Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]
Protein Classification
pentatricopeptide repeat-containing protein( domain architecture ID 1000225)
pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| PLN03081 super family | cl33631 | pentatricopeptide (PPR) repeat-containing protein; Provisional |
42-559 | 4.56e-134 | ||||||||
pentatricopeptide (PPR) repeat-containing protein; Provisional The actual alignment was detected with superfamily member PLN03081: Pssm-ID: 215563 [Multi-domain] Cd Length: 697 Bit Score: 406.18 E-value: 4.56e-134
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| Name | Accession | Description | Interval | E-value | ||||||||
| PLN03081 | PLN03081 | pentatricopeptide (PPR) repeat-containing protein; Provisional |
42-559 | 4.56e-134 | ||||||||
pentatricopeptide (PPR) repeat-containing protein; Provisional Pssm-ID: 215563 [Multi-domain] Cd Length: 697 Bit Score: 406.18 E-value: 4.56e-134
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| DYW_deaminase | pfam14432 | DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ... |
467-559 | 1.04e-47 | ||||||||
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems. Pssm-ID: 464172 [Multi-domain] Cd Length: 93 Bit Score: 161.05 E-value: 1.04e-47
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| PPR | TIGR00756 | pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ... |
252-286 | 4.71e-06 | ||||||||
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Pssm-ID: 273253 [Multi-domain] Cd Length: 35 Bit Score: 43.21 E-value: 4.71e-06
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| Name | Accession | Description | Interval | E-value | |||||||||
| PLN03081 | PLN03081 | pentatricopeptide (PPR) repeat-containing protein; Provisional |
42-559 | 4.56e-134 | |||||||||
pentatricopeptide (PPR) repeat-containing protein; Provisional Pssm-ID: 215563 [Multi-domain] Cd Length: 697 Bit Score: 406.18 E-value: 4.56e-134
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| PLN03077 | PLN03077 | Protein ECB2; Provisional |
55-557 | 1.17e-117 | |||||||||
Protein ECB2; Provisional Pssm-ID: 215561 [Multi-domain] Cd Length: 857 Bit Score: 368.02 E-value: 1.17e-117
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| DYW_deaminase | pfam14432 | DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ... |
467-559 | 1.04e-47 | |||||||||
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems. Pssm-ID: 464172 [Multi-domain] Cd Length: 93 Bit Score: 161.05 E-value: 1.04e-47
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| PLN03077 | PLN03077 | Protein ECB2; Provisional |
62-368 | 1.04e-29 | |||||||||
Protein ECB2; Provisional Pssm-ID: 215561 [Multi-domain] Cd Length: 857 Bit Score: 124.58 E-value: 1.04e-29
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| PLN03218 | PLN03218 | maturation of RBCL 1; Provisional |
62-376 | 1.02e-17 | |||||||||
maturation of RBCL 1; Provisional Pssm-ID: 215636 [Multi-domain] Cd Length: 1060 Bit Score: 87.24 E-value: 1.02e-17
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| PPR_2 | pfam13041 | PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ... |
249-298 | 5.62e-13 | |||||||||
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Pssm-ID: 463778 [Multi-domain] Cd Length: 50 Bit Score: 63.54 E-value: 5.62e-13
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| PLN03077 | PLN03077 | Protein ECB2; Provisional |
153-421 | 2.06e-12 | |||||||||
Protein ECB2; Provisional Pssm-ID: 215561 [Multi-domain] Cd Length: 857 Bit Score: 69.88 E-value: 2.06e-12
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| PLN03218 | PLN03218 | maturation of RBCL 1; Provisional |
130-369 | 2.36e-11 | |||||||||
maturation of RBCL 1; Provisional Pssm-ID: 215636 [Multi-domain] Cd Length: 1060 Bit Score: 66.82 E-value: 2.36e-11
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| PPR_long | pfam17177 | Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ... |
227-391 | 6.54e-09 | |||||||||
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: 56.25 E-value: 6.54e-09
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| PPR_long | pfam17177 | Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ... |
262-434 | 6.49e-08 | |||||||||
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: 53.17 E-value: 6.49e-08
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| PLN03218 | PLN03218 | maturation of RBCL 1; Provisional |
86-296 | 4.66e-07 | |||||||||
maturation of RBCL 1; Provisional Pssm-ID: 215636 [Multi-domain] Cd Length: 1060 Bit Score: 52.96 E-value: 4.66e-07
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| PPR | TIGR00756 | pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ... |
252-286 | 4.71e-06 | |||||||||
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Pssm-ID: 273253 [Multi-domain] Cd Length: 35 Bit Score: 43.21 E-value: 4.71e-06
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| E_motif | pfam20431 | E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ... |
387-430 | 4.81e-06 | |||||||||
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding. Pssm-ID: 466580 [Multi-domain] Cd Length: 63 Bit Score: 44.07 E-value: 4.81e-06
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| PPR_2 | pfam13041 | PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ... |
116-159 | 8.51e-06 | |||||||||
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Pssm-ID: 463778 [Multi-domain] Cd Length: 50 Bit Score: 43.12 E-value: 8.51e-06
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| PPR | pfam01535 | PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ... |
252-282 | 2.60e-05 | |||||||||
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR. Pssm-ID: 366695 [Multi-domain] Cd Length: 31 Bit Score: 41.30 E-value: 2.60e-05
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| PPR | pfam01535 | PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ... |
150-180 | 3.28e-05 | |||||||||
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR. Pssm-ID: 366695 [Multi-domain] Cd Length: 31 Bit Score: 40.91 E-value: 3.28e-05
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| PPR_3 | pfam13812 | Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ... |
273-333 | 4.18e-05 | |||||||||
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. Pssm-ID: 316342 [Multi-domain] Cd Length: 63 Bit Score: 41.57 E-value: 4.18e-05
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| PPR | pfam01535 | PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ... |
119-142 | 3.57e-04 | |||||||||
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR. Pssm-ID: 366695 [Multi-domain] Cd Length: 31 Bit Score: 37.83 E-value: 3.57e-04
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| PPR_2 | pfam13041 | PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ... |
147-180 | 4.34e-04 | |||||||||
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Pssm-ID: 463778 [Multi-domain] Cd Length: 50 Bit Score: 38.11 E-value: 4.34e-04
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| PPR | TIGR00756 | pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ... |
150-180 | 2.66e-03 | |||||||||
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Pssm-ID: 273253 [Multi-domain] Cd Length: 35 Bit Score: 35.51 E-value: 2.66e-03
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| Blast search parameters | ||||
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