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Conserved domains on  [gi|74867485|sp|Q9V6Q2|]
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RecName: Full=Histone H3-like centromeric protein cid; AltName: Full=CENP-A homolog; AltName: Full=Centromere identifier protein

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 ...
 126-219 2.96e-32

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 cd22911:

Pssm-ID: 480273  Cd Length: 95  Bit Score: 112.63  E-value: 2.96e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485 126 PMSRAKRMDREIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDEpLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRV 205
Cdd:cd22911   2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKD-LRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                        90
                ....*....|....
gi 74867485 206 TLEVRDMALMAYIC 219
Cdd:cd22911  81 TLMPKDMQLARRIR 94
 
Name Accession Description Interval E-value
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 126-219 2.96e-32

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: 112.63  E-value: 2.96e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485 126 PMSRAKRMDREIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDEpLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRV 205
Cdd:cd22911   2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKD-LRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                        90
                ....*....|....
gi 74867485 206 TLEVRDMALMAYIC 219
Cdd:cd22911  81 TLMPKDMQLARRIR 94
H3 smart00428
Histone H3;
135-219 5.84e-19

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 78.64  E-value: 5.84e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485    135 REIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDEPLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMAL 214
Cdd:smart00428  17 REIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQL 96


                   ....*
gi 74867485    215 MAYIC 219
Cdd:smart00428  97 ARRIR 101
Histone pfam00125
Core histone H2A/H2B/H3/H4;
94-219 1.07e-18

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 78.63  E-value: 1.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485    94 QTRRMTVQQESKTRAAGPVAAQNQTRRRKAANPMSRAKRmdrEIRRLQHHPGTLIPKLPFSRLVREfiVKYSDDEPLRVT 173
Cdd:pfam00125   6 NKANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALK---EIRKYQSSTDLLIYKLPFARVVRE--VVQSTKTDLRIS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 74867485   174 EGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMALMAYIC 219
Cdd:pfam00125  81 ADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PTZ00018 PTZ00018
histone H3; Provisional
 135-225 9.91e-13

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 63.00  E-value: 9.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485  135 REIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDepLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMAL 214
Cdd:PTZ00018  50 REIRRYQKSTELLIRKLPFQRLVREIAQDFKTD--LRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 127

                         90
                 ....*....|.
gi 74867485  215 MAYIcdRGRQF 225
Cdd:PTZ00018 128 ARRI--RGERS 136
 
Name Accession Description Interval E-value
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 126-219 2.96e-32

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: 112.63  E-value: 2.96e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485 126 PMSRAKRMDREIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDEpLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRV 205
Cdd:cd22911   2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKD-LRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                        90
                ....*....|....
gi 74867485 206 TLEVRDMALMAYIC 219
Cdd:cd22911  81 TLMPKDMQLARRIR 94
H3 smart00428
Histone H3;
135-219 5.84e-19

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 78.64  E-value: 5.84e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485    135 REIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDEPLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMAL 214
Cdd:smart00428  17 REIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQL 96


                   ....*
gi 74867485    215 MAYIC 219
Cdd:smart00428  97 ARRIR 101
Histone pfam00125
Core histone H2A/H2B/H3/H4;
94-219 1.07e-18

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 78.63  E-value: 1.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485    94 QTRRMTVQQESKTRAAGPVAAQNQTRRRKAANPMSRAKRmdrEIRRLQHHPGTLIPKLPFSRLVREfiVKYSDDEPLRVT 173
Cdd:pfam00125   6 NKANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALK---EIRKYQSSTDLLIYKLPFARVVRE--VVQSTKTDLRIS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 74867485   174 EGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMALMAYIC 219
Cdd:pfam00125  81 ADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PTZ00018 PTZ00018
histone H3; Provisional
 135-225 9.91e-13

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 63.00  E-value: 9.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485  135 REIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDepLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMAL 214
Cdd:PTZ00018  50 REIRRYQKSTELLIRKLPFQRLVREIAQDFKTD--LRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 127

                         90
                 ....*....|.
gi 74867485  215 MAYIcdRGRQF 225
Cdd:PTZ00018 128 ARRI--RGERS 136
PLN00161 PLN00161
histone H3; Provisional
 90-214 2.57e-12

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 61.94  E-value: 2.57e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485   90 TRSPQTRRMTVQQESKTRAAGPVAAQnQTRRRKAANPMSRAKRmdrEIRRLQHHPGTLIPKLPFSRLVREfIVKYSDDEP 169
Cdd:PLN00161   2 ARRLQGKRFRKGKKPQKEASGVTRQE-LDKKPHRYRPGTVALR---EIRKYQKSTELLIRKLPFARLVRE-ISNEMLREP 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 74867485  170 LRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMAL 214
Cdd:PLN00161  77 FRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQL 121
PLN00121 PLN00121
histone H3; Provisional
 135-218 5.16e-10

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 55.83  E-value: 5.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485  135 REIRRLQHHPGTLIPKLPFSRLVREFIVKYSDDepLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMAL 214
Cdd:PLN00121  50 REIRKYQKSTELLIRKLPFQRLVREIAQDFKTD--LRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 127


                 ....
gi 74867485  215 MAYI 218
Cdd:PLN00121 128 ARRI 131
PLN00160 PLN00160
histone H3; Provisional
 127-218 3.32e-09

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 52.74  E-value: 3.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74867485  127 MSRAKRMDREIRRLQHHPGTLIPKLPFSRLVREFIVKYSdDEPLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVT 206
Cdd:PLN00160   1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMS-REAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVT 79

                         90
                 ....*....|..
gi 74867485  207 LEVRDMALMAYI 218
Cdd:PLN00160  80 IMPKDMQLARRI 91
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 149-214 3.86e-03

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 34.89  E-value: 3.86e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 74867485   149 PKLPFSRLVRefIVKySDDEPLRVTEGALLAMQESCEMYLTQRLADSYMLTKHRNRVTLEVRDMAL 214
Cdd:pfam00808   1 AELPIARVKR--IMK-SDPDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQ 63
 
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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