKAPRKQLATKAARKSApatggvKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD-LRFQS 79
Cdd:PLN00161   8 KRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREpFRWTA 81

                         90       100       110
                 ....*....|....*....|....*....|
gi 37788229   80 SAVMALQEASEAYLVGLFEDTNLCAIHAKR 109
Cdd:PLN00161  82 EALLALQEATEDFLVHLFEDCNLCAIHAKR 111
PLN00160 PLN00160
histone H3; Provisional
 35-109 4.93e-29

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 100.51  E-value: 4.93e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 37788229   35 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 109
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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