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Conserved domains on  [gi|564352046|ref|XP_006238600|]
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single-stranded DNA-binding protein 3 isoform X7 [Rattus norvegicus]

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 ...
 81-346 1.80e-61

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: 199.41  E-value: 1.80e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046   81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFF------------------------------QPFMSP 127
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFqsppshpssqpsphaqppphnpatmmgphsQPFMGP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  128 RYAGGPRPPIRMGNQPP--GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRG--MGPMGPgpqtdpwlslQNYGSG 203
Cdd:pfam04503  81 RYPGGPRPSVRMPQQGNdfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGpgMGPMGP----------QSYGPG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  204 MR-PPPNSLGP--AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGT-YVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMI 279
Cdd:pfam04503 151 MRgPPPNSTDGpgGMPPMNMGPGGRRPWPQPNASNPLPYSSSSPGSyGGPPGGGGPPGPTPIMPSPQDSTNSGENMYTLM 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564352046  280 NPVPPGGSRSNFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDDG 346
Cdd:pfam04503 231 NPVGPGGNRANFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPREDG 293
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 7.10e-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: 7.10e-03
                           10        20
                   ....*....|....*....|....*..
gi 564352046    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 ...
 81-346 1.80e-61

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: 199.41  E-value: 1.80e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046   81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFF------------------------------QPFMSP 127
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFqsppshpssqpsphaqppphnpatmmgphsQPFMGP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  128 RYAGGPRPPIRMGNQPP--GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRG--MGPMGPgpqtdpwlslQNYGSG 203
Cdd:pfam04503  81 RYPGGPRPSVRMPQQGNdfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGpgMGPMGP----------QSYGPG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  204 MR-PPPNSLGP--AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGT-YVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMI 279
Cdd:pfam04503 151 MRgPPPNSTDGpgGMPPMNMGPGGRRPWPQPNASNPLPYSSSSPGSyGGPPGGGGPPGPTPIMPSPQDSTNSGENMYTLM 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564352046  280 NPVPPGGSRSNFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDDG 346
Cdd:pfam04503 231 NPVGPGGNRANFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPREDG 293
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 124-236 5.19e-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: 51.35  E-value: 5.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  124 FMSPRyAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHP---NMGGSMQRMNPPRGMGPMGPGPQTDPWLSLQNy 200
Cdd:TIGR01628 375 FMQLQ-PRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPrmsMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQN- 452

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 564352046  201 gsgmRPPPNSLGP--AMPGINMGPgAGRPWPNPNSANS 236
Cdd:TIGR01628 453 ----AAQKPPMQPvmYPPNYQSLP-LSQDLPQPQSTAS 485
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 7.10e-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: 7.10e-03
                           10        20
                   ....*....|....*....|....*..
gi 564352046    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 ...
 81-346 1.80e-61

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: 199.41  E-value: 1.80e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046   81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFF------------------------------QPFMSP 127
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFqsppshpssqpsphaqppphnpatmmgphsQPFMGP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  128 RYAGGPRPPIRMGNQPP--GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRG--MGPMGPgpqtdpwlslQNYGSG 203
Cdd:pfam04503  81 RYPGGPRPSVRMPQQGNdfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGpgMGPMGP----------QSYGPG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  204 MR-PPPNSLGP--AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGT-YVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMI 279
Cdd:pfam04503 151 MRgPPPNSTDGpgGMPPMNMGPGGRRPWPQPNASNPLPYSSSSPGSyGGPPGGGGPPGPTPIMPSPQDSTNSGENMYTLM 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564352046  280 NPVPPGGSRSNFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDDG 346
Cdd:pfam04503 231 NPVGPGGNRANFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPREDG 293
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 124-236 5.19e-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: 51.35  E-value: 5.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564352046  124 FMSPRyAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHP---NMGGSMQRMNPPRGMGPMGPGPQTDPWLSLQNy 200
Cdd:TIGR01628 375 FMQLQ-PRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPrmsMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQN- 452

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 564352046  201 gsgmRPPPNSLGP--AMPGINMGPgAGRPWPNPNSANS 236
Cdd:TIGR01628 453 ----AAQKPPMQPvmYPPNYQSLP-LSQDLPQPQSTAS 485
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 7.10e-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: 7.10e-03
                           10        20
                   ....*....|....*....|....*..
gi 564352046    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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