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Conserved domains on  [gi|1832250487|ref|NP_001368793|]
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uncharacterized protein LOC4348823 [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
545-577 1.94e-07

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


:

Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 47.87  E-value: 1.94e-07
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1832250487  545 SKMVVSELKTELEAQGLPTDGTRQVLYQRVQKA 577
Cdd:smart00513   2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEA 34
PPR_long super family cl38513
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 103-184 4.06e-05

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


The actual alignment was detected with superfamily member pfam17177:

Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 45.85  E-value: 4.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487 103 IYDMVAAGLSPGPRSFHGLVAAHVLAGDAEGAMQSLRRELSSGVRPLHETFVALVRVFAKKGlatRGMEILAAMERYKYD 182
Cdd:pfam17177 113 VKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAG---RADKVYAYLHRLRDA 189


                  ..
gi 1832250487 183 IR 184
Cdd:pfam17177 190 VR 191
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 104-316 7.64e-04

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 43.33  E-value: 7.64e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487  104 YDMVAAGLSPGPRSFHGLVAAHVLAGD---AEGAMQSLRrelSSGVRPLHETFVALVRVFAKKGLATRGMEILAAMERYK 180
Cdd:PLN03218   496 HEMVNAGVEANVHTFGALIDGCARAGQvakAFGAYGIMR---SKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET 572

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487  181 YDIRKAWLI---LVEELVNNNYLEDANTVFLKGTEGGLQGTDEIYDLLIEEDCKAGDHSNALTVAYKMEASGRMATTFHF 257
Cdd:PLN03218   573 HPIDPDHITvgaLMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFF 652

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1832250487  258 NCLLSVQATCGIPEIAFATFENMEYGGegyMKPDTESYNWVIQAFTRATSYDRAGDVAE 316
Cdd:PLN03218   653 SALVDVAGHAGDLDKAFEILQDARKQG---IKLGTVSYSSLMGACSNAKNWKKALELYE 708
 
Name Accession Description Interval E-value
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
545-577 1.94e-07

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 47.87  E-value: 1.94e-07
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1832250487  545 SKMVVSELKTELEAQGLPTDGTRQVLYQRVQKA 577
Cdd:smart00513   2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEA 34
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 545-577 4.74e-07

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 46.62  E-value: 4.74e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1832250487 545 SKMVVSELKTELEAQGLPTDGTRQVLYQRVQKA 577
Cdd:pfam02037   2 SKLTVAELKEELRKRGLPTSGKKAELIERLQEY 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 103-184 4.06e-05

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 45.85  E-value: 4.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487 103 IYDMVAAGLSPGPRSFHGLVAAHVLAGDAEGAMQSLRRELSSGVRPLHETFVALVRVFAKKGlatRGMEILAAMERYKYD 182
Cdd:pfam17177 113 VKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAG---RADKVYAYLHRLRDA 189


                  ..
gi 1832250487 183 IR 184
Cdd:pfam17177 190 VR 191
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 104-316 7.64e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 43.33  E-value: 7.64e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487  104 YDMVAAGLSPGPRSFHGLVAAHVLAGD---AEGAMQSLRrelSSGVRPLHETFVALVRVFAKKGLATRGMEILAAMERYK 180
Cdd:PLN03218   496 HEMVNAGVEANVHTFGALIDGCARAGQvakAFGAYGIMR---SKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET 572

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487  181 YDIRKAWLI---LVEELVNNNYLEDANTVFLKGTEGGLQGTDEIYDLLIEEDCKAGDHSNALTVAYKMEASGRMATTFHF 257
Cdd:PLN03218   573 HPIDPDHITvgaLMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFF 652

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1832250487  258 NCLLSVQATCGIPEIAFATFENMEYGGegyMKPDTESYNWVIQAFTRATSYDRAGDVAE 316
Cdd:PLN03218   653 SALVDVAGHAGDLDKAFEILQDARKQG---IKLGTVSYSSLMGACSNAKNWKKALELYE 708
 
Name Accession Description Interval E-value
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
545-577 1.94e-07

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 47.87  E-value: 1.94e-07
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1832250487  545 SKMVVSELKTELEAQGLPTDGTRQVLYQRVQKA 577
Cdd:smart00513   2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEA 34
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 545-577 4.74e-07

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 46.62  E-value: 4.74e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1832250487 545 SKMVVSELKTELEAQGLPTDGTRQVLYQRVQKA 577
Cdd:pfam02037   2 SKLTVAELKEELRKRGLPTSGKKAELIERLQEY 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 103-184 4.06e-05

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 45.85  E-value: 4.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487 103 IYDMVAAGLSPGPRSFHGLVAAHVLAGDAEGAMQSLRRELSSGVRPLHETFVALVRVFAKKGlatRGMEILAAMERYKYD 182
Cdd:pfam17177 113 VKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAG---RADKVYAYLHRLRDA 189


                  ..
gi 1832250487 183 IR 184
Cdd:pfam17177 190 VR 191
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 104-316 7.64e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 43.33  E-value: 7.64e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487  104 YDMVAAGLSPGPRSFHGLVAAHVLAGD---AEGAMQSLRrelSSGVRPLHETFVALVRVFAKKGLATRGMEILAAMERYK 180
Cdd:PLN03218   496 HEMVNAGVEANVHTFGALIDGCARAGQvakAFGAYGIMR---SKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET 572

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832250487  181 YDIRKAWLI---LVEELVNNNYLEDANTVFLKGTEGGLQGTDEIYDLLIEEDCKAGDHSNALTVAYKMEASGRMATTFHF 257
Cdd:PLN03218   573 HPIDPDHITvgaLMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFF 652

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1832250487  258 NCLLSVQATCGIPEIAFATFENMEYGGegyMKPDTESYNWVIQAFTRATSYDRAGDVAE 316
Cdd:PLN03218   653 SALVDVAGHAGDLDKAFEILQDARKQG---IKLGTVSYSSLMGACSNAKNWKKALELYE 708
 
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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