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Conserved domains on  [gi|334187687|ref|NP_197005|]
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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

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 289-509 1.70e-19

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 93.02  E-value: 1.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  289 VWMEMGNVGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTME-EEK 367
Cdd:PLN03218  494 VFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKaETH 573

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  368 GIEPNVVTYNSLIKPLCKARKTEEAKQV-----------------------------------FDEMLEKGLFPTIRTYH 412
Cdd:PLN03218  574 PIDPDHITVGALMKACANAGQVDRAKEVyqmiheynikgtpevytiavnscsqkgdwdfalsiYDDMKKKGVKPDEVFFS 653

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  413 AFMRIL---RTGEEVFELLAKMRKMGCEPTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNG 489
Cdd:PLN03218  654 ALVDVAghaGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

                         250       260
                  ....*....|....*....|
gi 334187687  490 KIEEAYGYYKEMKDKGMRPN 509
Cdd:PLN03218  734 QLPKALEVLSEMKRLGLCPN 753
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 289-509 1.70e-19

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 93.02  E-value: 1.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  289 VWMEMGNVGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTME-EEK 367
Cdd:PLN03218  494 VFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKaETH 573

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  368 GIEPNVVTYNSLIKPLCKARKTEEAKQV-----------------------------------FDEMLEKGLFPTIRTYH 412
Cdd:PLN03218  574 PIDPDHITVGALMKACANAGQVDRAKEVyqmiheynikgtpevytiavnscsqkgdwdfalsiYDDMKKKGVKPDEVFFS 653

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  413 AFMRIL---RTGEEVFELLAKMRKMGCEPTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNG 489
Cdd:PLN03218  654 ALVDVAghaGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

                         250       260
                  ....*....|....*....|
gi 334187687  490 KIEEAYGYYKEMKDKGMRPN 509
Cdd:PLN03218  734 QLPKALEVLSEMKRLGLCPN 753
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 371-411 9.78e-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: 59.68  E-value: 9.78e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 334187687  371 PNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTY 411
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 374-408 1.30e-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: 45.14  E-value: 1.30e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334187687  374 VTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTI 408
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 289-509 1.70e-19

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 93.02  E-value: 1.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  289 VWMEMGNVGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTME-EEK 367
Cdd:PLN03218  494 VFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKaETH 573

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  368 GIEPNVVTYNSLIKPLCKARKTEEAKQV-----------------------------------FDEMLEKGLFPTIRTYH 412
Cdd:PLN03218  574 PIDPDHITVGALMKACANAGQVDRAKEVyqmiheynikgtpevytiavnscsqkgdwdfalsiYDDMKKKGVKPDEVFFS 653

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  413 AFMRIL---RTGEEVFELLAKMRKMGCEPTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNG 489
Cdd:PLN03218  654 ALVDVAghaGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

                         250       260
                  ....*....|....*....|
gi 334187687  490 KIEEAYGYYKEMKDKGMRPN 509
Cdd:PLN03218  734 QLPKALEVLSEMKRLGLCPN 753
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 277-475 5.29e-19

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 91.48  E-value: 5.29e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  277 CNVIGSPREAERVWMEMGNVGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEA 356
Cdd:PLN03218  589 CANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKA 668

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  357 RNLMKTMEEEkGIEPNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTYHAFMRILRTGEEV---FELLAKMRK 433
Cdd:PLN03218  669 FEILQDARKQ-GIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLpkaLEVLSEMKR 747

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 334187687  434 MGCEPTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDL 475
Cdd:PLN03218  748 LGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNL 789
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 220-509 7.05e-18

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 87.62  E-value: 7.05e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  220 FHAYKRFKLEMGIDDFQSLLSALCRYKNVSDA--GHLIFCNKDKYPfDAKSFNIVLNGwCNVIGSPREAERVWMEMG--N 295
Cdd:PLN03218  495 FHEMVNAGVEANVHTFGALIDGCARAGQVAKAfgAYGIMRSKNVKP-DRVVFNALISA-CGQSGAVDRAFDVLAEMKaeT 572

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  296 VGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTMEEeKGIEPNVVT 375
Cdd:PLN03218  573 HPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKK-KGVKPDEVF 651

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  376 YNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTYHAFMRI---LRTGEEVFELLAKMRKMGCEPTVETYIMLIRKLCR 452
Cdd:PLN03218  652 FSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGAcsnAKNWKKALELYEDIKSIKLRPTVSTMNALITALCE 731

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 334187687  453 WRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGMRPN 509
Cdd:PLN03218  732 GNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPN 788
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 297-508 3.45e-15

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 79.15  E-value: 3.45e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  297 GVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTMeEEKGIEPNVVTY 376
Cdd:PLN03218  467 GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIM-RSKNVKPDRVVF 545

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  377 NSLIKPLCKARKTEEAKQVFDEML--EKGLFPTIRTYHAFMRILRTGEEV---FELLAKMRKMGCEPTVETYIMLIRKLC 451
Cdd:PLN03218  546 NALISACGQSGAVDRAFDVLAEMKaeTHPIDPDHITVGALMKACANAGQVdraKEVYQMIHEYNIKGTPEVYTIAVNSCS 625

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334187687  452 RWRDFDNVLLLWDEMKEKTVGPD---LSSYI-VMIHGlflnGKIEEAYGYYKEMKDKGMRP 508
Cdd:PLN03218  626 QKGDWDFALSIYDDMKKKGVKPDevfFSALVdVAGHA----GDLDKAFEILQDARKQGIKL 682
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 371-411 9.78e-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: 59.68  E-value: 9.78e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 334187687  371 PNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTY 411
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 367-399 8.19e-11

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: 56.97  E-value: 8.19e-11
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334187687  367 KGIEPNVVTYNSLIKPLCKARKTEEAKQVFDEM 399
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 310-448 2.56e-10

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: 60.49  E-value: 2.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  310 SCySKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSE---------ARNLMKTMEEeKGIEPNVVTYNSLI 380
Cdd:pfam17177  20 KC-SKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDlkpqlaadrGFEVFEAMKA-QGVSPNEATYTAVA 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334187687  381 KPLCKARKTEEAKQVFDEMLEKGLFPTIRTY----HAFMRILRTgEEVFELLAKMRKMGCEPTVETYIMLIR 448
Cdd:pfam17177  98 RLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYspalHAYCEAGDA-DKAYEVEEHMLAHGVELEEPELAALLK 168
PLN03077 PLN03077
Protein ECB2; Provisional
 299-399 5.85e-10

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 62.17  E-value: 5.85e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 299 KHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTMEEEKGIEPNVVTYNS 378
Cdd:PLN03077 551 EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYAC 630

                         90       100
                 ....*....|....*....|.
gi 334187687 379 LIKPLCKARKTEEAKQVFDEM 399
Cdd:PLN03077 631 VVDLLGRAGKLTEAYNFINKM 651
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 301-385 4.82e-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: 52.37  E-value: 4.82e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  301 DVVSYSSMISCYSKGGSLNKVLKLFDRMKKeciepdrkvynavvhalakasfvsearnlmktmeeeKGIEPNVVTYNSLI 380
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKK------------------------------------RGVKPNVYTYTILI 45


                  ....*
gi 334187687  381 KPLCK 385
Cdd:pfam13041  46 NGLCK 50
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 301-506 1.88e-08

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 57.19  E-value: 1.88e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 301 DVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTMEEEkgiepNVVTYNSLI 380
Cdd:PLN03081 122 PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPER-----NLASWGTII 196

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 381 KPLCKARKTEEAKQVFDEMLEKGLFPTIRTYHAFMR------ILRTGEEVFELLAKMRKMGceptvETYIM--LIRKLCR 452
Cdd:PLN03081 197 GGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRasaglgSARAGQQLHCCVLKTGVVG-----DTFVScaLIDMYSK 271

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 334187687 453 WRDFDNVLLLWDEMKEKTVgpdlSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGM 506
Cdd:PLN03081 272 CGDIEDARCVFDGMPEKTT----VAWNSMLAGYALHGYSEEALCLYYEMRDSGV 321
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 318-442 3.41e-08

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 54.32  E-value: 3.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  318 LNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTMEEeKGIEPNVVTYNSLIKPLCKARKTEEAKQVFD 397
Cdd:pfam17177  71 ADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEA-AGVSPRLRSYSPALHAYCEAGDADKAYEVEE 149

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 334187687  398 EMLEKGLFPTIRTYHAFMRI-LRTGEE--VFELLAKMRKMGCEPTVET 442
Cdd:pfam17177 150 HMLAHGVELEEPELAALLKVsAKAGRAdkVYAYLHRLRDAVRQVSEST 197
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 365-415 4.17e-08

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: 50.05  E-value: 4.17e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 334187687  365 EEKGIEPNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTYHAFM 415
Cdd:pfam13812   7 VRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PLN03077 PLN03077
Protein ECB2; Provisional
 280-434 5.10e-08

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 56.01  E-value: 5.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 280 IGSPREAERVWMEMGnvgvKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNL 359
Cdd:PLN03077 336 LGSWGEAEKVFSRME----TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKL 411

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334187687 360 MKtMEEEKGIEPNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFptirTYHAFMRILRTGEEVFELLAKMRKM 434
Cdd:PLN03077 412 HE-LAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVI----SWTSIIAGLRLNNRCFEALIFFRQM 481
PLN03077 PLN03077
Protein ECB2; Provisional
 301-509 1.04e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 51.77  E-value: 1.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 301 DVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNlMKTMEEEKGIEPNVVTYNSLI 380
Cdd:PLN03077 252 DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGRE-MHGYVVKTGFAVDVSVCNSLI 330

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 381 KPLCKARKTEEAKQVFDEM--------------LEKGLFP--TIRTYhAFMRI----------------------LRTGE 422
Cdd:PLN03077 331 QMYLSLGSWGEAEKVFSRMetkdavswtamisgYEKNGLPdkALETY-ALMEQdnvspdeitiasvlsacaclgdLDVGV 409

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 423 EVFELLAKMRKMgceptveTYIM----LIRKLCRWRDFDNVLLLWDEMKEKtvgpDLSSYIVMIHGLFLNGKIEEAYGYY 498
Cdd:PLN03077 410 KLHELAERKGLI-------SYVVvanaLIEMYSKCKCIDKALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFF 478

                        250
                 ....*....|.
gi 334187687 499 KEMKDKgMRPN 509
Cdd:PLN03077 479 RQMLLT-LKPN 488
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 374-408 1.30e-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: 45.14  E-value: 1.30e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334187687  374 VTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTI 408
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 275-507 2.21e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 50.64  E-value: 2.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 275 GWCNVI------GSPREAERVWMEMGNVGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALA 348
Cdd:PLN03081 292 AWNSMLagyalhGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYS 371

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 349 KASFVSEARNLMKTMEEEkgiepNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTYHAFMRILR------TGE 422
Cdd:PLN03081 372 KWGRMEDARNVFDRMPRK-----NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRysglseQGW 446

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 423 EVFELLA-----KMRKM---------GCEPTVETYIMLIRK-------------LCRWRDFDNvLLLWDEMKEK--TVGP 473
Cdd:PLN03081 447 EIFQSMSenhriKPRAMhyacmiellGREGLLDEAYAMIRRapfkptvnmwaalLTACRIHKN-LELGRLAAEKlyGMGP 525

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 334187687 474 D-LSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGMR 507
Cdd:PLN03081 526 EkLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLS 560
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 303-336 2.47e-06

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 43.98  E-value: 2.47e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334187687  303 VSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPD 336
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 265-314 5.08e-06

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 43.51  E-value: 5.08e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334187687  265 DAKSFNIVLNGWCNViGSPREAERVWMEMGNVGVKHDVVSYSSMISCYSK 314
Cdd:pfam13041   2 DVVTYNTLINGYCKK-GKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 473-510 5.13e-06

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 43.51  E-value: 5.13e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 334187687  473 PDLSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGMRPNE 510
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNV 38
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 288-349 7.24e-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: 43.89  E-value: 7.24e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334187687  288 RVWMEMGNVGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAK 349
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 323-381 7.31e-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: 7.31e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 334187687  323 KLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTMEEeKGIEPNVVTYNSLIK 381
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKK-KGIKPTLDTYNAILG 58
PLN03077 PLN03077
Protein ECB2; Provisional
 214-434 8.54e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 48.69  E-value: 8.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 214 GKAIntfHAYKrFKLEMGIDDF--QSLLSALCRYKNVSDAGHLiFCNKDKypfDAKSFNIVLNGWCNViGSPREAERVWM 291
Cdd:PLN03077 508 GKEI---HAHV-LRTGIGFDGFlpNALLDLYVRCGRMNYAWNQ-FNSHEK---DVVSWNILLTGYVAH-GKGSMAVELFN 578

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 292 EMGNVGVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKE-CIEPDRKVYNAVVHALAKASFVSEARNLMKTMEeekgIE 370
Cdd:PLN03077 579 RMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYACVVDLLGRAGKLTEAYNFINKMP----IT 654

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334187687 371 PNVVTYNSLIKPLCKARKTE----EAKQVFDemlekgLFPTIRTYHAFMRILRTGEEVFELLAKMRKM 434
Cdd:PLN03077 655 PDPAVWGALLNACRIHRHVElgelAAQHIFE------LDPNSVGYYILLCNLYADAGKWDEVARVRKT 716
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 327-510 9.36e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 48.72  E-value: 9.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  327 RMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKTMEEeKGIEPNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFP 406
Cdd:PLN03218  427 RFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQE-AGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEA 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  407 TIRTYHAFMR----------------ILRTG----------------------EEVFELLAKMRKMG--CEPTVETYIML 446
Cdd:PLN03218  506 NVHTFGALIDgcaragqvakafgaygIMRSKnvkpdrvvfnalisacgqsgavDRAFDVLAEMKAEThpIDPDHITVGAL 585

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334187687  447 IRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGMRPNE 510
Cdd:PLN03218  586 MKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDE 649
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 438-485 1.70e-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: 42.35  E-value: 1.70e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 334187687  438 PTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGL 485
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 374-404 2.06e-05

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 41.30  E-value: 2.06e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334187687  374 VTYNSLIKPLCKARKTEEAKQVFDEMLEKGL 404
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 303-333 2.16e-05

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 41.30  E-value: 2.16e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334187687  303 VSYSSMISCYSKGGSLNKVLKLFDRMKKECI 333
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 376-509 3.29e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 46.79  E-value: 3.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  376 YNSLIKplckARKTEEAKQVFDEMLEKGLFPTIRTYHA-FMRIL---RTGEEVFELLAKMRkmgcEPTVETYIMLIRKLC 451
Cdd:PLN03218  377 YNRLLR----DGRIKDCIDLLEDMEKRGLLDMDKIYHAkFFKACkkqRAVKEAFRFAKLIR----NPTLSTFNMLMSVCA 448

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334187687  452 RWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGMRPN 509
Cdd:PLN03218  449 SSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEAN 506
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 477-510 5.28e-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: 40.52  E-value: 5.28e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334187687  477 SYIVMIHGLFLNGKIEEAYGYYKEMKDKGMRPNE 510
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 424-510 1.66e-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: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  424 VFELLAKMRKMGCEPTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNGKIEEAYGYYKEMKD 503
Cdd:pfam17177  74 GFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLA 153


                  ....*..
gi 334187687  504 KGMRPNE 510
Cdd:pfam17177 154 HGVELEE 160
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 336-512 2.84e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 44.10  E-value: 2.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  336 DRKVYNAVVHALAKASFVSEARNLMKTMEEEKGIEPNVVTYNSLIKpLCKARKT-EEAKQVFDEMLEkglfPTIRTYHAF 414
Cdd:PLN03218  369 KSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFK-ACKKQRAvKEAFRFAKLIRN----PTLSTFNML 443

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687  415 MRILRTGEEV---FELLAKMRKMGCEPTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMIHGLFLNGKI 491
Cdd:PLN03218  444 MSVCASSQDIdgaLRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQV 523

                         170       180
                  ....*....|....*....|.
gi 334187687  492 EEAYGYYKEMKDKGMRPNENV 512
Cdd:PLN03218  524 AKAFGAYGIMRSKNVKPDRVV 544
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 297-329 3.87e-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: 38.10  E-value: 3.87e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334187687  297 GVKHDVVSYSSMISCYSKGGSLNKVLKLFDRMK 329
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 461-509 5.51e-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: 38.49  E-value: 5.51e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334187687  461 LLWDEMKEKTVGPDLSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGMRPN 509
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPT 49
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 476-506 5.51e-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: 5.51e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334187687  476 SSYIVMIHGLFLNGKIEEAYGYYKEMKDKGM 506
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 395-447 6.45e-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: 6.45e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 334187687  395 VFDEMLEKGLFPTIRTY----HAFMRIlRTGEEVFELLAKMRKMGCEPTVETYIMLI 447
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYthllHAYANV-GNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 281-499 1.93e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 41.01  E-value: 1.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 281 GSPREAERVWMEMGnvgvKHDVVSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLM 360
Cdd:PLN03081 273 GDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAH 348

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 361 KTMEEeKGIEPNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFptirTYHAFMRILRT---GEEVFELLAKMRKMGCE 437
Cdd:PLN03081 349 AGLIR-TGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLI----SWNALIAGYGNhgrGTKAVEMFERMIAEGVA 423

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 438 PTVETYIMLIRKlCR--------WRDFdnvLLLWDEMKEKtvgPDLSSYIVMIHGLFLNGKIEEAYGYYK 499
Cdd:PLN03081 424 PNHVTFLAVLSA-CRysglseqgWEIF---QSMSENHRIK---PRAMHYACMIELLGREGLLDEAYAMIR 486
PLN03077 PLN03077
Protein ECB2; Provisional
 225-510 4.23e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.22  E-value: 4.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 225 RFKLEMGiddfQSLLSALCRYKNVSDAGHLIFCNKDKypfDAKSFNIVLNGWCNViGSPREAERVWMEMGNVGVKHDVVS 304
Cdd:PLN03077 118 SLGVRLG----NAMLSMFVRFGELVHAWYVFGKMPER---DLFSWNVLVGGYAKA-GYFDEALCLYHRMLWAGVRPDVYT 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 305 YSSMI-SCyskGGSLNKvlklfdRMKKEC--------IEPDRKVYNAVVHALAKASFVSEARNLMKTMEEEkgiepNVVT 375
Cdd:PLN03077 190 FPCVLrTC---GGIPDL------ARGREVhahvvrfgFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR-----DCIS 255

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334187687 376 YNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTYHAFMRILRT-GEEVF--ELLAKMRKMGCEPTVETYIMLIR---K 449
Cdd:PLN03077 256 WNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELlGDERLgrEMHGYVVKTGFAVDVSVCNSLIQmylS 335

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334187687 450 LCRWRDFDNVlllWDEMKEKtvgpDLSSYIVMIHGLFLNGKIEEAYGYYKEMKDKGMRPNE 510
Cdd:PLN03077 336 LGSWGEAEKV---FSRMETK----DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDE 389
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 442-474 8.97e-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: 33.97  E-value: 8.97e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334187687  442 TYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPD 474
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 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.
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