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Conserved domains on  [gi|444730861|gb|ELW71234|]
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Sp110 nuclear body protein [Tupaia chinensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 5-103 1.36e-56

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


:

Pssm-ID: 460835  Cd Length: 99  Bit Score: 182.35  E-value: 1.36e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444730861    5 LEAALFQHFSHQKLEIAYAIDKPFPFFEGLWDKSFISDRQYGESMEACRNLVPIAKVVHSTLTQLETRFSVPLLKTLFSR 84
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80

                          90
                  ....*....|....*....
gi 444730861   85 INLVEYPKLNTICQSFRNG 103
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 382-428 1.37e-17

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


:

Pssm-ID: 460167  Cd Length: 76  Bit Score: 76.85  E-value: 1.37e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 444730861  382 SSEKCIQNkEGVWFTPKEFELEGKKKNSKDWKRSLHCGGQTVRQLLE 428
Cdd:pfam01342  27 ISGKCIQN-EDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIE 72
Bromodomain super family cl02556
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 429-461 4.12e-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 cd05501:

Pssm-ID: 445827  Cd Length: 102  Bit Score: 39.72  E-value: 4.12e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 444730861 429 IRDYGEPFKEALWLILVTERLAEEVY-VVAWLCR 461
Cdd:cd05501   30 IRDYCQGIKEPMWLNKVKERLNERVYhTVEGFVR 63
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 5-103 1.36e-56

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


Pssm-ID: 460835  Cd Length: 99  Bit Score: 182.35  E-value: 1.36e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444730861    5 LEAALFQHFSHQKLEIAYAIDKPFPFFEGLWDKSFISDRQYGESMEACRNLVPIAKVVHSTLTQLETRFSVPLLKTLFSR 84
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80

                          90
                  ....*....|....*....
gi 444730861   85 INLVEYPKLNTICQSFRNG 103
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 382-428 1.37e-17

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 460167  Cd Length: 76  Bit Score: 76.85  E-value: 1.37e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 444730861  382 SSEKCIQNkEGVWFTPKEFELEGKKKNSKDWKRSLHCGGQTVRQLLE 428
Cdd:pfam01342  27 ISGKCIQN-EDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIE 72
SAND smart00258
SAND domain;
382-428 2.38e-13

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 65.06  E-value: 2.38e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 444730861   382 SSEKCIQNkEGVWFTPKEFELEGKKKNSKDWKRSLHCGGQTVRQLLE 428
Cdd:smart00258  23 ISVKCIQY-EDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLME 68
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 429-461 4.12e-04

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 39.72  E-value: 4.12e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 444730861 429 IRDYGEPFKEALWLILVTERLAEEVY-VVAWLCR 461
Cdd:cd05501   30 IRDYCQGIKEPMWLNKVKERLNERVYhTVEGFVR 63
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 5-103 1.36e-56

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


Pssm-ID: 460835  Cd Length: 99  Bit Score: 182.35  E-value: 1.36e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444730861    5 LEAALFQHFSHQKLEIAYAIDKPFPFFEGLWDKSFISDRQYGESMEACRNLVPIAKVVHSTLTQLETRFSVPLLKTLFSR 84
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80

                          90
                  ....*....|....*....
gi 444730861   85 INLVEYPKLNTICQSFRNG 103
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 382-428 1.37e-17

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 460167  Cd Length: 76  Bit Score: 76.85  E-value: 1.37e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 444730861  382 SSEKCIQNkEGVWFTPKEFELEGKKKNSKDWKRSLHCGGQTVRQLLE 428
Cdd:pfam01342  27 ISGKCIQN-EDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIE 72
SAND smart00258
SAND domain;
382-428 2.38e-13

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 65.06  E-value: 2.38e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 444730861   382 SSEKCIQNkEGVWFTPKEFELEGKKKNSKDWKRSLHCGGQTVRQLLE 428
Cdd:smart00258  23 ISVKCIQY-EDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLME 68
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 429-461 4.12e-04

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 39.72  E-value: 4.12e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 444730861 429 IRDYGEPFKEALWLILVTERLAEEVY-VVAWLCR 461
Cdd:cd05501   30 IRDYCQGIKEPMWLNKVKERLNERVYhTVEGFVR 63
 
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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