NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1229203753|ref|NP_001341119|]
View 

MYB transcription factor isoform 1 [Glycine max]

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 ...
 6-56 9.86e-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: 77.99  E-value: 9.86e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1229203753   6 QKWTAEEEQALKAGVVKHGVGKWRTILKDPEFSSVlylRSNVDLKDKWRNL 56
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFVNN---RTSVDLKDKWRNL 48
H15 smart00526
Domain in histone families 1 and 5;
118-180 7.02e-10

Domain in histone families 1 and 5;


:

Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 54.12  E-value: 7.02e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1229203753  118 KRSNLSLDKLIMEAITCLKENGGSNKTAIAAFIEDQYWALP-GLKSMLSAKLKFLTASGKLIKV 180
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 ...
 6-56 9.86e-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: 77.99  E-value: 9.86e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1229203753   6 QKWTAEEEQALKAGVVKHGVGKWRTILKDPEFSSVlylRSNVDLKDKWRNL 56
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFVNN---RTSVDLKDKWRNL 48
H15 smart00526
Domain in histone families 1 and 5;
118-180 7.02e-10

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 54.12  E-value: 7.02e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1229203753  118 KRSNLSLDKLIMEAITCLKENGGSNKTAIAAFIEDQYWALP-GLKSMLSAKLKFLTASGKLIKV 180
Cdd:smart00526   1 PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPnNFRKLLKLALKRLVASGKLVQV 64
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 127-180 1.52e-07

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: 48.39  E-value: 1.52e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1229203753 127 LIMEAITCLKENGGSNKTAIAAFIEDQYWALP-GLKSMLSAKLKFLTASGKLIKV 180
Cdd:cd00073    10 MVTEAIKALKERKGSSLQAIKKYIEAKYKVDDeNFNKLLKLALKKGVAKGKLVQV 64
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
5-56 2.77e-07

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 46.45  E-value: 2.77e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1229203753    5 KQKWTAEEEQALKAGVVKHGVGKWRTIlkdpefSSVLYLRSNVDLKDKWRNL 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 ...
 123-183 4.70e-06

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: 43.67  E-value: 4.70e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1229203753 123 SLDKLIMEAITCLKENGGSNKTAIAAFIEDQYWAL--PGLKSMLSAKLKFLTASGKLIKVNRK 183
Cdd:pfam00538   3 PYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGdvAKFNSLLKRALKKGVEKGTLVQPKGT 65
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 5-56 9.55e-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: 42.11  E-value: 9.55e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1229203753   5 KQKWTAEEEQALKAGVVKHGvGKWRTILKdpefssVLYLRSNVDLKDKWRNL 56
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKIAK------LLPGRTDNQCKNRWQNY 45
 
Name Accession Description Interval E-value
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 6-56 9.86e-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: 77.99  E-value: 9.86e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1229203753   6 QKWTAEEEQALKAGVVKHGVGKWRTILKDPEFSSVlylRSNVDLKDKWRNL 56
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFVNN---RTSVDLKDKWRNL 48
H15 smart00526
Domain in histone families 1 and 5;
118-180 7.02e-10

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 54.12  E-value: 7.02e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1229203753  118 KRSNLSLDKLIMEAITCLKENGGSNKTAIAAFIEDQYWALP-GLKSMLSAKLKFLTASGKLIKV 180
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 9.68e-08

'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: 47.57  E-value: 9.68e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1229203753   7 KWTAEEEQALKAGVVKHGVGKWRTIlkdpefSSVLYLRSNVDLKDKWRNL 56
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGKNNWEKI------AKELPGRTPKQCRERWRNL 44
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 127-180 1.52e-07

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: 48.39  E-value: 1.52e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1229203753 127 LIMEAITCLKENGGSNKTAIAAFIEDQYWALP-GLKSMLSAKLKFLTASGKLIKV 180
Cdd:cd00073    10 MVTEAIKALKERKGSSLQAIKKYIEAKYKVDDeNFNKLLKLALKKGVAKGKLVQV 64
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
5-56 2.77e-07

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 46.45  E-value: 2.77e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1229203753    5 KQKWTAEEEQALKAGVVKHGVGKWRTIlkdpefSSVLYLRSNVDLKDKWRNL 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 ...
 123-183 4.70e-06

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: 43.67  E-value: 4.70e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1229203753 123 SLDKLIMEAITCLKENGGSNKTAIAAFIEDQYWAL--PGLKSMLSAKLKFLTASGKLIKVNRK 183
Cdd:pfam00538   3 PYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGdvAKFNSLLKRALKKGVEKGTLVQPKGT 65
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 5-56 9.55e-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: 42.11  E-value: 9.55e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1229203753   5 KQKWTAEEEQALKAGVVKHGvGKWRTILKdpefssVLYLRSNVDLKDKWRNL 56
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKIAK------LLPGRTDNQCKNRWQNY 45
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 8-71 1.84e-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: 36.13  E-value: 1.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1229203753   8 WTAEEEQALKAGVVKHGvGKWRTIlkdpefSSVLYLRSNVDLKDKWRNL--SVMANG-WSSREKSRL 71
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYG-NDWKQI------AKELGRRTPKQCFDRWRRKlnPKISRGpWSKEEDQRL 60
 
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