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Conserved domains on  [gi|15220068|ref|NP_178132|]
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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
 58-376 2.58e-13

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 71.83  E-value: 2.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068    58 FKANATNRLVIENRFAfeDTVSRLAGAGRLDFIE-DLLEHQKTLPQGRREGFI---VRIIMLygkagMTKQALDTFfNMD 133
Cdd:PLN03218  372 EYIDAYNRLLRDGRIK--DCIDLLEDMEKRGLLDmDKIYHAKFFKACKKQRAVkeaFRFAKL-----IRNPTLSTF-NML 443

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   134 LYGCKRSvKSFNAALQVLSFnpdlhtiwefLHDApskyGIDIDAVSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDVV 213
Cdd:PLN03218  444 MSVCASS-QDIDGALRVLRL----------VQEA----GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVH 508

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   214 TYTTLISALYKHERCVIGNGLWNLMVLKGCKPNLTTFNVRIQfLVNRRRAWD-ANDLLLLM-----PklqVEPDSITYNM 287
Cdd:PLN03218  509 TFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALIS-ACGQSGAVDrAFDVLAEMkaethP---IDPDHITVGA 584

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   288 VIKGFFLARFPDMAERVYTAMHGKGYKPNLKIYQTMIHYLCKAGNFDLAYTMCKDCMRKKWYPNldtvEMLLKGLVK--- 364
Cdd:PLN03218  585 LMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPD----EVFFSALVDvag 660

                         330
                  ....*....|...
gi 15220068   365 -KGQLDQAKSIME 376
Cdd:PLN03218  661 hAGDLDKAFEILQ 673
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 58-376 2.58e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 71.83  E-value: 2.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068    58 FKANATNRLVIENRFAfeDTVSRLAGAGRLDFIE-DLLEHQKTLPQGRREGFI---VRIIMLygkagMTKQALDTFfNMD 133
Cdd:PLN03218  372 EYIDAYNRLLRDGRIK--DCIDLLEDMEKRGLLDmDKIYHAKFFKACKKQRAVkeaFRFAKL-----IRNPTLSTF-NML 443

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   134 LYGCKRSvKSFNAALQVLSFnpdlhtiwefLHDApskyGIDIDAVSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDVV 213
Cdd:PLN03218  444 MSVCASS-QDIDGALRVLRL----------VQEA----GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVH 508

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   214 TYTTLISALYKHERCVIGNGLWNLMVLKGCKPNLTTFNVRIQfLVNRRRAWD-ANDLLLLM-----PklqVEPDSITYNM 287
Cdd:PLN03218  509 TFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALIS-ACGQSGAVDrAFDVLAEMkaethP---IDPDHITVGA 584

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   288 VIKGFFLARFPDMAERVYTAMHGKGYKPNLKIYQTMIHYLCKAGNFDLAYTMCKDCMRKKWYPNldtvEMLLKGLVK--- 364
Cdd:PLN03218  585 LMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPD----EVFFSALVDvag 660

                         330
                  ....*....|...
gi 15220068   365 -KGQLDQAKSIME 376
Cdd:PLN03218  661 hAGDLDKAFEILQ 673
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 176-224 1.78e-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: 55.83  E-value: 1.78e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15220068   176 DAVSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDVVTYTTLISALYK 224
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 178-212 5.17e-04

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: 37.05  E-value: 5.17e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15220068   178 VSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDV 212
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 58-376 2.58e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 71.83  E-value: 2.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068    58 FKANATNRLVIENRFAfeDTVSRLAGAGRLDFIE-DLLEHQKTLPQGRREGFI---VRIIMLygkagMTKQALDTFfNMD 133
Cdd:PLN03218  372 EYIDAYNRLLRDGRIK--DCIDLLEDMEKRGLLDmDKIYHAKFFKACKKQRAVkeaFRFAKL-----IRNPTLSTF-NML 443

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   134 LYGCKRSvKSFNAALQVLSFnpdlhtiwefLHDApskyGIDIDAVSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDVV 213
Cdd:PLN03218  444 MSVCASS-QDIDGALRVLRL----------VQEA----GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVH 508

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   214 TYTTLISALYKHERCVIGNGLWNLMVLKGCKPNLTTFNVRIQfLVNRRRAWD-ANDLLLLM-----PklqVEPDSITYNM 287
Cdd:PLN03218  509 TFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALIS-ACGQSGAVDrAFDVLAEMkaethP---IDPDHITVGA 584

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   288 VIKGFFLARFPDMAERVYTAMHGKGYKPNLKIYQTMIHYLCKAGNFDLAYTMCKDCMRKKWYPNldtvEMLLKGLVK--- 364
Cdd:PLN03218  585 LMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPD----EVFFSALVDvag 660

                         330
                  ....*....|...
gi 15220068   365 -KGQLDQAKSIME 376
Cdd:PLN03218  661 hAGDLDKAFEILQ 673
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 176-224 1.78e-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: 55.83  E-value: 1.78e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15220068   176 DAVSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDVVTYTTLISALYK 224
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 118-329 6.74e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 61.05  E-value: 6.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   118 KAGMTKQALDTFFNMDLYGCKRSVKSFNAALQVLSFNPDlhtiWEF---LHDAPSKYGIDIDAVSFNIAIKSFCELGILD 194
Cdd:PLN03218  591 NAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGD----WDFalsIYDDMKKKGVKPDEVFFSALVDVAGHAGDLD 666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   195 GAYMAMREMEKSGLTPDVVTYTTLISALykherCVIGNGLWNLMVLKGCK-----PNLTTFNVRIQFLVNRRRAWDANDL 269
Cdd:PLN03218  667 KAFEILQDARKQGIKLGTVSYSSLMGAC-----SNAKNWKKALELYEDIKsiklrPTVSTMNALITALCEGNQLPKALEV 741

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   270 LLLMPKLQVEPDSITYNMVIKGFFLARFPDMAERVYTAMHGKGYKPNLKIYQTMIHyLCK 329
Cdd:PLN03218  742 LSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITG-LCL 800
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 112-342 1.67e-07

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 53.34  E-value: 1.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  112 IIMLYGKAGMTKQALDTFFNMDlygcKRSVKSFNAALQVLSFNPDLHTIWEFLHDApSKYGIDIDAVSFNIAIKSFCELG 191
Cdd:PLN03081 265 LIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEM-RDSGVSIDQFTFSIMIRIFSRLA 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  192 ILDGAYMAMREMEKSGLTPDVVTYTTLISALYKHERCVIGNGLWNLMVLKgckpNLTTFNVRIQFLVNRRRAWDANDLLL 271
Cdd:PLN03081 340 LLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFE 415

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15220068  272 LMPKLQVEPDSITYNMVIKGFFLARFPDMAERVYTAM-HGKGYKPNLKIYQTMIHYLCKAGNFDLAYTMCKD 342
Cdd:PLN03081 416 RMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMsENHRIKPRAMHYACMIELLGREGLLDEAYAMIRR 487
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 210-252 2.61e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 46.97  E-value: 2.61e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 15220068   210 PDVVTYTTLISALYKHERCVIGNGLWNLMVLKGCKPNLTTFNV 252
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTI 43
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 280-329 2.15e-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: 44.28  E-value: 2.15e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15220068   280 PDSITYNMVIKGFFLARFPDMAERVYTAMHGKGYKPNLKIYQTMIHYLCK 329
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 201-260 8.01e-06

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 43.12  E-value: 8.01e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   201 REMEKSGLTPDVVTYTTLISALYKHERCVIGNGLWNLMVLKGCKPNLTTFNVRIQFLVNR 260
Cdd:pfam13812   4 REMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PLN03077 PLN03077
Protein ECB2; Provisional
 116-316 1.41e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 47.15  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  116 YGKAGMTKQALDTFFNMDLYGCKRSVKSFNAALQVLSFNPDLHTIWEF-LHDAPSKYGIDIDAV---------------- 178
Cdd:PLN03077 162 YAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVhAHVVRFGFELDVDVVnalitmyvkcgdvvsa 241

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  179 -------------SFNIAIKSFCELGI-LDG--AYMAMREMEksgLTPDVVTYTTLISA--LYKHERcvIGNGLWNLMVL 240
Cdd:PLN03077 242 rlvfdrmprrdciSWNAMISGYFENGEcLEGleLFFTMRELS---VDPDLMTITSVISAceLLGDER--LGREMHGYVVK 316

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15220068  241 KGCKPNLTTFNVRIQFLVNRRRAWDANDLLLLMPKlqvePDSITYNMVIKGFFLARFPDMAERVYTAMHGKGYKPN 316
Cdd:PLN03077 317 TGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----KDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPD 388
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 273-382 2.77e-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: 42.00  E-value: 2.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068   273 MPKLQVEPDSITYNMVIKGFFLARFPDMAERVYTAMHGKGYKPNLKIYQTMIHYLCKAGNFDLAYTMcKDCMRKKWY-PN 351
Cdd:pfam17177  81 MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEV-EEHMLAHGVeLE 159

                          90       100       110
                  ....*....|....*....|....*....|.
gi 15220068   352 LDTVEMLLKGLVKKGQLDQAKSIMELVHRRV 382
Cdd:pfam17177 160 EPELAALLKVSAKAGRADKVYAYLHRLRDAV 190
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 178-212 5.17e-04

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: 37.05  E-value: 5.17e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15220068   178 VSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDV 212
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 283-316 7.23e-04

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: 36.66  E-value: 7.23e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15220068   283 ITYNMVIKGFFLARFPDMAERVYTAMHGKGYKPN 316
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 303-371 8.19e-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: 40.46  E-value: 8.19e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15220068   303 RVYTAMHGKGYKPNLKIYQTMIHYLCKAGNFDLAYTMCKDCMRKKWYPNLDTVEMLLKGLVKKGQLDQA 371
Cdd:pfam17177  76 EVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKA 144
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 315-364 1.14e-03

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 36.57  E-value: 1.14e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15220068   315 PNLKIYQTMIHYLCKAGNFDLAYTMCKDCMRKKWYPNLDTVEMLLKGLVK 364
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 172-204 1.65e-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: 35.78  E-value: 1.65e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15220068   172 GIDIDAVSFNIAIKSFCELGILDGAYMAMREME 204
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 176-302 1.94e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 1.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  176 DAVSFNIAIKSFCELGILDGAYMAMREMEKSGLTPDVVTYTTLISALYKHERCVIGNGLWNLMVLK-GCKPNLTTFNVRI 254
Cdd:PLN03077 553 DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYACVV 632

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15220068  255 QFLVNRRRAWDANDLLLLMPklqVEPDSITYNMVIKGFFLARFPDMAE 302
Cdd:PLN03077 633 DLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACRIHRHVELGE 677
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 207-222 4.91e-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: 34.24  E-value: 4.91e-03
                          10
                  ....*....|....*.
gi 15220068   207 GLTPDVVTYTTLISAL 222
Cdd:pfam12854   2 GLKPDVVTYNTLINGL 17
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 311-345 5.11e-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: 34.24  E-value: 5.11e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15220068   311 KGYKPNLKIYQTMIHYLCKAGNFDLAYTMCkDCMR 345
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELL-DEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 112-337 8.80e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 38.29  E-value: 8.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  112 IIMLYGKAGMTKQALDTFFNMDLYGCK------RSVKSFNAALQVLSFNPDLHTI------------------------- 160
Cdd:PLN03077 360 MISGYEKNGLPDKALETYALMEQDNVSpdeitiASVLSACACLGDLDVGVKLHELaerkglisyvvvanaliemyskckc 439

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  161 ----WEFLHDAPSKygidiDAVSFNIAIKSFCELGILDGAYMAMREMeKSGLTPDVVTYTTLISA------------LYK 224
Cdd:PLN03077 440 idkaLEVFHNIPEK-----DVISWTSIIAGLRLNNRCFEALIFFRQM-LLTLKPNSVTLIAALSAcarigalmcgkeIHA 513

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220068  225 HE-RCVIG------NGLWNLMVLKG-----------CKPNLTTFNVRIQFLVNRRRAWDANDLLLLMPKLQVEPDSITY- 285
Cdd:PLN03077 514 HVlRTGIGfdgflpNALLDLYVRCGrmnyawnqfnsHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFi 593

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15220068  286 ---------NMVIKGFFLarFPDMAERVYTAmhgkgykPNLKIYQTMIHYLCKAGNFDLAY 337
Cdd:PLN03077 594 sllcacsrsGMVTQGLEY--FHSMEEKYSIT-------PNLKHYACVVDLLGRAGKLTEAY 645
 
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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