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Conserved domains on  [gi|1435650149|ref|XP_025872703|]
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LOW QUALITY PROTEIN: histone H1oo [Vulpes vulpes]

Protein Classification

histone H1/H5 family protein( domain architecture ID 10049384)

histone H1/H5 family protein similar to a linker histone (H1 or H5), which is a chromatin-associated protein that binds to the exterior of nucleosomes and dramatically stabilizes the highly condensed states of chromatin fibers

CATH:  1.10.10.10
Gene Ontology:  GO:0006334|GO:0003677|GO:0030527|GO:0000786
PubMed:  26212454|16345076|10973918|11149891
SCOP:  4000178

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 43-133 9.69e-21

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: 84.98  E-value: 9.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1435650149  43 GRRHPPVLRMVLEALQAGEQRRGTSVAAIKVYILQKYPTVDViRLKYLLKQALATGMHRGLLVRPtnsKAKGATGSFKLV 122
Cdd:cd00073     1 PPSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDE-NFNKLLKLALKKGVAKGKLVQV---KGTGASGSFKLS 76

                          90
                  ....*....|.
gi 1435650149 123 PKHKRKVQPRK 133
Cdd:cd00073    77 KKKKKKKKPAK 87
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 132-254 4.64e-03

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 38.73  E-value: 4.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1435650149 132 RKTSTMTAPRrpgE*QGGGPKKPKEAKKDP-PNPDKVTRGPRKPGEARTAPPKPGTAKEKAPKKGSQTKNQEARVSEARK 210
Cdd:PRK12678   47 RKGELIAAIK---EARGGGAAAAAATPAAPaAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPE 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1435650149 211 VSQQPDKATQALPRATGPSGKSKVKGRRNSQGGETHRKTKAGSQ 254
Cdd:PRK12678  124 AAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEE 167
 
Name Accession Description Interval E-value
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 43-133 9.69e-21

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: 84.98  E-value: 9.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1435650149  43 GRRHPPVLRMVLEALQAGEQRRGTSVAAIKVYILQKYPTVDViRLKYLLKQALATGMHRGLLVRPtnsKAKGATGSFKLV 122
Cdd:cd00073     1 PPSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDE-NFNKLLKLALKKGVAKGKLVQV---KGTGASGSFKLS 76

                          90
                  ....*....|.
gi 1435650149 123 PKHKRKVQPRK 133
Cdd:cd00073    77 KKKKKKKKPAK 87
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 46-119 5.13e-20

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: 82.57  E-value: 5.13e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1435650149  46 HPPVLRMVLEALQAGEQRRGTSVAAIKVYILQKYPTVDVIRLKYLLKQALATGMHRGLLVRPtnsKAKGATGSF 119
Cdd:pfam00538   1 HPPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNSLLKRALKKGVEKGTLVQP---KGTGASGSF 71
H15 smart00526
Domain in histone families 1 and 5;
46-109 2.90e-10

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 55.66  E-value: 2.90e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1435650149   46 HPPVLRMVLEALQAGEQRRGTSVAAIKVYILQKYpTVDVIRLKYLLKQALATGMHRGLLVRPTN 109
Cdd:smart00526   4 HPPYSEMIVEAISALKERKGSSLQAIKKYIEANY-KVLPNNFRKLLKLALKRLVASGKLVQVKG 66
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 132-254 4.64e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 38.73  E-value: 4.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1435650149 132 RKTSTMTAPRrpgE*QGGGPKKPKEAKKDP-PNPDKVTRGPRKPGEARTAPPKPGTAKEKAPKKGSQTKNQEARVSEARK 210
Cdd:PRK12678   47 RKGELIAAIK---EARGGGAAAAAATPAAPaAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPE 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1435650149 211 VSQQPDKATQALPRATGPSGKSKVKGRRNSQGGETHRKTKAGSQ 254
Cdd:PRK12678  124 AAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEE 167
 
Name Accession Description Interval E-value
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 43-133 9.69e-21

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: 84.98  E-value: 9.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1435650149  43 GRRHPPVLRMVLEALQAGEQRRGTSVAAIKVYILQKYPTVDViRLKYLLKQALATGMHRGLLVRPtnsKAKGATGSFKLV 122
Cdd:cd00073     1 PPSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDE-NFNKLLKLALKKGVAKGKLVQV---KGTGASGSFKLS 76

                          90
                  ....*....|.
gi 1435650149 123 PKHKRKVQPRK 133
Cdd:cd00073    77 KKKKKKKKPAK 87
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 46-119 5.13e-20

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: 82.57  E-value: 5.13e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1435650149  46 HPPVLRMVLEALQAGEQRRGTSVAAIKVYILQKYPTVDVIRLKYLLKQALATGMHRGLLVRPtnsKAKGATGSF 119
Cdd:pfam00538   1 HPPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNSLLKRALKKGVEKGTLVQP---KGTGASGSF 71
H15 smart00526
Domain in histone families 1 and 5;
46-109 2.90e-10

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 55.66  E-value: 2.90e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1435650149   46 HPPVLRMVLEALQAGEQRRGTSVAAIKVYILQKYpTVDVIRLKYLLKQALATGMHRGLLVRPTN 109
Cdd:smart00526   4 HPPYSEMIVEAISALKERKGSSLQAIKKYIEANY-KVLPNNFRKLLKLALKRLVASGKLVQVKG 66
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 132-254 4.64e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 38.73  E-value: 4.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1435650149 132 RKTSTMTAPRrpgE*QGGGPKKPKEAKKDP-PNPDKVTRGPRKPGEARTAPPKPGTAKEKAPKKGSQTKNQEARVSEARK 210
Cdd:PRK12678   47 RKGELIAAIK---EARGGGAAAAAATPAAPaAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPE 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1435650149 211 VSQQPDKATQALPRATGPSGKSKVKGRRNSQGGETHRKTKAGSQ 254
Cdd:PRK12678  124 AAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEE 167
 
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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