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Conserved domains on  [gi|1063720074|ref|NP_001320017|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1003726)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner; similar to Arabidopsis pentatricopeptide repeat proteins that play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts

Gene Ontology:  GO:0003723
PubMed:  23635770

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 253-582 2.88e-13

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.99  E-value: 2.88e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  253 CKIYTNLVECYSRNGEFDAVFSLIHEMDDKKLELSFCSYGCVLDDACRLGDAEFIDKVLCLMVEKK-------FVTL--- 322
Cdd:PLN03218   472 CKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNvkpdrvvFNALisa 551

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  323 -GDSAVNDKIIERLCDMGktfasemlfrkacnGET--VRLWDSTYGCMLKALSRKKRTKEAVDVYRMICRKGITVLDEsC 399
Cdd:PLN03218   552 cGQSGAVDRAFDVLAEMK--------------AEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPE-V 616

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  400 YIEFANAlCRDDNSSEEEEELLVDVIKRGFVPCTHKLSEVLASMCRKRRWKSAEKLLDSVMEMEVYFDSFACGLLMERYC 479
Cdd:PLN03218   617 YTIAVNS-CSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACS 695

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  480 RSGKLEKALVLHEKIKKMKGSLDVNAYNAvldrlmmrqkemveeavvvfeymkeinsvnsksftiMIQGLCRVKEMKKAM 559
Cdd:PLN03218   696 NAKNWKKALELYEDIKSIKLRPTVSTMNA------------------------------------LITALCEGNQLPKAL 739

                          330       340
                   ....*....|....*....|...
gi 1063720074  560 RSHDEMLRLGLKPDLVTYKRLIL 582
Cdd:PLN03218   740 EVLSEMKRLGLCPNTITYSILLV 762
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 502-551 3.57e-07

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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 46.97  E-value: 3.57e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063720074 502 DVNAYNAVLDRLMmrQKEMVEEAVVVFEYMKEIN-SVNSKSFTIMIQGLCR 551
Cdd:pfam13041   2 DVVTYNTLINGYC--KKGKVEEAFKLFNEMKKRGvKPNVYTYTILINGLCK 50
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 186-226 3.85e-05

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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 41.19  E-value: 3.85e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063720074 186 PSQSAYNSLLGSLVKENQFRVALCLYSAMVRNGIVSDELTW 226
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 253-582 2.88e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.99  E-value: 2.88e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  253 CKIYTNLVECYSRNGEFDAVFSLIHEMDDKKLELSFCSYGCVLDDACRLGDAEFIDKVLCLMVEKK-------FVTL--- 322
Cdd:PLN03218   472 CKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNvkpdrvvFNALisa 551

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  323 -GDSAVNDKIIERLCDMGktfasemlfrkacnGET--VRLWDSTYGCMLKALSRKKRTKEAVDVYRMICRKGITVLDEsC 399
Cdd:PLN03218   552 cGQSGAVDRAFDVLAEMK--------------AEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPE-V 616

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  400 YIEFANAlCRDDNSSEEEEELLVDVIKRGFVPCTHKLSEVLASMCRKRRWKSAEKLLDSVMEMEVYFDSFACGLLMERYC 479
Cdd:PLN03218   617 YTIAVNS-CSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACS 695

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  480 RSGKLEKALVLHEKIKKMKGSLDVNAYNAvldrlmmrqkemveeavvvfeymkeinsvnsksftiMIQGLCRVKEMKKAM 559
Cdd:PLN03218   696 NAKNWKKALELYEDIKSIKLRPTVSTMNA------------------------------------LITALCEGNQLPKAL 739

                          330       340
                   ....*....|....*....|...
gi 1063720074  560 RSHDEMLRLGLKPDLVTYKRLIL 582
Cdd:PLN03218   740 EVLSEMKRLGLCPNTITYSILLV 762
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 538-584 4.29e-08

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: 49.67  E-value: 4.29e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063720074 538 NSKSFTIMIQGLCRVKEMKKAMRSHDEMLRLGLKPDLVTYKRLILGF 584
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 502-551 3.57e-07

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: 46.97  E-value: 3.57e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063720074 502 DVNAYNAVLDRLMmrQKEMVEEAVVVFEYMKEIN-SVNSKSFTIMIQGLCR 551
Cdd:pfam13041   2 DVVTYNTLINGYC--KKGKVEEAFKLFNEMKKRGvKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 186-226 3.85e-05

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: 41.19  E-value: 3.85e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063720074 186 PSQSAYNSLLGSLVKENQFRVALCLYSAMVRNGIVSDELTW 226
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 541-573 2.03e-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: 35.89  E-value: 2.03e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063720074 541 SFTIMIQGLCRVKEMKKAMRSHDEMLRLGLKPD 573
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 253-582 2.88e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.99  E-value: 2.88e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  253 CKIYTNLVECYSRNGEFDAVFSLIHEMDDKKLELSFCSYGCVLDDACRLGDAEFIDKVLCLMVEKK-------FVTL--- 322
Cdd:PLN03218   472 CKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNvkpdrvvFNALisa 551

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  323 -GDSAVNDKIIERLCDMGktfasemlfrkacnGET--VRLWDSTYGCMLKALSRKKRTKEAVDVYRMICRKGITVLDEsC 399
Cdd:PLN03218   552 cGQSGAVDRAFDVLAEMK--------------AEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPE-V 616

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  400 YIEFANAlCRDDNSSEEEEELLVDVIKRGFVPCTHKLSEVLASMCRKRRWKSAEKLLDSVMEMEVYFDSFACGLLMERYC 479
Cdd:PLN03218   617 YTIAVNS-CSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACS 695

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074  480 RSGKLEKALVLHEKIKKMKGSLDVNAYNAvldrlmmrqkemveeavvvfeymkeinsvnsksftiMIQGLCRVKEMKKAM 559
Cdd:PLN03218   696 NAKNWKKALELYEDIKSIKLRPTVSTMNA------------------------------------LITALCEGNQLPKAL 739

                          330       340
                   ....*....|....*....|...
gi 1063720074  560 RSHDEMLRLGLKPDLVTYKRLIL 582
Cdd:PLN03218   740 EVLSEMKRLGLCPNTITYSILLV 762
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 538-584 4.29e-08

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: 49.67  E-value: 4.29e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063720074 538 NSKSFTIMIQGLCRVKEMKKAMRSHDEMLRLGLKPDLVTYKRLILGF 584
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 502-551 3.57e-07

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: 46.97  E-value: 3.57e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063720074 502 DVNAYNAVLDRLMmrQKEMVEEAVVVFEYMKEIN-SVNSKSFTIMIQGLCR 551
Cdd:pfam13041   2 DVVTYNTLINGYC--KKGKVEEAFKLFNEMKKRGvKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 186-226 3.85e-05

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: 41.19  E-value: 3.85e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063720074 186 PSQSAYNSLLGSLVKENQFRVALCLYSAMVRNGIVSDELTW 226
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 200-305 1.32e-03

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: 40.46  E-value: 1.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720074 200 KENQFRVALCLYSAMVRNGI--------------VSDELTWDLIAQILCEQGRSksVFKLMET-GVESCK-IYTNLVECY 263
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVrlaqyhynvllylcSKAADATDLKPQLAADRGFE--VFEAMKAqGVSPNEaTYTAVARLA 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1063720074 264 SRNGEFDAVFSLIHEMDDKKLELSFCSYGCVLDDACRLGDAE 305
Cdd:pfam17177 101 AAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDAD 142
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 541-573 2.03e-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: 35.89  E-value: 2.03e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063720074 541 SFTIMIQGLCRVKEMKKAMRSHDEMLRLGLKPD 573
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 467-511 5.29e-03

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: 35.03  E-value: 5.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063720074 467 DSFACGLLMERYCRSGKLEKALVLHEKIKKMKGSLDVNAYNAVLD 511
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 255-300 7.18e-03

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: 34.65  E-value: 7.18e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063720074 255 IYTNLVECYSRNGEFDAVFSLIHEMDDKKLELSFCSYGCVLDDACR 300
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
 
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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