NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2026127178|ref|NP_001381291|]
View 

single-stranded DNA-binding protein 3 isosform f [Homo sapiens]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 81-318 3.85e-53

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: 176.69  E-value: 3.85e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178  81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFFQPP--------------------------------- 124
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFQSPpshpssqpsphaqppphnpatmmgphsqpfmgp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 125 -------------------GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGMGPMGPGPQNYGSGMR-PPPNSLG 184
Cdd:pfam04503  81 rypggprpsvrmpqqgndfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGPGMGPMGPQSYGPGMRgPPPNSTD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 185 P--AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGT-YVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMINPVPPGGSRS 261
Cdd:pfam04503 161 GpgGMPPMNMGPGGRRPWPQPNASNPLPYSSSSPGSyGGPPGGGGPPGPTPIMPSPQDSTNSGENMYTLMNPVGPGGNRA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2026127178 262 NFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDDG 318
Cdd:pfam04503 241 NFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPREDG 293
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 6.57e-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: 6.57e-03
                           10        20
                   ....*....|....*....|....*..
gi 2026127178   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 ...
 81-318 3.85e-53

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: 176.69  E-value: 3.85e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178  81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFFQPP--------------------------------- 124
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFQSPpshpssqpsphaqppphnpatmmgphsqpfmgp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 125 -------------------GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGMGPMGPGPQNYGSGMR-PPPNSLG 184
Cdd:pfam04503  81 rypggprpsvrmpqqgndfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGPGMGPMGPQSYGPGMRgPPPNSTD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 185 P--AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGT-YVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMINPVPPGGSRS 261
Cdd:pfam04503 161 GpgGMPPMNMGPGGRRPWPQPNASNPLPYSSSSPGSyGGPPGGGGPPGPTPIMPSPQDSTNSGENMYTLMNPVGPGGNRA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2026127178 262 NFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDDG 318
Cdd:pfam04503 241 NFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPREDG 293
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 120-208 9.57e-06

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: 47.11  E-value: 9.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 120 FFQPPGGVPGtqpllPNSMDPTRQQGHP---NMGGSMQRMNPPRGMGPMGPGPQNYGSGMR---PPPNSLGP--AMPGIN 191
Cdd:TIGR01628 395 MGQPPYYGQG-----PQQQFNGQPLGWPrmsMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAqnaAQKPPMQPvmYPPNYQ 469

                          90
                  ....*....|....*..
gi 2026127178 192 MGPgAGRPWPNPNSANS 208
Cdd:TIGR01628 470 SLP-LSQDLPQPQSTAS 485
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 6.57e-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: 6.57e-03
                           10        20
                   ....*....|....*....|....*..
gi 2026127178   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 ...
 81-318 3.85e-53

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: 176.69  E-value: 3.85e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178  81 EHSSEAKAFHDYSA---AAAPSPVLGNIPPNDGMPGGPIPPGFFQPP--------------------------------- 124
Cdd:pfam04503   1 EHSSEAKAFHDYSFvssAAAPSPVMGQMPPGDGMPGGPMPPGFFQSPpshpssqpsphaqppphnpatmmgphsqpfmgp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 125 -------------------GGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGMGPMGPGPQNYGSGMR-PPPNSLG 184
Cdd:pfam04503  81 rypggprpsvrmpqqgndfNGPPGQQPMMPNSMDPTRPGGHPNMGGPMQRMNPPRGPGMGPMGPQSYGPGMRgPPPNSTD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 185 P--AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGT-YVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMINPVPPGGSRS 261
Cdd:pfam04503 161 GpgGMPPMNMGPGGRRPWPQPNASNPLPYSSSSPGSyGGPPGGGGPPGPTPIMPSPQDSTNSGENMYTLMNPVGPGGNRA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2026127178 262 NFPMGPGSDgPMGGMGGMEPHHMNGSLGSGDIDGLpKNSPNNIsgISNPPGTPRDDG 318
Cdd:pfam04503 241 NFPMGPGLE-GPMGPNGMEPHHSNGSLGSGDMDGM-KNSPANV--LSNGPGTPREDG 293
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 120-208 9.57e-06

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: 47.11  E-value: 9.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026127178 120 FFQPPGGVPGtqpllPNSMDPTRQQGHP---NMGGSMQRMNPPRGMGPMGPGPQNYGSGMR---PPPNSLGP--AMPGIN 191
Cdd:TIGR01628 395 MGQPPYYGQG-----PQQQFNGQPLGWPrmsMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAqnaAQKPPMQPvmYPPNYQ 469

                          90
                  ....*....|....*..
gi 2026127178 192 MGPgAGRPWPNPNSANS 208
Cdd:TIGR01628 470 SLP-LSQDLPQPQSTAS 485
LisH smart00667
Lissencephaly type-1-like homology motif; Alpha-helical motif present in Lis1, treacle, ...
 17-43 6.57e-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: 6.57e-03
                           10        20
                   ....*....|....*....|....*..
gi 2026127178   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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH