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Conserved domains on  [gi|197386154|ref|NP_001128070|]
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huntingtin-interacting protein M [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
H2A super family cl30547
Histone 2A;
21-82 1.72e-07

Histone 2A;


The actual alignment was detected with superfamily member smart00414:

Pssm-ID: 197711  Cd Length: 106  Bit Score: 45.79  E-value: 1.72e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 197386154    21 SSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNIS 82
Cdd:smart00414   3 SARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRIT 64
 
Name Accession Description Interval E-value
H2A smart00414
Histone 2A;
21-82 1.72e-07

Histone 2A;


Pssm-ID: 197711  Cd Length: 106  Bit Score: 45.79  E-value: 1.72e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 197386154    21 SSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNIS 82
Cdd:smart00414   3 SARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRIT 64
HFD_H2A cd00074
histone-fold domain found in histone H2A and similar proteins; Histone H2A is the core ...
 21-105 2.07e-07

histone-fold domain found in histone H2A and similar proteins; Histone H2A is the core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467020  Cd Length: 89  Bit Score: 45.22  E-value: 2.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197386154  21 SSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNISQdRERQR--ENDREPPQA 98
Cdd:cd00074    4 SKRAGLQFPVGRIHRLLKKGTYAKRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKKRITP-RHIQLaiRNDEELNKL 82


                 ....*..
gi 197386154  99 FKNAPFS 105
Cdd:cd00074   83 FKGVTIA 89
PLN00153 PLN00153
histone H2A; Provisional
 3-81 1.40e-06

histone H2A; Provisional


Pssm-ID: 165721 [Multi-domain]  Cd Length: 129  Bit Score: 43.94  E-value: 1.40e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 197386154   3 GKKSQEKACSDnkqtedpSSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNI 81
Cdd:PLN00153   7 GKTSGKKAVSR-------SAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRI 78
HTA1 COG5262
Histone H2A [Chromatin structure and dynamics];
12-81 5.77e-05

Histone H2A [Chromatin structure and dynamics];


Pssm-ID: 227587 [Multi-domain]  Cd Length: 132  Bit Score: 39.85  E-value: 5.77e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197386154  12 SDNKQTEDPSSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNI 81
Cdd:COG5262   11 ADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRI 80
 
Name Accession Description Interval E-value
H2A smart00414
Histone 2A;
21-82 1.72e-07

Histone 2A;


Pssm-ID: 197711  Cd Length: 106  Bit Score: 45.79  E-value: 1.72e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 197386154    21 SSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNIS 82
Cdd:smart00414   3 SARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRIT 64
HFD_H2A cd00074
histone-fold domain found in histone H2A and similar proteins; Histone H2A is the core ...
 21-105 2.07e-07

histone-fold domain found in histone H2A and similar proteins; Histone H2A is the core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467020  Cd Length: 89  Bit Score: 45.22  E-value: 2.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197386154  21 SSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNISQdRERQR--ENDREPPQA 98
Cdd:cd00074    4 SKRAGLQFPVGRIHRLLKKGTYAKRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKKRITP-RHIQLaiRNDEELNKL 82


                 ....*..
gi 197386154  99 FKNAPFS 105
Cdd:cd00074   83 FKGVTIA 89
PLN00153 PLN00153
histone H2A; Provisional
 3-81 1.40e-06

histone H2A; Provisional


Pssm-ID: 165721 [Multi-domain]  Cd Length: 129  Bit Score: 43.94  E-value: 1.40e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 197386154   3 GKKSQEKACSDnkqtedpSSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNI 81
Cdd:PLN00153   7 GKTSGKKAVSR-------SAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRI 78
PLN00157 PLN00157
histone H2A; Provisional
 1-81 2.00e-06

histone H2A; Provisional


Pssm-ID: 177758  Cd Length: 132  Bit Score: 43.69  E-value: 2.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197386154   1 MSGKKSQEKACSDNKQTEDpSSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQN 80
Cdd:PLN00157   1 MSGRGKRKGGGGGKKATSR-SAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSR 79


                 .
gi 197386154  81 I 81
Cdd:PLN00157  80 I 80
HTA1 COG5262
Histone H2A [Chromatin structure and dynamics];
12-81 5.77e-05

Histone H2A [Chromatin structure and dynamics];


Pssm-ID: 227587 [Multi-domain]  Cd Length: 132  Bit Score: 39.85  E-value: 5.77e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 197386154  12 SDNKQTEDPSSRPEVQVPVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEANINSQQNI 81
Cdd:COG5262   11 ADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRI 80
HFD_SOS1_rpt2 cd22915
second histone-fold domain found in son of sevenless homolog 1 (SOS-1) and similar proteins; ...
 29-84 6.99e-05

second histone-fold domain found in son of sevenless homolog 1 (SOS-1) and similar proteins; SOS-1 is a guanine nucleotide exchange factor for Ras that binds to GRB2. It promotes the exchange of Ras-bound GDP by GTP. It is a catalytic component of a trimeric complex that participates in transduction of signals from Ras to Rac, by promoting the Rac-specific guanine nucleotide exchange factor (GEF) activity. SOS-1 contains tandem histone folds at the N-terminal region. The model corresponds to the second repeat.


Pssm-ID: 467040  Cd Length: 75  Bit Score: 38.37  E-value: 6.99e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 197386154  29 PVNYVYRLLQEEQYTPCLGSTTSDFLLAMLDYLTDYILEVVGSEA-NINSQQNISQD 84
Cdd:cd22915    3 PVDKIHPLLKKDLLVYKVDPQVSLYLVAVLEYIAADILKLAGNYVrNIRHYEITSQD 59
 
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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