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Conserved domains on  [gi|1958801935|ref|XP_038939331|]
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sp110 nuclear body protein isoform X2 [Rattus norvegicus]

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 ...
 8-106 1.08e-57

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: 185.05  E-value: 1.08e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935   8 LEKALLQHFIYTKLDIAYAINKPFPFFEALRDNSFITERMYKESLEACQNLVPLSKVVHNILTSLEQTFDPSMLLILFSK 87
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80

                          90
                  ....*....|....*....
gi 1958801935  88 VNLREYPSLGAICRSFRNV 106
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 361-437 1.43e-34

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: 123.46  E-value: 1.43e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958801935 361 DFLSPTLSVTCGEARGTLFKEKLKQGSSEKCIQNEaGAWLTVKEFLKKGGKATSKDWKKAIRCNKKTLRSLEQDGFL 437
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNE-DSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
ftsN super family cl37078
cell division protein FtsN; FtsN is a poorly conserved protein active in cell division in a ...
 206-403 5.22e-04

cell division protein FtsN; FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions matched by pfam05036 (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis. [Cellular processes, Cell division]


The actual alignment was detected with superfamily member TIGR02223:

Pssm-ID: 274041 [Multi-domain]  Cd Length: 298  Bit Score: 41.99  E-value: 5.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935 206 EDSQEMPHHPSGPEAVVQDNSPAPNdPEVPQEAPCTPANKKARKRKSCIWSNSKRRRQKKKPPQHKMMGVASPGPGVQEK 285
Cdd:TIGR02223  67 ENGETAADLPPKPEERWSYIEELEA-REVLINDPEEPSNGGGVEESAQLTAEQRQLLEQMQADMRAAEKVLATAPSEQTV 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935 286 LKVVGQRTLN-QDDSTRNVKVVTRTLRERTRCAQTSSSQEISKEASKPRARKRPQKRPHTAGRTIHVPEKSKDDAVDFLS 364
Cdd:TIGR02223 146 AVEARKQTAEkKPQKARTAEAQKTPVETEKIASKVKEAKQKQKALPKQTAETQSNSKPIETAPKADKADKTKPKPKEKAE 225

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1958801935 365 PTLSVTCGEARGTLFKEKLK-----QGSSEKCIQNEAGAWLTVK 403
Cdd:TIGR02223 226 RAAALQCGAYANKEQAESVRaklafLGISSKITTTDGGKWYRVV 269
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 8-106 1.08e-57

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: 185.05  E-value: 1.08e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935   8 LEKALLQHFIYTKLDIAYAINKPFPFFEALRDNSFITERMYKESLEACQNLVPLSKVVHNILTSLEQTFDPSMLLILFSK 87
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80

                          90
                  ....*....|....*....
gi 1958801935  88 VNLREYPSLGAICRSFRNV 106
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 361-437 1.43e-34

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: 123.46  E-value: 1.43e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958801935 361 DFLSPTLSVTCGEARGTLFKEKLKQGSSEKCIQNEaGAWLTVKEFLKKGGKATSKDWKKAIRCNKKTLRSLEQDGFL 437
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNE-DSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
SAND smart00258
SAND domain;
365-437 1.51e-23

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 93.56  E-value: 1.51e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958801935  365 PTLSVTCGEARGTLFKEKLKQGSSEKCIQNEaGAWLTVKEFLKKGGKATSKDWKKAIRCNKKTLRSLEQDGFL 437
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQYE-DKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTL 72
ftsN TIGR02223
cell division protein FtsN; FtsN is a poorly conserved protein active in cell division in a ...
 206-403 5.22e-04

cell division protein FtsN; FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions matched by pfam05036 (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis. [Cellular processes, Cell division]


Pssm-ID: 274041 [Multi-domain]  Cd Length: 298  Bit Score: 41.99  E-value: 5.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935 206 EDSQEMPHHPSGPEAVVQDNSPAPNdPEVPQEAPCTPANKKARKRKSCIWSNSKRRRQKKKPPQHKMMGVASPGPGVQEK 285
Cdd:TIGR02223  67 ENGETAADLPPKPEERWSYIEELEA-REVLINDPEEPSNGGGVEESAQLTAEQRQLLEQMQADMRAAEKVLATAPSEQTV 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935 286 LKVVGQRTLN-QDDSTRNVKVVTRTLRERTRCAQTSSSQEISKEASKPRARKRPQKRPHTAGRTIHVPEKSKDDAVDFLS 364
Cdd:TIGR02223 146 AVEARKQTAEkKPQKARTAEAQKTPVETEKIASKVKEAKQKQKALPKQTAETQSNSKPIETAPKADKADKTKPKPKEKAE 225

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1958801935 365 PTLSVTCGEARGTLFKEKLK-----QGSSEKCIQNEAGAWLTVK 403
Cdd:TIGR02223 226 RAAALQCGAYANKEQAESVRaklafLGISSKITTTDGGKWYRVV 269
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 8-106 1.08e-57

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: 185.05  E-value: 1.08e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935   8 LEKALLQHFIYTKLDIAYAINKPFPFFEALRDNSFITERMYKESLEACQNLVPLSKVVHNILTSLEQTFDPSMLLILFSK 87
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80

                          90
                  ....*....|....*....
gi 1958801935  88 VNLREYPSLGAICRSFRNV 106
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 361-437 1.43e-34

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: 123.46  E-value: 1.43e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958801935 361 DFLSPTLSVTCGEARGTLFKEKLKQGSSEKCIQNEaGAWLTVKEFLKKGGKATSKDWKKAIRCNKKTLRSLEQDGFL 437
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNE-DSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
SAND smart00258
SAND domain;
365-437 1.51e-23

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 93.56  E-value: 1.51e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958801935  365 PTLSVTCGEARGTLFKEKLKQGSSEKCIQNEaGAWLTVKEFLKKGGKATSKDWKKAIRCNKKTLRSLEQDGFL 437
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQYE-DKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTL 72
ftsN TIGR02223
cell division protein FtsN; FtsN is a poorly conserved protein active in cell division in a ...
 206-403 5.22e-04

cell division protein FtsN; FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions matched by pfam05036 (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis. [Cellular processes, Cell division]


Pssm-ID: 274041 [Multi-domain]  Cd Length: 298  Bit Score: 41.99  E-value: 5.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935 206 EDSQEMPHHPSGPEAVVQDNSPAPNdPEVPQEAPCTPANKKARKRKSCIWSNSKRRRQKKKPPQHKMMGVASPGPGVQEK 285
Cdd:TIGR02223  67 ENGETAADLPPKPEERWSYIEELEA-REVLINDPEEPSNGGGVEESAQLTAEQRQLLEQMQADMRAAEKVLATAPSEQTV 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801935 286 LKVVGQRTLN-QDDSTRNVKVVTRTLRERTRCAQTSSSQEISKEASKPRARKRPQKRPHTAGRTIHVPEKSKDDAVDFLS 364
Cdd:TIGR02223 146 AVEARKQTAEkKPQKARTAEAQKTPVETEKIASKVKEAKQKQKALPKQTAETQSNSKPIETAPKADKADKTKPKPKEKAE 225

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1958801935 365 PTLSVTCGEARGTLFKEKLK-----QGSSEKCIQNEAGAWLTVK 403
Cdd:TIGR02223 226 RAAALQCGAYANKEQAESVRaklafLGISSKITTTDGGKWYRVV 269
 
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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