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Conserved domains on  [gi|1235799950|gb|ASU91906|]
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histone 3, partial [Staleochlora viridicata viridicata]

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 ...
 1-98 4.49e-66

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: 195.12  E-value: 4.49e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950   1 ATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYL 80
Cdd:PTZ00018   22 ASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYL 101

                          90
                  ....*....|....*...
gi 1235799950  81 VGLFEDTNLCAIHAKRVT 98
Cdd:PTZ00018  102 VGLFEDTNLCAIHAKRVT 119
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-98 4.49e-66

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 195.12  E-value: 4.49e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950   1 ATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYL 80
Cdd:PTZ00018   22 ASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYL 101

                          90
                  ....*....|....*...
gi 1235799950  81 VGLFEDTNLCAIHAKRVT 98
Cdd:PTZ00018  102 VGLFEDTNLCAIHAKRVT 119
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 19-98 1.33e-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: 164.25  E-value: 1.33e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950 19 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 97
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80


                 .
gi 1235799950 98 T 98
Cdd:cd22911   81 T 81
H3 smart00428
Histone H3;
13-98 5.62e-51

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 155.68  E-value: 5.62e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950   13 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 90
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*...
gi 1235799950   91 AIHAKRVT 98
Cdd:smart00428  81 AIHAKRVT 88
Histone pfam00125
Core histone H2A/H2B/H3/H4;
16-98 3.42e-40

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 129.09  E-value: 3.42e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950  16 KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAK 95
Cdd:pfam00125  31 KKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAK 110


                  ...
gi 1235799950  96 RVT 98
Cdd:pfam00125 111 RVT 113
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-98 4.49e-66

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 195.12  E-value: 4.49e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950   1 ATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYL 80
Cdd:PTZ00018   22 ASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYL 101

                          90
                  ....*....|....*...
gi 1235799950  81 VGLFEDTNLCAIHAKRVT 98
Cdd:PTZ00018  102 VGLFEDTNLCAIHAKRVT 119
PLN00121 PLN00121
histone H3; Provisional
 1-98 9.66e-61

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 181.41  E-value: 9.66e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950   1 ATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYL 80
Cdd:PLN00121   22 ATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYL 101

                          90
                  ....*....|....*...
gi 1235799950  81 VGLFEDTNLCAIHAKRVT 98
Cdd:PLN00121  102 VGLFEDTNLCAIHAKRVT 119
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 19-98 1.33e-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: 164.25  E-value: 1.33e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950 19 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 97
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80


                 .
gi 1235799950 98 T 98
Cdd:cd22911   81 T 81
H3 smart00428
Histone H3;
13-98 5.62e-51

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 155.68  E-value: 5.62e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950   13 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLC 90
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80


                   ....*...
gi 1235799950   91 AIHAKRVT 98
Cdd:smart00428  81 AIHAKRVT 88
Histone pfam00125
Core histone H2A/H2B/H3/H4;
16-98 3.42e-40

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 129.09  E-value: 3.42e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950  16 KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAK 95
Cdd:pfam00125  31 KKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAK 110


                  ...
gi 1235799950  96 RVT 98
Cdd:pfam00125 111 RVT 113
PLN00161 PLN00161
histone H3; Provisional
 1-98 1.59e-37

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 122.80  E-value: 1.59e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1235799950   1 ATKAARKSAPATGGV--KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASE 77
Cdd:PLN00161   13 GKKPQKEASGVTRQEldKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREpFRWTAEALLALQEATE 92

                          90       100
                  ....*....|....*....|.
gi 1235799950  78 AYLVGLFEDTNLCAIHAKRVT 98
Cdd:PLN00161   93 DFLVHLFEDCNLCAIHAKRVT 113
PLN00160 PLN00160
histone H3; Provisional
 22-98 2.86e-31

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 105.51  E-value: 2.86e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1235799950 22 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVT 98
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMsREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVT 79
 
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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