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Conserved domains on  [gi|17537523|ref|NP_497064|]
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Bromodomain associated domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
HFD_SF super family cl45933
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
11-95 6.57e-07

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


The actual alignment was detected with superfamily member cd22916:

Pssm-ID: 480273  Cd Length: 92  Bit Score: 47.21  E-value: 6.57e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537523  11 LRDSVSRIVENLGFSSIDEVAHAKLVGLLANGLDSMSQTCRGLLENSGRTAISLNTVDLkhAFRIHRVDLPGLVDYTRQV 90
Cdd:cd22916   8 LRVVVAQICQNVGWHSIQSSPLDLLTDVLQRYLLELARSAHRYAEQYGRTEPNLDDLGL--AFKDMGISLNELEDYVLNV 85

                ....*
gi 17537523  91 RPFPP 95
Cdd:cd22916  86 EPVPF 90
 
Name Accession Description Interval E-value
HFD_TAF3 cd22916
histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and ...
11-95 6.57e-07

histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and similar proteins; TAF3, also called TATA Binding Protein (TBP) associated factor 3, 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, or transcription initiation factor TFIID 140 kDa subunit (TAF(II)140, TAF140, TAFII-140,TAFII140), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors.


Pssm-ID: 467041  Cd Length: 92  Bit Score: 47.21  E-value: 6.57e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537523  11 LRDSVSRIVENLGFSSIDEVAHAKLVGLLANGLDSMSQTCRGLLENSGRTAISLNTVDLkhAFRIHRVDLPGLVDYTRQV 90
Cdd:cd22916   8 LRVVVAQICQNVGWHSIQSSPLDLLTDVLQRYLLELARSAHRYAEQYGRTEPNLDDLGL--AFKDMGISLNELEDYVLNV 85

                ....*
gi 17537523  91 RPFPP 95
Cdd:cd22916  86 EPVPF 90
 
Name Accession Description Interval E-value
HFD_TAF3 cd22916
histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and ...
11-95 6.57e-07

histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and similar proteins; TAF3, also called TATA Binding Protein (TBP) associated factor 3, 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, or transcription initiation factor TFIID 140 kDa subunit (TAF(II)140, TAF140, TAFII-140,TAFII140), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors.


Pssm-ID: 467041  Cd Length: 92  Bit Score: 47.21  E-value: 6.57e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537523  11 LRDSVSRIVENLGFSSIDEVAHAKLVGLLANGLDSMSQTCRGLLENSGRTAISLNTVDLkhAFRIHRVDLPGLVDYTRQV 90
Cdd:cd22916   8 LRVVVAQICQNVGWHSIQSSPLDLLTDVLQRYLLELARSAHRYAEQYGRTEPNLDDLGL--AFKDMGISLNELEDYVLNV 85

                ....*
gi 17537523  91 RPFPP 95
Cdd:cd22916  86 EPVPF 90
 
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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