NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|18398498|ref|NP_565422|]
View 

Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000098)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 149-431 5.43e-23

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 102.65  E-value: 5.43e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   149 LMVNNGLEPDQVTTDIAVRSLCETGRVDEAKDLMKELTEKHSP--PDTYTYNFLLKHLCKCKDLHVVYEfVDEMRDDFDV 226
Cdd:PLN03218  532 IMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPidPDHITVGALMKACANAGQVDRAKE-VYQMIHEYNI 610

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   227 KPDLVSFTILIdNVCnsknlreamylvSKLGNAGFkpdcflyntimkgfctlskgseAVGVYKKMKEEGVEPDQITYNTL 306
Cdd:PLN03218  611 KGTPEVYTIAV-NSC------------SQKGDWDF----------------------ALSIYDDMKKKGVKPDEVFFSAL 655

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   307 IFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKGESLGALSLLEEMEARGCAPNDCTYNTLLHGLCKARLM 386
Cdd:PLN03218  656 VDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQL 735

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 18398498   387 DKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVFDYA 431
Cdd:PLN03218  736 PKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQA 780
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 149-431 5.43e-23

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 102.65  E-value: 5.43e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   149 LMVNNGLEPDQVTTDIAVRSLCETGRVDEAKDLMKELTEKHSP--PDTYTYNFLLKHLCKCKDLHVVYEfVDEMRDDFDV 226
Cdd:PLN03218  532 IMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPidPDHITVGALMKACANAGQVDRAKE-VYQMIHEYNI 610

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   227 KPDLVSFTILIdNVCnsknlreamylvSKLGNAGFkpdcflyntimkgfctlskgseAVGVYKKMKEEGVEPDQITYNTL 306
Cdd:PLN03218  611 KGTPEVYTIAV-NSC------------SQKGDWDF----------------------ALSIYDDMKKKGVKPDEVFFSAL 655

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   307 IFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKGESLGALSLLEEMEARGCAPNDCTYNTLLHGLCKARLM 386
Cdd:PLN03218  656 VDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQL 735

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 18398498   387 DKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVFDYA 431
Cdd:PLN03218  736 PKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQA 780
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 284-429 4.56e-19

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: 85.53  E-value: 4.56e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   284 AVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYL---------KTMVDAGYEPDTATYTSLMNGMCRKGESLGA 354
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPQLaadrgfevfEAMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18398498   355 LSLLEEMEARGCAPNDCTYNTLLHGLCKARLMDKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVFD 429
Cdd:pfam17177 110 FDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAYLH 184
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 371-403 2.94e-07

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: 46.68  E-value: 2.94e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 18398498   371 CTYNTLLHGLCKARLMDKGMELYEMMKSSGVKL 403
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 149-431 5.43e-23

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 102.65  E-value: 5.43e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   149 LMVNNGLEPDQVTTDIAVRSLCETGRVDEAKDLMKELTEKHSP--PDTYTYNFLLKHLCKCKDLHVVYEfVDEMRDDFDV 226
Cdd:PLN03218  532 IMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPidPDHITVGALMKACANAGQVDRAKE-VYQMIHEYNI 610

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   227 KPDLVSFTILIdNVCnsknlreamylvSKLGNAGFkpdcflyntimkgfctlskgseAVGVYKKMKEEGVEPDQITYNTL 306
Cdd:PLN03218  611 KGTPEVYTIAV-NSC------------SQKGDWDF----------------------ALSIYDDMKKKGVKPDEVFFSAL 655

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   307 IFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKGESLGALSLLEEMEARGCAPNDCTYNTLLHGLCKARLM 386
Cdd:PLN03218  656 VDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQL 735

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 18398498   387 DKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVFDYA 431
Cdd:PLN03218  736 PKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQA 780
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 111-384 4.10e-22

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 99.95  E-value: 4.10e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   111 ILKSQpNFRPGRSTFLILLShACrapdSSISNVHRVLNLMVNNGLE-----PDQVTTDIAVRSLCETGRVDEAKDLMKEL 185
Cdd:PLN03218  532 IMRSK-NVKPDRVVFNALIS-AC----GQSGAVDRAFDVLAEMKAEthpidPDHITVGALMKACANAGQVDRAKEVYQMI 605

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   186 TEKH--SPPDTYTynfLLKHLCKCK-DLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFK 262
Cdd:PLN03218  606 HEYNikGTPEVYT---IAVNSCSQKgDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK 681

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   263 PDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLM 342
Cdd:PLN03218  682 LGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL 761

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 18398498   343 NGMCRKGESLGALSLLEEMEARGCAPNDCTYNTLLhGLCKAR 384
Cdd:PLN03218  762 VASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLCLRR 802
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 228-429 1.71e-20

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 94.94  E-value: 1.71e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   228 PDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLI 307
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   308 FGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKGESLGALSLLEEM--EARGCAPNDCTYNTLLHGLCKARL 385
Cdd:PLN03218  515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMkaETHPIDPDHITVGALMKACANAGQ 594

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 18398498   386 MDKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVFD 429
Cdd:PLN03218  595 VDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYD 638
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 284-429 4.56e-19

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: 85.53  E-value: 4.56e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   284 AVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYL---------KTMVDAGYEPDTATYTSLMNGMCRKGESLGA 354
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPQLaadrgfevfEAMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18398498   355 LSLLEEMEARGCAPNDCTYNTLLHGLCKARLMDKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVFD 429
Cdd:pfam17177 110 FDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAYLH 184
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 107-425 4.11e-18

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 87.23  E-value: 4.11e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  107 LFQhILKSQPNFRPGRSTFLILLSHACRApdSSISNVHRVLNLMVNNGLEPDQVTTDIAVRSLCETGRVDEAKDLMKELT 186
Cdd:PLN03081 109 LFE-ILEAGCPFTLPASTYDALVEACIAL--KSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMP 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  187 EKhsppDTYTYNFLLKHLCKCKDLHVVYEFVDEMRDDFDvKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFKPDCF 266
Cdd:PLN03081 186 ER----NLASWGTIIGGLVDAGNYREAFALFREMWEDGS-DAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTF 260

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  267 L-------------------------------YNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGR 315
Cdd:PLN03081 261 VscalidmyskcgdiedarcvfdgmpekttvaWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLAL 340

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  316 VEEARMYLKTMVDAGYEPD----TA---------------------------TYTSLMNGMCRKGESLGALSLLEEMEAR 364
Cdd:PLN03081 341 LEHAKQAHAGLIRTGFPLDivanTAlvdlyskwgrmedarnvfdrmprknliSWNALIAGYGNHGRGTKAVEMFERMIAE 420

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18398498  365 GCAPNDCTYNTLLHGLCKARLMDKGMELYEMM-KSSGVKLESNGYATLVRSLVKSGKVAEAY 425
Cdd:PLN03081 421 GVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMsENHRIKPRAMHYACMIELLGREGLLDEAY 482
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 333-382 1.61e-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: 73.17  E-value: 1.61e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 18398498   333 PDTATYTSLMNGMCRKGESLGALSLLEEMEARGCAPNDCTYNTLLHGLCK 382
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 120-463 9.01e-16

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 80.31  E-value: 9.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   120 PGRSTFLILLSHACRAPDssISNVHRVLNLMVNNGLEPDQV--TTDIavrSLC-ETGRVDEAKDLMKELTEKHSPPDTYT 196
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQD--IDGALRVLRLVQEAGLKADCKlyTTLI---STCaKSGKVDAMFEVFHEMVNAGVEANVHT 509

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   197 YNFLLKHLCKCKDLHVVYEFVDEMRDDfDVKPDLVSFTILIdNVCnsknlreamylvsklGNAGfkpdcflynTIMKGFC 276
Cdd:PLN03218  510 FGALIDGCARAGQVAKAFGAYGIMRSK-NVKPDRVVFNALI-SAC---------------GQSG---------AVDRAFD 563

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   277 TLSKgseavgvykkMKEEG--VEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKGESLGA 354
Cdd:PLN03218  564 VLAE----------MKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFA 633

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   355 LSLLEEMEARGCAPNDCTYNTLLHGLCKARLMDKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVFDYAVDS 434
Cdd:PLN03218  634 LSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI 713

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 18398498   435 KSLSDASAYSTLETTL---KWLKKA-------KEQGLVP 463
Cdd:PLN03218  714 KLRPTVSTMNALITALcegNQLPKAlevlsemKRLGLCP 752
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 298-347 1.00e-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: 65.08  E-value: 1.00e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 18398498   298 PDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCR 347
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 263-312 1.51e-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: 62.00  E-value: 1.51e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 18398498   263 PDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSK 312
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 84-427 7.83e-12

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 67.57  E-value: 7.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   84 DLKFHNSVLQSYGSIAVVNDTVKLFqhilkSQPNFRPGRS-TFLILLSHACRAPDSSISnvhrVLNLMVNNGLEPDQVTT 162
Cdd:PLN03077 322 DVSVCNSLIQMYLSLGSWGEAEKVF-----SRMETKDAVSwTAMISGYEKNGLPDKALE----TYALMEQDNVSPDEITI 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  163 dIAVRSLCET-GRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDLHVVYEFVDEMRDDfdvkpDLVSFTILIDNVC 241
Cdd:PLN03077 393 -ASVLSACAClGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK-----DVISWTSIIAGLR 466

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  242 NSKNLREAMY---------------LVSKL------------------------GNAGFKPDCFL--------------- 267
Cdd:PLN03077 467 LNNRCFEALIffrqmlltlkpnsvtLIAALsacarigalmcgkeihahvlrtgiGFDGFLPNALLdlyvrcgrmnyawnq 546

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  268 ----------YNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTM-VDAGYEPDTA 336
Cdd:PLN03077 547 fnshekdvvsWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMeEKYSITPNLK 626

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  337 TYTSLMNGMCRKGESLGALSLLEEMEARgcaPNDCTYNTLLHGlCKarlMDKGMELYEMMKSSGVKLESN--GYATLVRS 414
Cdd:PLN03077 627 HYACVVDLLGRAGKLTEAYNFINKMPIT---PDPAVWGALLNA-CR---IHRHVELGELAAQHIFELDPNsvGYYILLCN 699

                        410
                 ....*....|....
gi 18398498  415 L-VKSGKVAEAYEV 427
Cdd:PLN03077 700 LyADAGKWDEVARV 713
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 192-242 9.06e-10

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: 53.91  E-value: 9.06e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18398498   192 PDTYTYNFLLKHLCKCKDLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCN 242
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKR-GVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 364-397 4.08e-09

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: 51.58  E-value: 4.08e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 18398498   364 RGCAPNDCTYNTLLHGLCKARLMDKGMELYEMMK 397
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 368-417 1.66e-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: 50.44  E-value: 1.66e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 18398498   368 PNDCTYNTLLHGLCKARLMDKGMELYEMMKSSGVKLESNGYATLVRSLVK 417
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 157-206 2.48e-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: 50.05  E-value: 2.48e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 18398498   157 PDQVTTDIAVRSLCETGRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCK 206
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 294-327 5.84e-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: 48.50  E-value: 5.84e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 18398498   294 EGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMV 327
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 297-427 1.14e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.50  E-value: 1.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   297 EPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKGESLGALSLLEEMEARGCAPNDCTYNTL 376
Cdd:PLN03218  434 NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGAL 513

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18398498   377 LHGLCKARLMDKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEV 427
Cdd:PLN03218  514 IDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDV 564
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 323-384 1.54e-07

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: 48.12  E-value: 1.54e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18398498   323 LKTMVDAGYEPDTATYTSLMNGMCRKGESLGALSLLEEMEARGCAPNDCTYNTLLhGLCKAR 384
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL-GVIGGR 63
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 371-403 2.94e-07

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: 46.68  E-value: 2.94e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 18398498   371 CTYNTLLHGLCKARLMDKGMELYEMMKSSGVKL 403
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 330-362 3.09e-07

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: 46.57  E-value: 3.09e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 18398498   330 GYEPDTATYTSLMNGMCRKGESLGALSLLEEME 362
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 372-401 5.52e-07

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: 45.53  E-value: 5.52e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 18398498   372 TYNTLLHGLCKARLMDKGMELYEMMKSSGV 401
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03077 PLN03077
Protein ECB2; Provisional
 5-428 6.29e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 52.16  E-value: 6.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498    5 PSSFRSMPANLLVRKTTPSP-PAPPRDFR-NRTAVGGDSAKLPQNTQAPREPSLRNPFKSPNLSDAKSLFNSIAATsRIP 82
Cdd:PLN03077   5 HFYLNPGKPNLFQLASHKAPnVLPYWNFHgRKRSRGLSVAASSSSSTHDSNSQLRALCSHGQLEQALKLLESMQEL-RVP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   83 LDLKFHNSVLQSYGSIAVVNDTVKLFQHILKSQPNF--RPGRStfliLLSHACRAPDssISNVHRVLNLMVnnglEPDQV 160
Cdd:PLN03077  84 VDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLgvRLGNA----MLSMFVRFGE--LVHAWYVFGKMP----ERDLF 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  161 TTDIAVRSLCETGRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDL--------HVV-YEFvdemRDDFDVKPDLV 231
Cdd:PLN03077 154 SWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLargrevhaHVVrFGF----ELDVDVVNALI 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  232 SFTILIDNVCNSKNLREAMYlvsklgnagfKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQIT--------- 302
Cdd:PLN03077 230 TMYVKCGDVVSARLVFDRMP----------RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTitsvisace 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  303 --------------------------YNTLIFGLSKAGRVEEARMYLKTMvdagYEPDTATYTSLMNGMCRKGESLGALS 356
Cdd:PLN03077 300 llgderlgremhgyvvktgfavdvsvCNSLIQMYLSLGSWGEAEKVFSRM----ETKDAVSWTAMISGYEKNGLPDKALE 375

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18398498  357 LLEEMEARGCAPNDCTYNTLLHGLCKARLMDKGMELYEMMKSSGVKLesngYATLVRSLV----KSGKVAEAYEVF 428
Cdd:PLN03077 376 TYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLIS----YVVVANALIemysKCKCIDKALEVF 447
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 301-335 6.32e-07

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: 45.52  E-value: 6.32e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 18398498   301 ITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDT 335
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 337-370 1.22e-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: 44.75  E-value: 1.22e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 18398498   337 TYTSLMNGMCRKGESLGALSLLEEMEARGCAPND 370
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 266-299 5.20e-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: 42.83  E-value: 5.20e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 18398498   266 FLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPD 299
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 337-366 5.97e-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: 5.97e-06
                          10        20        30
                  ....*....|....*....|....*....|
gi 18398498   337 TYTSLMNGMCRKGESLGALSLLEEMEARGC 366
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 301-330 4.41e-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: 40.14  E-value: 4.41e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 18398498   301 ITYNTLIFGLSKAGRVEEARMYLKTMVDAG 330
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 252-307 5.51e-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: 40.80  E-value: 5.51e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 18398498   252 LVSKLGNAGFKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLI 307
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 334-428 1.41e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 44.48  E-value: 1.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   334 DTATYTSLMNGMCRKGESLGALSLLEEMEARG---------------CA-----------------PNDCTYNTLLHGLC 381
Cdd:PLN03218  369 KSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGlldmdkiyhakffkaCKkqravkeafrfaklirnPTLSTFNMLMSVCA 448

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 18398498   382 KARLMDKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKVAEAYEVF 428
Cdd:PLN03218  449 SSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVF 495
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 99-228 1.93e-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: 42.77  E-value: 1.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498    99 AVVNDTVKLFQHILksqpnfrpgrSTFLILLSHACRAPDS----SISNVHRVLNLMVNNGLEPDQVTTDIAVRSLCETGR 174
Cdd:pfam17177  36 AAKAEGVRLAQYHY----------NVLLYLCSKAADATDLkpqlAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGD 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 18398498   175 VDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDLHVVYEfVDEMRDDFDVKP 228
Cdd:pfam17177 106 GDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYE-VEEHMLAHGVEL 158
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 266-296 4.22e-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: 37.44  E-value: 4.22e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 18398498   266 FLYNTIMKGFCTLSKGSEAVGVYKKMKEEGV 296
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 217-275 5.55e-04

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: 38.11  E-value: 5.55e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 18398498   217 VDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFKPDCFLYNTIMKGF 275
Cdd:pfam13812   3 LREMVRD-GIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 356-402 5.66e-04

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: 38.11  E-value: 5.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 18398498   356 SLLEEMEARGCAPNDCTYNTLLHGLCKARLMDKGMELYEMMKSSGVK 402
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIK 47
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 192-221 5.67e-04

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: 37.33  E-value: 5.67e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 18398498   192 PDTYTYNFLLKHLCKCKDLHVVYEFVDEMR 221
Cdd:pfam12854   5 PDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 345-427 7.72e-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: 40.84  E-value: 7.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498   345 MC-RKGESLGALSLLEEMEARGCAPNDCTYNTLLHgLC----------KARLMDKGMELYEMMKSSGVKLESNGYATLVR 413
Cdd:pfam17177  20 KCsKHADATGALALYDAAKAEGVRLAQYHYNVLLY-LCskaadatdlkPQLAADRGFEVFEAMKAQGVSPNEATYTAVAR 98

                          90
                  ....*....|....
gi 18398498   414 SLVKSGKVAEAYEV 427
Cdd:pfam17177  99 LAAAKGDGDLAFDL 112
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 153-184 1.18e-03

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: 36.17  E-value: 1.18e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 18398498   153 NGLEPDQVTTDIAVRSLCETGRVDEAKDLMKE 184
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDE 32
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 260-292 1.47e-03

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: 36.17  E-value: 1.47e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 18398498   260 GFKPDCFLYNTIMKGFCtlSKG--SEAVGVYKKMK 292
Cdd:pfam12854   2 GLKPDVVTYNTLINGLC--RAGrvDEAFELLDEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 153-334 4.52e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 39.45  E-value: 4.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  153 NGLEPDQVTTDIAVRSLCETGRVDEAKDLMKELTEKHSPPDTYTYNFLLkhlCKCKDLHVV---YEFVDEMRDDFDVKPD 229
Cdd:PLN03077 548 NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLL---CACSRSGMVtqgLEYFHSMEEKYSITPN 624

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  230 LVSFTILIDNVCNSKNLREAMYLVSKLgnaGFKPDCFLYNTIMKGfCTLSKGSEAVGVYKKMKEEgVEPDQITYNTLIFG 309
Cdd:PLN03077 625 LKHYACVVDLLGRAGKLTEAYNFINKM---PITPDPAVWGALLNA-CRIHRHVELGELAAQHIFE-LDPNSVGYYILLCN 699

                        170       180
                 ....*....|....*....|....*.
gi 18398498  310 L-SKAGRVEEARMYLKTMVDAGYEPD 334
Cdd:PLN03077 700 LyADAGKWDEVARVRKTMRENGLTVD 725
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 218-421 5.10e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 39.47  E-value: 5.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  218 DEMRDDFDVKPDLVSFTILIDNVCNSKNLREAMYLVSKL-GNAGFKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGV 296
Cdd:PLN03081  75 DARLDDTQIRKSGVSLCSQIEKLVACGRHREALELFEILeAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGF 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398498  297 EPDQITYNTLIfglskagrveeaRMYLKTmvdagyepdtatytslmnGMCrkgesLGALSLLEEMEARgcapNDCTYNTL 376
Cdd:PLN03081 155 EPDQYMMNRVL------------LMHVKC------------------GML-----IDARRLFDEMPER----NLASWGTI 195

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 18398498  377 LHGLCKARLMDKGMELYEMMKSSGVKLESNGYATLVRSLVKSGKV 421
Cdd:PLN03081 196 IGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSA 240
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 195-229 5.68e-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: 34.35  E-value: 5.68e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 18398498   195 YTYNFLLKHLCKCKDLHVVYEFVDEMRDDfDVKPD 229
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKER-GIEPD 34
 
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