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Conserved domains on  [gi|17553562|ref|NP_499073|]
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Histone H3-like centromeric protein cpar-1 [Caenorhabditis elegans]

Protein Classification

histone H3 family protein( domain architecture ID 11269512)

histone H3 family protein similar to histone H3-like nucleosomal protein that is specifically found in centromeric nucleosomes

Gene Ontology:  GO:0003677|GO:0046982|GO:0034080|GO:0005654
PubMed:  8121801
SCOP:  4000793

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
H3 smart00428
Histone H3;
156-261 2.94e-59

Histone H3;


:

Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 183.42  E-value: 2.94e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562    156 NRISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTSTPFSsDLRIRSDAINALQEASEALLVQMFDGSSL 235
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGV-DLRFQSSAIMALQEAAEAYLVGLFEDTNL 79

                           90       100
                   ....*....|....*....|....*.
gi 17553562    236 ISAHSKRATLTTTDVQLYRRLCLPNL 261
Cdd:smart00428  80 LAIHAKRVTIMPKDIQLARRIRGERL 105
 
Name Accession Description Interval E-value
H3 smart00428
Histone H3;
156-261 2.94e-59

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 183.42  E-value: 2.94e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562    156 NRISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTSTPFSsDLRIRSDAINALQEASEALLVQMFDGSSL 235
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGV-DLRFQSSAIMALQEAAEAYLVGLFEDTNL 79

                           90       100
                   ....*....|....*....|....*.
gi 17553562    236 ISAHSKRATLTTTDVQLYRRLCLPNL 261
Cdd:smart00428  80 LAIHAKRVTIMPKDIQLARRIRGERL 105
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 162-257 3.55e-45

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: 146.92  E-value: 3.55e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562 162 RRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTSTPfsSDLRIRSDAINALQEASEALLVQMFDGSSLISAHSK 241
Cdd:cd22911   1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKT--KDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAK 78

                        90
                ....*....|....*.
gi 17553562 242 RATLTTTDVQLYRRLC 257
Cdd:cd22911  79 RVTLMPKDMQLARRIR 94
Histone pfam00125
Core histone H2A/H2B/H3/H4;
133-257 9.78e-40

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 134.10  E-value: 9.78e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562   133 TNGRNGSRAGSSSSDRVRMIAGRNRISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTstpFSSDLRIRS 212
Cdd:pfam00125   5 KNKANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQS---TKTDLRISA 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 17553562   213 DAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDVQLYRRLC 257
Cdd:pfam00125  82 DAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PTZ00018 PTZ00018
histone H3; Provisional
 158-256 4.67e-34

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 120.01  E-value: 4.67e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562  158 ISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTstpFSSDLRIRSDAINALQEASEALLVQMFDGSSLIS 237
Cdd:PTZ00018  36 IKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD---FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCA 112

                         90
                 ....*....|....*....
gi 17553562  238 AHSKRATLTTTDVQLYRRL 256
Cdd:PTZ00018 113 IHAKRVTIMPKDIQLARRI 131
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
185-256 1.27e-04

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 39.43  E-value: 1.27e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17553562 185 IPKAPFARLVREImqtstpfsSDLRIRSDAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDVQLYRRL 256
Cdd:COG2036   2 LPVAPVDRIIKKA--------GAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
 
Name Accession Description Interval E-value
H3 smart00428
Histone H3;
156-261 2.94e-59

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 183.42  E-value: 2.94e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562    156 NRISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTSTPFSsDLRIRSDAINALQEASEALLVQMFDGSSL 235
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGV-DLRFQSSAIMALQEAAEAYLVGLFEDTNL 79

                           90       100
                   ....*....|....*....|....*.
gi 17553562    236 ISAHSKRATLTTTDVQLYRRLCLPNL 261
Cdd:smart00428  80 LAIHAKRVTIMPKDIQLARRIRGERL 105
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 162-257 3.55e-45

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: 146.92  E-value: 3.55e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562 162 RRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTSTPfsSDLRIRSDAINALQEASEALLVQMFDGSSLISAHSK 241
Cdd:cd22911   1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKT--KDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAK 78

                        90
                ....*....|....*.
gi 17553562 242 RATLTTTDVQLYRRLC 257
Cdd:cd22911  79 RVTLMPKDMQLARRIR 94
Histone pfam00125
Core histone H2A/H2B/H3/H4;
133-257 9.78e-40

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 134.10  E-value: 9.78e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562   133 TNGRNGSRAGSSSSDRVRMIAGRNRISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTstpFSSDLRIRS 212
Cdd:pfam00125   5 KNKANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQS---TKTDLRISA 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 17553562   213 DAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDVQLYRRLC 257
Cdd:pfam00125  82 DAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PTZ00018 PTZ00018
histone H3; Provisional
 158-256 4.67e-34

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 120.01  E-value: 4.67e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562  158 ISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTstpFSSDLRIRSDAINALQEASEALLVQMFDGSSLIS 237
Cdd:PTZ00018  36 IKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD---FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCA 112

                         90
                 ....*....|....*....
gi 17553562  238 AHSKRATLTTTDVQLYRRL 256
Cdd:PTZ00018 113 IHAKRVTIMPKDIQLARRI 131
PLN00121 PLN00121
histone H3; Provisional
 158-256 5.43e-31

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 112.07  E-value: 5.43e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562  158 ISKTRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTstpFSSDLRIRSDAINALQEASEALLVQMFDGSSLIS 237
Cdd:PLN00121  36 VKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQD---FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCA 112

                         90
                 ....*....|....*....
gi 17553562  238 AHSKRATLTTTDVQLYRRL 256
Cdd:PLN00121 113 IHAKRVTIMPKDIQLARRI 131
PLN00161 PLN00161
histone H3; Provisional
 132-256 1.03e-28

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 105.85  E-value: 1.03e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562  132 GTNGRNGSRAGSSSSDRVRMIAGRNRisktRRYRPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTSTPfsSDLRIR 211
Cdd:PLN00161   7 GKRFRKGKKPQKEASGVTRQELDKKP----HRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLR--EPFRWT 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 17553562  212 SDAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDVQLYRRL 256
Cdd:PLN00161  81 AEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125
PLN00160 PLN00160
histone H3; Provisional
 165-256 2.52e-24

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 93.57  E-value: 2.52e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562  165 RPGQKALEEIRKYQESEDLLIPKAPFARLVREIMQTSTpfSSDLRIRSDAINALQEASEALLVQMFDGSSLISAHSKRAT 244
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMS--REAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVT 79

                         90
                 ....*....|..
gi 17553562  245 LTTTDVQLYRRL 256
Cdd:PLN00160  80 IMPKDMQLARRI 91
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
185-256 1.27e-04

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 39.43  E-value: 1.27e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17553562 185 IPKAPFARLVREImqtstpfsSDLRIRSDAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDVQLYRRL 256
Cdd:COG2036   2 LPVAPVDRIIKKA--------GAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
HFD_POLE3_DPB4 cd22928
histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; ...
 181-250 1.45e-04

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.


Pssm-ID: 467053  Cd Length: 87  Bit Score: 39.80  E-value: 1.45e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553562 181 EDLLIPKAPFARLVREIMqtstpfSSDLRIRSDAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDV 250
Cdd:cd22928   1 DDLELPRAVITRIIKEAL------PEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDV 64
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 185-253 2.22e-04

histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.


Pssm-ID: 467045  Cd Length: 94  Bit Score: 39.46  E-value: 2.22e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17553562 185 IPKApfarLVREIMQTSTpfssDLRIRSDAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDVQLY 253
Cdd:cd22920   3 LPKS----LVKKLFKHFL----KRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVELL 63
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 185-255 4.11e-04

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 37.91  E-value: 4.11e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17553562 185 IPKAPFARLVREimqtstpfSSDLRIRSDAINALQEASEALLVQMFDGSSLISAHSKRATLTTTDVQLYRR 255
Cdd:cd22909   2 LPKAPVKRIIKK--------AGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
 
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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