NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|334184790|ref|NP_181376|]
View 

Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13329789)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner

CATH:  1.25.40.10
Gene Ontology:  GO:0003723
PubMed:  19004664|23635770|25882680|34065603|18031283|30809817
SCOP:  4001344

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 319-368 2.44e-16

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: 72.78  E-value: 2.44e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334184790  319 PDVYTYNVYINGLCKQNDIEGALKMMSSMNKLGSEPNVVTYNILIKALVK 368
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 181-421 1.74e-15

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 79.15  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  181 TFGILIDALCRIGEVDCATELVRYMSQDSVIVDPRLYSRLLSSvCKHKDSSCFDVIGYlEDLRKTRFSPGlrdyTVVMRF 260
Cdd:PLN03218  581 TVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS-CSQKGDWDFALSIY-DDMKKKGVKPD----EVFFSA 654

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  261 LVE----GGRGKEVVSVLNQMKCDRVEPDLVCYTiVLQGVIAD-EDYPKADKLFDELLLLGLAPDVYTYNVYINGLCKQN 335
Cdd:PLN03218  655 LVDvaghAGDLDKAFEILQDARKQGIKLGTVSYS-SLMGACSNaKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  336 DIEGALKMMSSMNKLGSEPNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNSHTFDIMISAYIEVDEVVCAHGLLE 415
Cdd:PLN03218  734 QLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPV 813


                  ....*.
gi 334184790  416 EAFNMN 421
Cdd:PLN03218  814 VSFDSG 819
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 319-368 2.44e-16

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: 72.78  E-value: 2.44e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334184790  319 PDVYTYNVYINGLCKQNDIEGALKMMSSMNKLGSEPNVVTYNILIKALVK 368
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 181-421 1.74e-15

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 79.15  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  181 TFGILIDALCRIGEVDCATELVRYMSQDSVIVDPRLYSRLLSSvCKHKDSSCFDVIGYlEDLRKTRFSPGlrdyTVVMRF 260
Cdd:PLN03218  581 TVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS-CSQKGDWDFALSIY-DDMKKKGVKPD----EVFFSA 654

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  261 LVE----GGRGKEVVSVLNQMKCDRVEPDLVCYTiVLQGVIAD-EDYPKADKLFDELLLLGLAPDVYTYNVYINGLCKQN 335
Cdd:PLN03218  655 LVDvaghAGDLDKAFEILQDARKQGIKLGTVSYS-SLMGACSNaKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  336 DIEGALKMMSSMNKLGSEPNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNSHTFDIMISAYIEVDEVVCAHGLLE 415
Cdd:PLN03218  734 QLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPV 813


                  ....*.
gi 334184790  416 EAFNMN 421
Cdd:PLN03218  814 VSFDSG 819
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 354-401 2.34e-12

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: 61.23  E-value: 2.34e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 334184790  354 PNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNSHTFDIMISAY 401
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 357-391 1.05e-05

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: 42.06  E-value: 1.05e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334184790  357 VTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNS 391
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 322-356 7.27e-05

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: 39.75  E-value: 7.27e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334184790  322 YTYNVYINGLCKQNDIEGALKMMSSMNKLGSEPNV 356
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 319-368 2.44e-16

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: 72.78  E-value: 2.44e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334184790  319 PDVYTYNVYINGLCKQNDIEGALKMMSSMNKLGSEPNVVTYNILIKALVK 368
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 181-421 1.74e-15

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 79.15  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  181 TFGILIDALCRIGEVDCATELVRYMSQDSVIVDPRLYSRLLSSvCKHKDSSCFDVIGYlEDLRKTRFSPGlrdyTVVMRF 260
Cdd:PLN03218  581 TVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS-CSQKGDWDFALSIY-DDMKKKGVKPD----EVFFSA 654

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  261 LVE----GGRGKEVVSVLNQMKCDRVEPDLVCYTiVLQGVIAD-EDYPKADKLFDELLLLGLAPDVYTYNVYINGLCKQN 335
Cdd:PLN03218  655 LVDvaghAGDLDKAFEILQDARKQGIKLGTVSYS-SLMGACSNaKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  336 DIEGALKMMSSMNKLGSEPNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNSHTFDIMISAYIEVDEVVCAHGLLE 415
Cdd:PLN03218  734 QLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPV 813


                  ....*.
gi 334184790  416 EAFNMN 421
Cdd:PLN03218  814 VSFDSG 819
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 354-401 2.34e-12

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: 61.23  E-value: 2.34e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 334184790  354 PNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNSHTFDIMISAY 401
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 284-333 8.34e-09

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: 51.21  E-value: 8.34e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334184790  284 PDLVCYTIVLQGVIADEDYPKADKLFDELLLLGLAPDVYTYNVYINGLCK 333
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 351-383 2.72e-08

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 49.27  E-value: 2.72e-08
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334184790  351 GSEPNVVTYNILIKALVKAGDLSRAKTLWKEME 383
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 121-334 3.27e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 52.96  E-value: 3.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  121 SGRIEEAIEVFFKIP--NFRCVPSAYT--LNAlllvlVRKRQSLELVPEILVKACRMGVRLEESTFGILIDALCRIGEVD 196
Cdd:PLN03218  592 AGQVDRAKEVYQMIHeyNIKGTPEVYTiaVNS-----CSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLD 666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  197 CATELVRYMSQDSVIVDPRLYSRLLSSVCKHKDSScfDVIGYLEDLRKTRFSPGLRDYTVVMRFLVEGGRGKEVVSVLNQ 276
Cdd:PLN03218  667 KAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWK--KALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSE 744

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334184790  277 MKCDRVEPDLVCYTIVLQGVIADEDYPKADKLFDELLLLGLAPDVYTYNVyINGLCKQ 334
Cdd:PLN03218  745 MKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRC-ITGLCLR 801
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 319-450 8.70e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 51.42  E-value: 8.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  319 PDVYTYNVYINGLCKQNDIEGALKMMSSMNKLGSEPNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNSHTFDIMI 398
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  399 SAyievdevvCAH-GLLEEAFNMNVFVKSSRIE-------EVISRLCEKGLMDQAVELLA 450
Cdd:PLN03218  515 DG--------CARaGQVAKAFGAYGIMRSKNVKpdrvvfnALISACGQSGAVDRAFDVLA 566
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 322-417 1.26e-06

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: 48.93  E-value: 1.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  322 YTYNVYINgLC----------KQNDIEGALKMMSSMNKLGSEPNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNS 391
Cdd:pfam17177  47 YHYNVLLY-LCskaadatdlkPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRL 125

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 334184790  392 HTFDIMISAY---------IEVDEVVCAHGL-LEEA 417
Cdd:pfam17177 126 RSYSPALHAYceagdadkaYEVEEHMLAHGVeLEEP 161
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 319-347 4.47e-06

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 43.10  E-value: 4.47e-06
                          10        20
                  ....*....|....*....|....*....
gi 334184790  319 PDVYTYNVYINGLCKQNDIEGALKMMSSM 347
Cdd:pfam12854   5 PDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 173-206 5.44e-06

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 42.72  E-value: 5.44e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334184790  173 MGVRLEESTFGILIDALCRIGEVDCATELVRYMS 206
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 357-387 5.46e-06

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: 42.84  E-value: 5.46e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334184790  357 VTYNILIKALVKAGDLSRAKTLWKEMETNGV 387
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 347-401 6.09e-06

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: 43.50  E-value: 6.09e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 334184790  347 MNKLGSEPNVVTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNSHTFDIMISAY 401
Cdd:pfam13812   6 MVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 307-368 8.33e-06

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: 43.12  E-value: 8.33e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334184790  307 KLFDELLLLGLAPDVYTYNVYINGLCKQNDIEGALKMMSSMNKLGSEPNVVTYNILIKALVK 368
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 357-391 1.05e-05

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: 42.06  E-value: 1.05e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334184790  357 VTYNILIKALVKAGDLSRAKTLWKEMETNGVNRNS 391
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 220-387 2.72e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 46.79  E-value: 2.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  220 LLSSVCKHKDsscfDVIGYLEDLRKTRfSPGLRD----YTVVMRFLVEGGRGKEVVSVLNQMKCDRVEPDLVCYTIVLQG 295
Cdd:PLN03218  442 MLMSVCASSQ----DIDGALRVLRLVQ-EAGLKAdcklYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDG 516

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  296 VIADEDYPKADKLFDELLLLGLAPDVYTYNVYINGLCKQNDIEGALKMMSSMnklGSE-----PNVVTYNILIKALVKAG 370
Cdd:PLN03218  517 CARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEM---KAEthpidPDHITVGALMKACANAG 593

                         170
                  ....*....|....*..
gi 334184790  371 DLSRAKTLWKEMETNGV 387
Cdd:PLN03218  594 QVDRAKEVYQMIHEYNI 610
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 322-356 7.27e-05

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: 39.75  E-value: 7.27e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334184790  322 YTYNVYINGLCKQNDIEGALKMMSSMNKLGSEPNV 356
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 254-295 8.68e-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: 40.04  E-value: 8.68e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 334184790  254 YTVVMRFLVEGGRGKEVVSVLNQMKCDRVEPDLVCYTIVLQG 295
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 273-371 1.08e-04

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: 43.15  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  273 VLNQMKCDRVEPDLVCYTIVLQGVIADEDYPKADKLFDELLLLGLAPDVYTYNVYINGLCKQNDIEGALKMMSSMNKLGS 352
Cdd:pfam17177  77 VFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGV 156

                          90
                  ....*....|....*....
gi 334184790  353 EPNVVTYNILIKALVKAGD 371
Cdd:pfam17177 157 ELEEPELAALLKVSAKAGR 175
Mtf2 pfam19189
Mtf2 family; This family appears to be distantly related to PPR repeats.
 355-436 5.13e-04

Mtf2 family; This family appears to be distantly related to PPR repeats.


Pssm-ID: 437034  Cd Length: 195  Bit Score: 41.24  E-value: 5.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790  355 NVVTYNILIKALVKA-GDLSRAKTLWKEMETNGVNRNSHTFDIMISAYIEVDEVVCAHGLLEEAFNMNVFVKSSRIEEVI 433
Cdd:pfam19189 110 TTDVYNELLRTRWEGfRDLYGVLSLLEEMKVNGVQGDLETREILEKIRREVGEQENDPKGVGVLWSKEDKRDLDELEKYL 189


                  ...
gi 334184790  434 SRL 436
Cdd:pfam19189 190 RKL 192
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 322-351 4.51e-03

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: 34.75  E-value: 4.51e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 334184790  322 YTYNVYINGLCKQNDIEGALKMMSSMNKLG 351
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PLN03077 PLN03077
Protein ECB2; Provisional
 188-413 7.40e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 38.68  E-value: 7.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790 188 ALCRIGEVDCATELVRYMSQDSVIVDPRLYSRLL------------SSVCKHKDSScfdvigyledlrKTRFspGLRDYT 255
Cdd:PLN03077  60 ALCSHGQLEQALKLLESMQELRVPVDEDAYVALFrlcewkraveegSRVCSRALSS------------HPSL--GVRLGN 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184790 256 VVMRFLVEGGRGKEVVSVLNQMKcdrvEPDLVCYTIVLQGVIADEDYPKADKLFDELLLLGLAPDVYTYNVYINGLCKQN 335
Cdd:PLN03077 126 AMLSMFVRFGELVHAWYVFGKMP----ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIP 201

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334184790 336 DIEGALKMMSSMNKLGSEPNVVTYNILIKALVKAGDLSRAKTLWKEMETngvnRNSHTFDIMISAYIEVDEvvCAHGL 413
Cdd:PLN03077 202 DLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPR----RDCISWNAMISGYFENGE--CLEGL 273
 
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