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Conserved domains on  [gi|1443052588|ref|XP_025877681|]
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uncharacterized protein [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Helitron_like_N super family cl16715
Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently ...
 337-495 1.06e-29

Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently recognized eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.


The actual alignment was detected with superfamily member pfam14214:

Pssm-ID: 464105  Cd Length: 199  Bit Score: 116.23  E-value: 1.06e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443052588 337 HYRKDEPNPFTCCGRLSDQLAanafsCIETSRLTYHALNQKKLRSE--THQGISDAVVRGDSDGKD---VGTKVILPSSF 411
Cdd:pfam14214   9 DGRFARHPRFLFVAFNLFQQA-----RAESRRLSFIRVNQKELRAEsyTGERLRDALEEETDDPEVlalLGSIVILPSSV 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443052588 412 IGGRRYMVQNYHDSMAICRSYGPPQIFSTFTCNSKWPEIIEAIRFE-----------AGQKPSDRSDMVTHVYHMKLDEY 480
Cdd:pfam14214  84 PGSPRYMLQLRQDAMAIVRRLGKPDLFITFTPNDLWPEIKRELARYrewklpgaqtrLRRLASDRPDIVARVFHRKLELF 163

                         170
                  ....*....|....*..
gi 1443052588 481 ITSIKNGE--AFGPIKA 495
Cdd:pfam14214 164 LKDLLRFKegVFGNVSA 180
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 556-622 5.04e-17

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


:

Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 76.14  E-value: 5.04e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443052588 556 VRVRVTRFSQFTTANepdKILRLDLVLLDEQGDMMDAQIPGRHVSQFKPLLKEDAVYYIKYFEVAEA 622
Cdd:cd04480     2 ICVRVLRLWDVYNNA---SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPN 65
 
Name Accession Description Interval E-value
Helitron_like_N pfam14214
Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently ...
 337-495 1.06e-29

Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently recognized eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.


Pssm-ID: 464105  Cd Length: 199  Bit Score: 116.23  E-value: 1.06e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443052588 337 HYRKDEPNPFTCCGRLSDQLAanafsCIETSRLTYHALNQKKLRSE--THQGISDAVVRGDSDGKD---VGTKVILPSSF 411
Cdd:pfam14214   9 DGRFARHPRFLFVAFNLFQQA-----RAESRRLSFIRVNQKELRAEsyTGERLRDALEEETDDPEVlalLGSIVILPSSV 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443052588 412 IGGRRYMVQNYHDSMAICRSYGPPQIFSTFTCNSKWPEIIEAIRFE-----------AGQKPSDRSDMVTHVYHMKLDEY 480
Cdd:pfam14214  84 PGSPRYMLQLRQDAMAIVRRLGKPDLFITFTPNDLWPEIKRELARYrewklpgaqtrLRRLASDRPDIVARVFHRKLELF 163

                         170
                  ....*....|....*..
gi 1443052588 481 ITSIKNGE--AFGPIKA 495
Cdd:pfam14214 164 LKDLLRFKegVFGNVSA 180
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 556-622 5.04e-17

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 76.14  E-value: 5.04e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443052588 556 VRVRVTRFSQFTTANepdKILRLDLVLLDEQGDMMDAQIPGRHVSQFKPLLKEDAVYYIKYFEVAEA 622
Cdd:cd04480     2 ICVRVLRLWDVYNNA---SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPN 65
 
Name Accession Description Interval E-value
Helitron_like_N pfam14214
Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently ...
 337-495 1.06e-29

Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently recognized eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.


Pssm-ID: 464105  Cd Length: 199  Bit Score: 116.23  E-value: 1.06e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443052588 337 HYRKDEPNPFTCCGRLSDQLAanafsCIETSRLTYHALNQKKLRSE--THQGISDAVVRGDSDGKD---VGTKVILPSSF 411
Cdd:pfam14214   9 DGRFARHPRFLFVAFNLFQQA-----RAESRRLSFIRVNQKELRAEsyTGERLRDALEEETDDPEVlalLGSIVILPSSV 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443052588 412 IGGRRYMVQNYHDSMAICRSYGPPQIFSTFTCNSKWPEIIEAIRFE-----------AGQKPSDRSDMVTHVYHMKLDEY 480
Cdd:pfam14214  84 PGSPRYMLQLRQDAMAIVRRLGKPDLFITFTPNDLWPEIKRELARYrewklpgaqtrLRRLASDRPDIVARVFHRKLELF 163

                         170
                  ....*....|....*..
gi 1443052588 481 ITSIKNGE--AFGPIKA 495
Cdd:pfam14214 164 LKDLLRFKegVFGNVSA 180
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 556-622 5.04e-17

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 76.14  E-value: 5.04e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443052588 556 VRVRVTRFSQFTTANepdKILRLDLVLLDEQGDMMDAQIPGRHVSQFKPLLKEDAVYYIKYFEVAEA 622
Cdd:cd04480     2 ICVRVLRLWDVYNNA---SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPN 65
RPA1_DBD_A cd04474
RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding ...
 544-622 2.18e-05

RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can.


Pssm-ID: 239920 [Multi-domain]  Cd Length: 104  Bit Score: 43.77  E-value: 2.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443052588 544 LRDVTQESHRWQVRVRVTRFSQFTTANEPDKILRL-DLVLLDEQGDMMDAQIPGRHVSQFKPLLKEDAVYYIKYFEVAEA 622
Cdd:cd04474     2 ISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLfSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKVA 81
 
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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