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Conserved domains on  [gi|1775480513|pdb|6KW4|A]
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Chain A, Chromatin structure-remodeling complex protein RSC58

Protein Classification

bromodomain-containing protein( domain architecture ID 267)

bromodomain-containing protein may act as transcription regulator involved in chromatin-based DNA damage response (DDR) pathways, which maintain genome integrity from cell-intrinsic and extrinsic DNA-damaging sources

CATH:  1.20.920.10
Gene Ontology:  GO:0005515
PubMed:  31582847|28847823|34548613|1350857|26472704

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Bromodomain super family cl02556
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 39-122 1.05e-04

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


The actual alignment was detected with superfamily member pfam00439:

Pssm-ID: 445827 [Multi-domain]  Cd Length: 84  Bit Score: 40.76  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KW4_A         39 FFEKNPDKIYESYCKFIKNRsnseglirnedkLVLTTINKRFENGEYEpiqgGFYKLYHDIKLVCTILIHFYPQGTRNYQ 118
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKKP------------MDLSTIKKKLENGEYK----SLAEFLADVKLIFSNARTYNGPGSVIYK 80


                  ....
6KW4_A        119 LVDK 122
Cdd:pfam00439  81 AAEK 84
 
Name Accession Description Interval E-value
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 39-122 1.05e-04

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 40.76  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KW4_A         39 FFEKNPDKIYESYCKFIKNRsnseglirnedkLVLTTINKRFENGEYEpiqgGFYKLYHDIKLVCTILIHFYPQGTRNYQ 118
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKKP------------MDLSTIKKKLENGEYK----SLAEFLADVKLIFSNARTYNGPGSVIYK 80


                  ....
6KW4_A        119 LVDK 122
Cdd:pfam00439  81 AAEK 84
BROMO smart00297
bromo domain;
31-131 2.22e-03

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 37.64  E-value: 2.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KW4_A          31 VDESFPAKFFEKNPDKI-YESYCKFIKNRsnseglirnedkLVLTTINKRFENGEYEpiqgGFYKLYHDIKLVCTILIHF 109
Cdd:smart00297  19 LDSHPLSWPFLKPVSRKeAPDYYDIIKKP------------MDLKTIKKKLENGKYS----SVEEFVADFNLMFSNARTY 82

                           90       100
                   ....*....|....*....|..
6KW4_A         110 YPQGTRNYQLVDKFYKFSSELL 131
Cdd:smart00297  83 NGPDSEVYKDAKKLEKFFEKKL 104
 
Name Accession Description Interval E-value
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 39-122 1.05e-04

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 40.76  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KW4_A         39 FFEKNPDKIYESYCKFIKNRsnseglirnedkLVLTTINKRFENGEYEpiqgGFYKLYHDIKLVCTILIHFYPQGTRNYQ 118
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKKP------------MDLSTIKKKLENGEYK----SLAEFLADVKLIFSNARTYNGPGSVIYK 80


                  ....
6KW4_A        119 LVDK 122
Cdd:pfam00439  81 AAEK 84
BROMO smart00297
bromo domain;
31-131 2.22e-03

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 37.64  E-value: 2.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KW4_A          31 VDESFPAKFFEKNPDKI-YESYCKFIKNRsnseglirnedkLVLTTINKRFENGEYEpiqgGFYKLYHDIKLVCTILIHF 109
Cdd:smart00297  19 LDSHPLSWPFLKPVSRKeAPDYYDIIKKP------------MDLKTIKKKLENGKYS----SVEEFVADFNLMFSNARTY 82

                           90       100
                   ....*....|....*....|..
6KW4_A         110 YPQGTRNYQLVDKFYKFSSELL 131
Cdd:smart00297  83 NGPDSEVYKDAKKLEKFFEKKL 104
 
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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