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Conserved domains on  [gi|15221913|ref|NP_175295|]
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high mobility group A5 [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;
78-136 7.04e-17

Domain in histone families 1 and 5;


:

Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 74.92  E-value: 7.04e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 15221913     78 YSDMICTAIAALNEPDGSSKQAISRYIERIYTGIPTAHGALLTHHLKTLKTSGILVMVK 136
Cdd:smart00526   7 YSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVK 65
 
Name Accession Description Interval E-value
H15 smart00526
Domain in histone families 1 and 5;
78-136 7.04e-17

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 74.92  E-value: 7.04e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 15221913     78 YSDMICTAIAALNEPDGSSKQAISRYIERIYTGIPTAHGALLTHHLKTLKTSGILVMVK 136
Cdd:smart00526   7 YSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVK 65
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 78-136 1.83e-11

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: 59.46  E-value: 1.83e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221913    78 YSDMICTAIAALNEPDGSSKQAISRYIERIYTGIPTAHGA-LLTHHLKTLKTSGILVMVK 136
Cdd:pfam00538   4 YSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNsLLKRALKKGVEKGTLVQPK 63
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 78-141 5.05e-11

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: 58.79  E-value: 5.05e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15221913  78 YSDMICTAIAALNEPDGSSKQAISRYIERIYTGIPTAHGALLTHHLKTLKTSGILVMVKK-----SYKL 141
Cdd:cd00073   7 YSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGtgasgSFKL 75
 
Name Accession Description Interval E-value
H15 smart00526
Domain in histone families 1 and 5;
78-136 7.04e-17

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 74.92  E-value: 7.04e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 15221913     78 YSDMICTAIAALNEPDGSSKQAISRYIERIYTGIPTAHGALLTHHLKTLKTSGILVMVK 136
Cdd:smart00526   7 YSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVK 65
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 78-136 1.83e-11

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: 59.46  E-value: 1.83e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15221913    78 YSDMICTAIAALNEPDGSSKQAISRYIERIYTGIPTAHGA-LLTHHLKTLKTSGILVMVK 136
Cdd:pfam00538   4 YSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNsLLKRALKKGVEKGTLVQPK 63
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 78-141 5.05e-11

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: 58.79  E-value: 5.05e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15221913  78 YSDMICTAIAALNEPDGSSKQAISRYIERIYTGIPTAHGALLTHHLKTLKTSGILVMVKK-----SYKL 141
Cdd:cd00073   7 YSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGtgasgSFKL 75
 
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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