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Conserved domains on  [gi|30685367|ref|NP_173195|]
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Homeodomain-like/winged-helix DNA-binding family protein [Arabidopsis thaliana]

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

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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 ...
 7-56 4.06e-20

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: 81.46  E-value: 4.06e-20
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30685367   7 KWTAEEEEALLAGVRKHGPGKWKNILRDPELaeqLSSRSNIDLKDKWRNL 56
Cdd:cd11660   2 KWTDEEDEALVEGVEKYGVGNWAKILKDYFF---VNNRTSVDLKDKWRNL 48
H15 smart00526
Domain in histone families 1 and 5;
124-188 1.83e-10

Domain in histone families 1 and 5;


:

Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 55.66  E-value: 1.83e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685367    124 PKNAPRYDGMIFEALSNLTDANGSDVSAIFNFIEQRQEV-PPNFRRMLSSRLRRLAAQGKLEKVSH 188
Cdd:smart00526   1 PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVlPNNFRKLLKLALKRLVASGKLVQVKG 66
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 7-56 4.06e-20

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: 81.46  E-value: 4.06e-20
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30685367   7 KWTAEEEEALLAGVRKHGPGKWKNILRDPELaeqLSSRSNIDLKDKWRNL 56
Cdd:cd11660   2 KWTDEEDEALVEGVEKYGVGNWAKILKDYFF---VNNRTSVDLKDKWRNL 48
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
5-56 1.15e-10

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 55.69  E-value: 1.15e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 30685367      5 KLKWTAEEEEALLAGVRKHGPGKWKNIlrdpelAEQLSSRSNIDLKDKWRNL 56
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKI------AKELPGRTAEQCRERWRNL 46
H15 smart00526
Domain in histone families 1 and 5;
124-188 1.83e-10

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 55.66  E-value: 1.83e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685367    124 PKNAPRYDGMIFEALSNLTDANGSDVSAIFNFIEQRQEV-PPNFRRMLSSRLRRLAAQGKLEKVSH 188
Cdd:smart00526   1 PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVlPNNFRKLLKLALKRLVASGKLVQVKG 66
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 5-56 2.13e-08

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: 49.42  E-value: 2.13e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 30685367     5 KLKWTAEEEEALLAGVRKHGpGKWKNIlrdpelAEQLSSRSNIDLKDKWRNL 56
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKI------AKLLPGRTDNQCKNRWQNY 45
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 128-158 1.91e-04

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: 39.05  E-value: 1.91e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 30685367   128 PRYDGMIFEALSNLTDANGSDVSAIFNFIEQ 158
Cdd:pfam00538   2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKA 32
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 128-195 3.50e-03

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: 36.06  E-value: 3.50e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30685367 128 PRYDGMIFEALSNLTDANGSDVSAIFNFIEQRQ-EVPPNFRRMLSSRLRRLAAQGKLEKVSHLKSTQNF 195
Cdd:cd00073   5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYkVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSF 73
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 7-56 4.06e-20

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: 81.46  E-value: 4.06e-20
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30685367   7 KWTAEEEEALLAGVRKHGPGKWKNILRDPELaeqLSSRSNIDLKDKWRNL 56
Cdd:cd11660   2 KWTDEEDEALVEGVEKYGVGNWAKILKDYFF---VNNRTSVDLKDKWRNL 48
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 7-56 3.27e-11

'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: 57.20  E-value: 3.27e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30685367   7 KWTAEEEEALLAGVRKHGPGKWKNIlrdpelAEQLSSRSNIDLKDKWRNL 56
Cdd:cd00167   1 PWTEEEDELLLEAVKKYGKNNWEKI------AKELPGRTPKQCRERWRNL 44
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
5-56 1.15e-10

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 55.69  E-value: 1.15e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 30685367      5 KLKWTAEEEEALLAGVRKHGPGKWKNIlrdpelAEQLSSRSNIDLKDKWRNL 56
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKI------AKELPGRTAEQCRERWRNL 46
H15 smart00526
Domain in histone families 1 and 5;
124-188 1.83e-10

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 55.66  E-value: 1.83e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685367    124 PKNAPRYDGMIFEALSNLTDANGSDVSAIFNFIEQRQEV-PPNFRRMLSSRLRRLAAQGKLEKVSH 188
Cdd:smart00526   1 PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVlPNNFRKLLKLALKRLVASGKLVQVKG 66
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 5-56 2.13e-08

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: 49.42  E-value: 2.13e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 30685367     5 KLKWTAEEEEALLAGVRKHGpGKWKNIlrdpelAEQLSSRSNIDLKDKWRNL 56
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKI------AKLLPGRTDNQCKNRWQNY 45
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 8-55 1.83e-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: 372817 [Multi-domain]  Cd Length: 60  Bit Score: 44.61  E-value: 1.83e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 30685367     8 WTAEEEEALLAGVRKHGpGKWKNIlrdpelAEQLSSRSNIDLKDKWRN 55
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYG-NDWKQI------AKELGRRTPKQCFDRWRR 41
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 128-158 1.91e-04

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: 39.05  E-value: 1.91e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 30685367   128 PRYDGMIFEALSNLTDANGSDVSAIFNFIEQ 158
Cdd:pfam00538   2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKA 32
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 128-195 3.50e-03

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: 36.06  E-value: 3.50e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30685367 128 PRYDGMIFEALSNLTDANGSDVSAIFNFIEQRQ-EVPPNFRRMLSSRLRRLAAQGKLEKVSHLKSTQNF 195
Cdd:cd00073   5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYkVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSF 73
 
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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