NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1002314898|ref|XP_015620818|]
View 

single myb histone 6 [Oryza sativa Japonica Group]

Protein Classification

histone H1/H5 family protein( domain architecture ID 10184773)

histone H1/H5 family protein such as Arabidopsis thaliana telomere repeat-binding factors that preferentially binds double-stranded telomeric repeats

CATH:  1.10.10.10|1.20.58.1880
Gene Ontology:  GO:0003691|GO:0003677|GO:0006355|GO:0003700
PubMed:  14576282|8882580|26212454|16345076|10973918
SCOP:  4000178|4000317

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 6-57 2.39e-19

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


:

Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 79.53  E-value: 2.39e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002314898   6 QKWTAEEESALKAGIAKHGAGKWRTILKDPDFSNvlrYRSNVDLKDKWRNMN 57
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFVN---NRTSVDLKDKWRNLK 49
H15 smart00526
Domain in histone families 1 and 5;
116-178 9.83e-11

Domain in histone families 1 and 5;


:

Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 56.43  E-value: 9.83e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002314898  116 KRSLSRLDNIIVEAVRSLNEPTGSYKTAIANYIEEQY-WPPADFDHVLSSKLNDLTASGKLIKV 178
Cdd:smart00526   1 PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYkVLPNNFRKLLKLALKRLVASGKLVQV 64
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 6-57 2.39e-19

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 79.53  E-value: 2.39e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002314898   6 QKWTAEEESALKAGIAKHGAGKWRTILKDPDFSNvlrYRSNVDLKDKWRNMN 57
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFVN---NRTSVDLKDKWRNLK 49
H15 smart00526
Domain in histone families 1 and 5;
116-178 9.83e-11

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 56.43  E-value: 9.83e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002314898  116 KRSLSRLDNIIVEAVRSLNEPTGSYKTAIANYIEEQY-WPPADFDHVLSSKLNDLTASGKLIKV 178
Cdd:smart00526   1 PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYkVLPNNFRKLLKLALKRLVASGKLVQV 64
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
5-56 4.50e-09

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 51.46  E-value: 4.50e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1002314898    5 KQKWTAEEESALKAGIAKHGAGKWRTIlkdpdfSNVLRYRSNVDLKDKWRNM 56
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKI------AKELPGRTAEQCRERWRNL 46
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 124-181 6.39e-07

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 45.98  E-value: 6.39e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314898 124 NIIVEAVRSLNEPTGSYKTAIANYIEEQYW--PPADFDHVLSSKLNDLTASGKLIKVNRK 181
Cdd:pfam00538   6 DMIKEAIKALKERKGSSRQAIKKYIKANYKvgDVAKFNSLLKRALKKGVEKGTLVQPKGT 65
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 5-56 5.05e-06

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 42.88  E-value: 5.05e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002314898   5 KQKWTAEEESALKAGIAKHGaGKWRTILKdpdfsnVLRYRSNVDLKDKWRNM 56
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKIAK------LLPGRTDNQCKNRWQNY 45
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 124-178 4.38e-05

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 41.45  E-value: 4.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002314898 124 NIIVEAVRSLNEPTGSYKTAIANYIEEQYWP-PADFDHVLSSKLNDLTASGKLIKV 178
Cdd:cd00073     9 EMVTEAIKALKERKGSSLQAIKKYIEAKYKVdDENFNKLLKLALKKGVAKGKLVQV 64
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 6-57 2.39e-19

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 79.53  E-value: 2.39e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002314898   6 QKWTAEEESALKAGIAKHGAGKWRTILKDPDFSNvlrYRSNVDLKDKWRNMN 57
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFVN---NRTSVDLKDKWRNLK 49
H15 smart00526
Domain in histone families 1 and 5;
116-178 9.83e-11

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 56.43  E-value: 9.83e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002314898  116 KRSLSRLDNIIVEAVRSLNEPTGSYKTAIANYIEEQY-WPPADFDHVLSSKLNDLTASGKLIKV 178
Cdd:smart00526   1 PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYkVLPNNFRKLLKLALKRLVASGKLVQV 64
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 7-56 2.02e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 52.19  E-value: 2.02e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002314898   7 KWTAEEESALKAGIAKHGAGKWRTIlkdpdfSNVLRYRSNVDLKDKWRNM 56
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGKNNWEKI------AKELPGRTPKQCRERWRNL 44
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
5-56 4.50e-09

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 51.46  E-value: 4.50e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1002314898    5 KQKWTAEEESALKAGIAKHGAGKWRTIlkdpdfSNVLRYRSNVDLKDKWRNM 56
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKI------AKELPGRTAEQCRERWRNL 46
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 124-181 6.39e-07

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 45.98  E-value: 6.39e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314898 124 NIIVEAVRSLNEPTGSYKTAIANYIEEQYW--PPADFDHVLSSKLNDLTASGKLIKVNRK 181
Cdd:pfam00538   6 DMIKEAIKALKERKGSSRQAIKKYIKANYKvgDVAKFNSLLKRALKKGVEKGTLVQPKGT 65
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 5-56 5.05e-06

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 42.88  E-value: 5.05e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002314898   5 KQKWTAEEESALKAGIAKHGaGKWRTILKdpdfsnVLRYRSNVDLKDKWRNM 56
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKIAK------LLPGRTDNQCKNRWQNY 45
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 124-178 4.38e-05

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 41.45  E-value: 4.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002314898 124 NIIVEAVRSLNEPTGSYKTAIANYIEEQYWP-PADFDHVLSSKLNDLTASGKLIKV 178
Cdd:cd00073     9 EMVTEAIKALKERKGSSLQAIKKYIEAKYKVdDENFNKLLKLALKKGVAKGKLVQV 64
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 8-56 9.93e-03

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 372817 [Multi-domain]  Cd Length: 60  Bit Score: 33.82  E-value: 9.93e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1002314898   8 WTAEEESALKAGIAKHGaGKWRTIlkdpdfSNVLRYRSNVDLKDKWRNM 56
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYG-NDWKQI------AKELGRRTPKQCFDRWRRK 42
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH