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Conserved domains on  [gi|568929778|ref|XP_006503474|]
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single-stranded DNA-binding protein 3 isoform X1 [Mus musculus]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 12218102)

single-stranded DNA-binding protein interacts with Lim domain binding proteins (LBDs) and stabilize LDBs by preventing their proteasomal degradation, thus promoting their functions in gene regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SSDP pfam04503
Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA ...
 81-387 1.19e-67

Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.


:

Pssm-ID: 461334 [Multi-domain]  Cd Length: 293  Bit Score: 216.36  E-value: 1.19e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778   81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPG---SQPSPHAQPPPHNPSSMMGPHSQPFMSP 154
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFQSPPShpsSQPSPHAQPPPHNPATMMGPHSQPFMGP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  155 RYAGGPRPPIRMGNQPP--GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRG--MGPMGPgpqtdpwlslQNYGSG 230
Cdd:pfam04503  81 RYPGGPRPSVRMPQQGNdfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGpgMGPMGP----------QSYGPG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  231 MR-PPPNSLGP--AMPGINMGPGAGRPWPNPNSANSgrqlqsmapessfqIPYSSSSPGT-YVGPPGGGGPPGTPIMPSP 306
Cdd:pfam04503 151 MRgPPPNSTDGpgGMPPMNMGPGGRRPWPQPNASNP--------------LPYSSSSPGSyGGPPGGGGPPGPTPIMPSP 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  307 ADSTNSSDNIYTMINPVPPGGSRSNFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDD 386
Cdd:pfam04503 217 QDSTNSGENMYTLMNPVGPGGNRANFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPRED 292


                  .
gi 568929778  387 G 387
Cdd:pfam04503 293 G 293
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 7.88e-03

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.


:

Pssm-ID: 128913  Cd Length: 34  Bit Score: 33.95  E-value: 7.88e-03
                           10        20
                   ....*....|....*....|....*..
gi 568929778    17 REKLALYVYEYLLHVGAQKSAQTFLSE 43
Cdd:smart00667   3 RSELNRLILEYLLRNGYEETAETLQKE 29
 
Name Accession Description Interval E-value
SSDP pfam04503
Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA ...
 81-387 1.19e-67

Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.


Pssm-ID: 461334 [Multi-domain]  Cd Length: 293  Bit Score: 216.36  E-value: 1.19e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778   81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPG---SQPSPHAQPPPHNPSSMMGPHSQPFMSP 154
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFQSPPShpsSQPSPHAQPPPHNPATMMGPHSQPFMGP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  155 RYAGGPRPPIRMGNQPP--GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRG--MGPMGPgpqtdpwlslQNYGSG 230
Cdd:pfam04503  81 RYPGGPRPSVRMPQQGNdfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGpgMGPMGP----------QSYGPG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  231 MR-PPPNSLGP--AMPGINMGPGAGRPWPNPNSANSgrqlqsmapessfqIPYSSSSPGT-YVGPPGGGGPPGTPIMPSP 306
Cdd:pfam04503 151 MRgPPPNSTDGpgGMPPMNMGPGGRRPWPQPNASNP--------------LPYSSSSPGSyGGPPGGGGPPGPTPIMPSP 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  307 ADSTNSSDNIYTMINPVPPGGSRSNFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDD 386
Cdd:pfam04503 217 QDSTNSGENMYTLMNPVGPGGNRANFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPRED 292


                  .
gi 568929778  387 G 387
Cdd:pfam04503 293 G 293
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 151-273 1.14e-07

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 53.66  E-value: 1.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  151 FMSPRyAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHP---NMGGSMQRMNPPRGMGPMGPGPQTDPWLSLQNy 227
Cdd:TIGR01628 375 FMQLQ-PRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPrmsMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQN- 452

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568929778  228 gsgmRPPPNSLGP--AMPGINMGPgAGRPWPNPNSA--------NSGRQLQSMAPE 273
Cdd:TIGR01628 453 ----AAQKPPMQPvmYPPNYQSLP-LSQDLPQPQSTasqggqnkKLAQVLASATPQ 503
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 7.88e-03

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.


Pssm-ID: 128913  Cd Length: 34  Bit Score: 33.95  E-value: 7.88e-03
                           10        20
                   ....*....|....*....|....*..
gi 568929778    17 REKLALYVYEYLLHVGAQKSAQTFLSE 43
Cdd:smart00667   3 RSELNRLILEYLLRNGYEETAETLQKE 29
 
Name Accession Description Interval E-value
SSDP pfam04503
Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA ...
 81-387 1.19e-67

Single-stranded DNA binding protein, SSDP; This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.


Pssm-ID: 461334 [Multi-domain]  Cd Length: 293  Bit Score: 216.36  E-value: 1.19e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778   81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPG---SQPSPHAQPPPHNPSSMMGPHSQPFMSP 154
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFQSPPShpsSQPSPHAQPPPHNPATMMGPHSQPFMGP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  155 RYAGGPRPPIRMGNQPP--GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRG--MGPMGPgpqtdpwlslQNYGSG 230
Cdd:pfam04503  81 RYPGGPRPSVRMPQQGNdfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGpgMGPMGP----------QSYGPG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  231 MR-PPPNSLGP--AMPGINMGPGAGRPWPNPNSANSgrqlqsmapessfqIPYSSSSPGT-YVGPPGGGGPPGTPIMPSP 306
Cdd:pfam04503 151 MRgPPPNSTDGpgGMPPMNMGPGGRRPWPQPNASNP--------------LPYSSSSPGSyGGPPGGGGPPGPTPIMPSP 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  307 ADSTNSSDNIYTMINPVPPGGSRSNFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDD 386
Cdd:pfam04503 217 QDSTNSGENMYTLMNPVGPGGNRANFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPRED 292


                  .
gi 568929778  387 G 387
Cdd:pfam04503 293 G 293
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 151-273 1.14e-07

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 53.66  E-value: 1.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  151 FMSPRyAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHP---NMGGSMQRMNPPRGMGPMGPGPQTDPWLSLQNy 227
Cdd:TIGR01628 375 FMQLQ-PRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPrmsMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQN- 452

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568929778  228 gsgmRPPPNSLGP--AMPGINMGPgAGRPWPNPNSA--------NSGRQLQSMAPE 273
Cdd:TIGR01628 453 ----AAQKPPMQPvmYPPNYQSLP-LSQDLPQPQSTasqggqnkKLAQVLASATPQ 503
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 94-241 1.32e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 41.17  E-value: 1.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778   94 AAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNPSSMMGPHSQPFMSPRyAGGPRPPIRMGNQPPGG 173
Cdd:pfam09770 209 KPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQ-SPQPDPAQPSIQPQAQQ 287

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568929778  174 VPGTQPllPNSMDPTRQQGHPNMGGSMQRMNPPRGMGPMGPGPqtdPWLSLQNYGSGMRPPPNSLGPA 241
Cdd:pfam09770 288 FHQQPP--PVPVQPTQILQNPNRLSAARVGYPQNPQPGVQPAP---AHQAHRQQGSFGRQAPIITHPQ 350
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 122-272 2.39e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 39.99  E-value: 2.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  122 QGPPGSQPSPHAQPPPHNPSSMMGPHSQPFMSPRYAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGSMQ 201
Cdd:pfam09606  68 GNGGMGGGQQGMPDPINALQNLAGQGTRPQMMGPMGPGPGGPMGQQMGGPGTASNLLASLGRPQMPMGGAGFPSQMSRVG 147

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568929778  202 RMNPPRGMGPMGPGPQTDPWLSLQNY-------GSGMRPPPNSLGPAMPGINMGPGAGRPWPnPNSANSGRQLQSMAP 272
Cdd:pfam09606 148 RMQPGGQAGGMMQPSSGQPGSGTPNQmgpnggpGQGQAGGMNGGQQGPMGGQMPPQMGVPGM-PGPADAGAQMGQQAQ 224
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 94-328 2.63e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 39.99  E-value: 2.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778   94 AAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNPssMMGPHSQPFMspryaGGPRPPIRMGNQPPGG 173
Cdd:pfam09606 226 NGGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQMQQMPQGVG--GGAGQGGPGQ-----PMGPPGQQPGAMPNVM 298

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  174 VPGTQPLLPNSMDPTRQQGhpnMGGSMQRMNPPRGMGPMGPGPQTDPWLSLQNYGSGMrpPPNSLGPAMPGINMGPGAGR 253
Cdd:pfam09606 299 SIGDQNNYQQQQTRQQQQQ---QGGNHPAAHQQQMNQSVGQGGQVVALGGLNHLETWN--PGNFGGLGANPMQRGQPGMM 373

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568929778  254 PWPNPNSANSGRQ---LQSMAPESSFQIPYSSSSPGTYVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMINPVPPGGS 328
Cdd:pfam09606 374 SSPSPVPGQQVRQvtpNQFMRQSPQPSVPSPQGPGSQPPQSHPGGMIPSPALIPSPSPQMSQQPAQQRTIGQDSPGGS 451
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 93-284 3.47e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 39.75  E-value: 3.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778   93 SAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNPSSMMgPHSQPFMSPRYAGGPRPPIRMGNQPPG 172
Cdd:pfam03154 315 PAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQL-PNPQSHKHPPHLSGPSPFQMNSNLPPP 393

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929778  173 gvPGTQPL--LPNSMDPTRQQGHPNMGGSMQRMNPPRGMGPMGPGPQTDPWLSLQ--NYGSGMRPPPNSLGPAMPGINMG 248
Cdd:pfam03154 394 --PALKPLssLSTHHPPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAAShpPTSGLHQVPSQSPFPQHPFVPGG 471

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 568929778  249 -----PGAGRPWPNPNSANSGRQLQSMAPESSFQIPYSSSS 284
Cdd:pfam03154 472 pppitPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSC 512
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 7.88e-03

Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.


Pssm-ID: 128913  Cd Length: 34  Bit Score: 33.95  E-value: 7.88e-03
                           10        20
                   ....*....|....*....|....*..
gi 568929778    17 REKLALYVYEYLLHVGAQKSAQTFLSE 43
Cdd:smart00667   3 RSELNRLILEYLLRNGYEETAETLQKE 29
 
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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