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Conserved domains on  [gi|42564980|ref|NP_188431|]
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winged-helix DNA-binding transcription factor family protein [Arabidopsis thaliana]

Protein Classification

histone H1/H5 domain-containing protein( domain architecture ID 10650008)

histone H1/H5 domain-containing protein similar to a linker histone (H1 or H5), which is a chromatin-associated protein that binds to the exterior of nucleosomes, and to plant high-mobility-group (HMG) proteins that bind to DNA and to nucleosomes and are involved in the regulation of DNA-dependent processes such as transcription, replication, recombination, and DNA repair

CATH:  1.10.10.10
Gene Ontology:  GO:0003677|GO:0000785
PubMed:  10196467|16345076
SCOP:  4000178

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
H15 smart00526
Domain in histone families 1 and 5;
64-126 5.51e-19

Domain in histone families 1 and 5;


:

Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 80.70  E-value: 5.51e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42564980     64 PHPPYSEMICAAIAALNEPDGSSKMAISRYIERCYTGLTSAHAALLTHHLKTLKTSGVLSMVK 126
Cdd:smart00526   3 SHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVK 65
 
Name Accession Description Interval E-value
H15 smart00526
Domain in histone families 1 and 5;
64-126 5.51e-19

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 80.70  E-value: 5.51e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42564980     64 PHPPYSEMICAAIAALNEPDGSSKMAISRYIERCYTGLTSAHAALLTHHLKTLKTSGVLSMVK 126
Cdd:smart00526   3 SHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVK 65
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 65-126 4.15e-13

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: 64.08  E-value: 4.15e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42564980    65 HPPYSEMICAAIAALNEPDGSSKMAISRYIERCYTGLTSAHAA-LLTHHLKTLKTSGVLSMVK 126
Cdd:pfam00538   1 HPPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNsLLKRALKKGVEKGTLVQPK 63
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 64-138 1.33e-12

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: 63.41  E-value: 1.33e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42564980  64 PHPPYSEMICAAIAALNEPDGSSKMAISRYIERCYTGLTSAHAALLTHHLKTLKTSGVLSMVKK-----SYKIAGSSTPP 138
Cdd:cd00073   3 SHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGtgasgSFKLSKKKKKK 82
 
Name Accession Description Interval E-value
H15 smart00526
Domain in histone families 1 and 5;
64-126 5.51e-19

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 80.70  E-value: 5.51e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42564980     64 PHPPYSEMICAAIAALNEPDGSSKMAISRYIERCYTGLTSAHAALLTHHLKTLKTSGVLSMVK 126
Cdd:smart00526   3 SHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVK 65
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 65-126 4.15e-13

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: 64.08  E-value: 4.15e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42564980    65 HPPYSEMICAAIAALNEPDGSSKMAISRYIERCYTGLTSAHAA-LLTHHLKTLKTSGVLSMVK 126
Cdd:pfam00538   1 HPPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNsLLKRALKKGVEKGTLVQPK 63
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 64-138 1.33e-12

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: 63.41  E-value: 1.33e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42564980  64 PHPPYSEMICAAIAALNEPDGSSKMAISRYIERCYTGLTSAHAALLTHHLKTLKTSGVLSMVKK-----SYKIAGSSTPP 138
Cdd:cd00073   3 SHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGtgasgSFKLSKKKKKK 82
 
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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