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Conserved domains on  [gi|970840034|gb|ALU66424|]
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histone 3, partial [Sphenarium macrophallicum]

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 ...
 1-106 1.59e-71

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: 208.99  E-value: 1.59e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034   1 APRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQE 80
Cdd:PTZ00018  16 APRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQE 95

                         90       100
                 ....*....|....*....|....*.
gi 970840034  81 ASEAYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:PTZ00018  96 AAEAYLVGLFEDTNLCAIHAKRVTIM 121
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-106 1.59e-71

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 208.99  E-value: 1.59e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034   1 APRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQE 80
Cdd:PTZ00018  16 APRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQE 95

                         90       100
                 ....*....|....*....|....*.
gi 970840034  81 ASEAYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:PTZ00018  96 AAEAYLVGLFEDTNLCAIHAKRVTIM 121
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 25-106 1.04e-55

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: 167.72  E-value: 1.04e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034  25 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 103
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80


                 ...
gi 970840034 104 TIM 106
Cdd:cd22911   81 TLM 83
H3 smart00428
Histone H3;
19-106 5.59e-52

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 158.38  E-value: 5.59e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034    19 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 96
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90
                   ....*....|
gi 970840034    97 AIHAKRVTIM 106
Cdd:smart00428  81 AIHAKRVTIM 90
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-106 1.23e-41

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 132.94  E-value: 1.23e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034    1 APRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQE 80
Cdd:pfam00125  16 APEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVALQE 89

                          90       100
                  ....*....|....*....|....*.
gi 970840034   81 ASEAYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:pfam00125  90 AVEDFLVELFEEANLLAIHAKRVTLT 115
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-106 1.59e-71

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 208.99  E-value: 1.59e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034   1 APRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQE 80
Cdd:PTZ00018  16 APRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQE 95

                         90       100
                 ....*....|....*....|....*.
gi 970840034  81 ASEAYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:PTZ00018  96 AAEAYLVGLFEDTNLCAIHAKRVTIM 121
PLN00121 PLN00121
histone H3; Provisional
 1-106 7.02e-66

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 194.89  E-value: 7.02e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034   1 APRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQE 80
Cdd:PLN00121  16 APRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQE 95

                         90       100
                 ....*....|....*....|....*.
gi 970840034  81 ASEAYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:PLN00121  96 AAEAYLVGLFEDTNLCAIHAKRVTIM 121
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 25-106 1.04e-55

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: 167.72  E-value: 1.04e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034  25 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 103
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80


                 ...
gi 970840034 104 TIM 106
Cdd:cd22911   81 TLM 83
H3 smart00428
Histone H3;
19-106 5.59e-52

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 158.38  E-value: 5.59e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034    19 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 96
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90
                   ....*....|
gi 970840034    97 AIHAKRVTIM 106
Cdd:smart00428  81 AIHAKRVTIM 90
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-106 1.23e-41

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 132.94  E-value: 1.23e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034    1 APRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQE 80
Cdd:pfam00125  16 APEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVALQE 89

                          90       100
                  ....*....|....*....|....*.
gi 970840034   81 ASEAYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:pfam00125  90 AVEDFLVELFEEANLLAIHAKRVTLT 115
PLN00161 PLN00161
histone H3; Provisional
 7-106 1.86e-38

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 125.50  E-value: 1.86e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034   7 ATKAARKSAPATGGV--KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASE 83
Cdd:PLN00161  13 GKKPQKEASGVTRQEldKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREpFRWTAEALLALQEATE 92

                         90       100
                 ....*....|....*....|...
gi 970840034  84 AYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:PLN00161  93 DFLVHLFEDCNLCAIHAKRVTIM 115
PLN00160 PLN00160
histone H3; Provisional
 28-106 5.09e-32

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 107.83  E-value: 5.09e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970840034  28 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM 106
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMsREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIM 81
 
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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