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Conserved domains on  [gi|1063712016|ref|NP_001326054|]
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pentatricopeptide (PPR) domain protein 40 [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13329975)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 49-455 1.26e-31

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 130.00  E-value: 1.26e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016   49 PSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNVFTYTILI 128
Cdd:PLN03218   435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  129 DGFLIAGRVDEALKQLEMMRVRKLNPNEATIRTFVHGIFRCLPPCKAFEVLVgfmEKDSNLQRVGYDAVLY------CLS 202
Cdd:PLN03218   515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLA---EMKAETHPIDPDHITVgalmkaCAN 591

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  203 NNSM--AKETGQFLRKIGERGYiPDSSTFnAAMSCLLKGhDLVETCRIFDGFVSRGVKPgfngylvlvqallnaqrfseg 280
Cdd:PLN03218   592 AGQVdrAKEVYQMIHEYNIKGT-PEVYTI-AVNSCSQKG-DWDFALSIYDDMKKKGVKP--------------------- 647

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  281 drylkqmgvDGLLSSvysynAVIDCLCKARRIENAAMFLTEMQDRGISPNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVH 360
Cdd:PLN03218   648 ---------DEVFFS-----ALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI 713

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  361 GFKPDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYN 440
Cdd:PLN03218   714 KLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCR 793

                          410
                   ....*....|....*
gi 1063712016  441 AtIQSFCKmRKVKKA 455
Cdd:PLN03218   794 C-ITGLCL-RRFEKA 806
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 434-481 4.84e-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: 60.45  E-value: 4.84e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063712016 434 PDLYAYNATIQSFCKMRKVKKAEELLKTMLRIGLKPDNFTYSTLIKAL 481
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 469-508 6.13e-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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 43.51  E-value: 6.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063712016 469 PDNFTYSTLIKALSESGRESEAREMFSSIERHGCVPDSYT 508
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 49-455 1.26e-31

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 130.00  E-value: 1.26e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016   49 PSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNVFTYTILI 128
Cdd:PLN03218   435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  129 DGFLIAGRVDEALKQLEMMRVRKLNPNEATIRTFVHGIFRCLPPCKAFEVLVgfmEKDSNLQRVGYDAVLY------CLS 202
Cdd:PLN03218   515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLA---EMKAETHPIDPDHITVgalmkaCAN 591

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  203 NNSM--AKETGQFLRKIGERGYiPDSSTFnAAMSCLLKGhDLVETCRIFDGFVSRGVKPgfngylvlvqallnaqrfseg 280
Cdd:PLN03218   592 AGQVdrAKEVYQMIHEYNIKGT-PEVYTI-AVNSCSQKG-DWDFALSIYDDMKKKGVKP--------------------- 647

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  281 drylkqmgvDGLLSSvysynAVIDCLCKARRIENAAMFLTEMQDRGISPNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVH 360
Cdd:PLN03218   648 ---------DEVFFS-----ALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI 713

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  361 GFKPDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYN 440
Cdd:PLN03218   714 KLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCR 793

                          410
                   ....*....|....*
gi 1063712016  441 AtIQSFCKmRKVKKA 455
Cdd:PLN03218   794 C-ITGLCL-RRFEKA 806
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 364-412 2.06e-17

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: 75.86  E-value: 2.06e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063712016 364 PDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCC 412
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 434-481 4.84e-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: 60.45  E-value: 4.84e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063712016 434 PDLYAYNATIQSFCKMRKVKKAEELLKTMLRIGLKPDNFTYSTLIKAL 481
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 367-401 1.20e-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: 47.84  E-value: 1.20e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063712016 367 ITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNE 401
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 469-508 6.13e-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: 6.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063712016 469 PDNFTYSTLIKALSESGRESEAREMFSSIERHGCVPDSYT 508
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 472-506 1.10e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 42.06  E-value: 1.10e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063712016 472 FTYSTLIKALSESGRESEAREMFSSIERHGCVPDS 506
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 49-455 1.26e-31

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 130.00  E-value: 1.26e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016   49 PSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNVFTYTILI 128
Cdd:PLN03218   435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  129 DGFLIAGRVDEALKQLEMMRVRKLNPNEATIRTFVHGIFRCLPPCKAFEVLVgfmEKDSNLQRVGYDAVLY------CLS 202
Cdd:PLN03218   515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLA---EMKAETHPIDPDHITVgalmkaCAN 591

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  203 NNSM--AKETGQFLRKIGERGYiPDSSTFnAAMSCLLKGhDLVETCRIFDGFVSRGVKPgfngylvlvqallnaqrfseg 280
Cdd:PLN03218   592 AGQVdrAKEVYQMIHEYNIKGT-PEVYTI-AVNSCSQKG-DWDFALSIYDDMKKKGVKP--------------------- 647

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  281 drylkqmgvDGLLSSvysynAVIDCLCKARRIENAAMFLTEMQDRGISPNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVH 360
Cdd:PLN03218   648 ---------DEVFFS-----ALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI 713

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  361 GFKPDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYN 440
Cdd:PLN03218   714 KLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCR 793

                          410
                   ....*....|....*
gi 1063712016  441 AtIQSFCKmRKVKKA 455
Cdd:PLN03218   794 C-ITGLCL-RRFEKA 806
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 224-530 2.03e-22

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 101.49  E-value: 2.03e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  224 PDSSTFNAAMSCLLKGHDLVETCRIFDGFVSRGVKPGFNGYLVLVQALLNAQRFSEGDRYLKQMGVDGLLSSVYSYNAVI 303
Cdd:PLN03218   435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  304 DCLCKARRIENAAMFLTEMQDRGISPNLVTFNTFLSGYSVRGDVKKVHGVLE--KLLVHGFKPDVITFSLIINCLCRAKE 381
Cdd:PLN03218   515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAemKAETHPIDPDHITVGALMKACANAGQ 594

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  382 IKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNATIQSFCKMRKVKKAEELLKT 461
Cdd:PLN03218   595 VDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQD 674

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  462 MLRIGLKPDNFTYSTLIKALSESGRESEAREMFSSIERHG---------------CVPDSYTKRLVEELDLRKSGLSRET 526
Cdd:PLN03218   675 ARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKlrptvstmnalitalCEGNQLPKALEVLSEMKRLGLCPNT 754


                   ....
gi 1063712016  527 VSAS 530
Cdd:PLN03218   755 ITYS 758
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 364-412 2.06e-17

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: 75.86  E-value: 2.06e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063712016 364 PDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCC 412
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 84-131 1.65e-15

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: 70.47  E-value: 1.65e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063712016  84 PDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNVFTYTILIDGF 131
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 382-514 8.59e-15

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: 73.20  E-value: 8.59e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 382 IKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNATIQSFCKMRKVKKAEELLKT 461
Cdd:pfam17177  71 ADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEH 150

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1063712016 462 MLRIGLKPDNFTYSTLIKALSESGRESEAREMFSSIERH-GCVPDSyTKRLVEE 514
Cdd:pfam17177 151 MLAHGVELEEPELAALLKVSAKAGRADKVYAYLHRLRDAvRQVSES-TAGVLEE 203
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 399-448 2.17e-12

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 61.61  E-value: 2.17e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063712016 399 PNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNATIQSFCK 448
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 80-113 2.56e-12

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: 60.82  E-value: 2.56e-12
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063712016  80 DGCKPDRFTYNILIHGVCKKGVVDEAIRLVKQME 113
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 ...
 434-481 4.84e-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: 60.45  E-value: 4.84e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063712016 434 PDLYAYNATIQSFCKMRKVKKAEELLKTMLRIGLKPDNFTYSTLIKAL 481
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 49-98 1.13e-11

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: 1.13e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063712016  49 PSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIHGVCK 98
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 33-505 1.38e-11

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 67.18  E-value: 1.38e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  33 KYCNDVFAQISFLGMkpstRLYNAVIDALVKSNSLDLAYLKFQQMRsdgcKPDRFTYNILIHGVCKKGVVDEAIRLVKQM 112
Cdd:PLN03077  107 RVCSRALSSHPSLGV----RLGNAMLSMFVRFGELVHAWYVFGKMP----ERDLFSWNVLVGGYAKAGYFDEALCLYHRM 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 113 EQEGNRPNVFTYTILIDGflIAGRVDEAL-KQLEMMRVR-----KLNPNEATIRTFVhgifRCLPPCKAFEVLVGFMEKD 186
Cdd:PLN03077  179 LWAGVRPDVYTFPCVLRT--CGGIPDLARgREVHAHVVRfgfelDVDVVNALITMYV----KCGDVVSARLVFDRMPRRD 252

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 187 snlqRVGYDAVLYCLSNNSMAKETGQFLRKIGERGYIPDSSTFNAAMS-CLLKGHdlVETCRIFDGFVsrgVKPGFNG-- 263
Cdd:PLN03077  253 ----CISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISaCELLGD--ERLGREMHGYV---VKTGFAVdv 323

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 264 --YLVLVQALLNAQRFSEGDRYLKQMGVDGLLS-----SVYSYNAVIDclcKArrIENAAMflteMQDRGISPNLVTFNT 336
Cdd:PLN03077  324 svCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSwtamiSGYEKNGLPD---KA--LETYAL----MEQDNVSPDEITIAS 394

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 337 FLSGYSVRGDVK---KVHGVLEKllvHGFKPDVITFSLIINCLCRAKEIKDAFDCFKEMLE-----WG------------ 396
Cdd:PLN03077  395 VLSACACLGDLDvgvKLHELAER---KGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEkdvisWTsiiaglrlnnrc 471

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 397 -------------IEPNEITYNILIRSCCSTGDTdRSVK------LFAKMKENGLSP----DLY---------------- 437
Cdd:PLN03077  472 fealiffrqmlltLKPNSVTLIAALSACARIGAL-MCGKeihahvLRTGIGFDGFLPnallDLYvrcgrmnyawnqfnsh 550

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063712016 438 -----AYNATIQSFCKMRKVKKAEELLKTMLRIGLKPDNFTYSTLIKALSESGRESEAREMFSSIE-RHGCVPD 505
Cdd:PLN03077  551 ekdvvSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEeKYSITPN 624
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 295-341 2.58e-11

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: 58.53  E-value: 2.58e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063712016 295 SVYSYNAVIDCLCKARRIENAAMFLTEMQDRGISPNLVTFNTFLSGY 341
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 52-499 3.15e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 62.58  E-value: 3.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  52 RLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYN--ILIHGVCkkGVVDEAIRLVKQMEQEgnrpNVFTYTILID 129
Cdd:PLN03081  124 STYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNrvLLMHVKC--GMLIDARRLFDEMPER----NLASWGTIIG 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 130 GFLIAGRVDEALKQLEMMRVrklNPNEATIRTFVHGIfrclppcKAFEVLvgfmekdsNLQRVGYDavLYCLSnnsmake 209
Cdd:PLN03081  198 GLVDAGNYREAFALFREMWE---DGSDAEPRTFVVML-------RASAGL--------GSARAGQQ--LHCCV------- 250

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 210 tgqflRKIGERGyipdsstfNAAMSCLL-----KGHDLVETCRIFDGFVSRgvkpgfngylvlvqallnaqrfsegdryl 284
Cdd:PLN03081  251 -----LKTGVVG--------DTFVSCALidmysKCGDIEDARCVFDGMPEK----------------------------- 288

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 285 kqmgvdgllsSVYSYNAVIDCLCKARRIENAAMFLTEMQDRGISPNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVHGFKP 364
Cdd:PLN03081  289 ----------TTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPL 358

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 365 DVITFSLIINCLCRAKEIKDAFDCFKEMlewgieP--NEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNAT 442
Cdd:PLN03081  359 DIVANTALVDLYSKWGRMEDARNVFDRM------PrkNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAV 432

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063712016 443 IQSFCKMRKVKKAEELLKTMLRI-GLKPDNFTYSTLIKALSESGRESEAremFSSIER 499
Cdd:PLN03081  433 LSACRYSGLSEQGWEIFQSMSENhRIKPRAMHYACMIELLGREGLLDEA---YAMIRR 487
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 329-378 4.70e-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: 55.06  E-value: 4.70e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063712016 329 PNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVHGFKPDVITFSLIINCLCR 378
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 22-316 2.81e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.89  E-value: 2.81e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016   22 LIGSWGRLGLAKYCNDVFAQISFLG--MKPSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIHGVCKK 99
Cdd:PLN03218   548 LISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQK 627

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  100 GVVDEAIRLVKQMEQEGNRPNVFTYTILIDGFLIAGRVDEALKQLEMMRVRKLNPneatirtfvhGIfrclppckafevl 179
Cdd:PLN03218   628 GDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKL----------GT------------- 684

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  180 vgfmekdsnlqrVGYDAVLYCLSNNSMAKETGQFLRKIGERGYIPDSSTFNAAMSCLLKGHDLVETCRIFDGFVSRGVKP 259
Cdd:PLN03218   685 ------------VSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCP 752

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063712016  260 GFNGYLVLVQALLNAQRFSEGDRYLKQMGVDGLlssvySYNAVI-DC---LCKaRRIENAA 316
Cdd:PLN03218   753 NTITYSILLVASERKDDADVGLDLLSQAKEDGI-----KPNLVMcRCitgLCL-RRFEKAC 807
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 389-449 4.74e-09

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: 52.75  E-value: 4.74e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063712016 389 FKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNATIQSFCKM 449
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 2-128 6.42e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 58.74  E-value: 6.42e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016    2 ELLKEIRDSGYRISDELMCVLIGSWGRLGLAKYCNDVFAQISFLGMKPSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDG 81
Cdd:PLN03218   670 EILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLG 749

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1063712016   82 CKPDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNVFTYTILI 128
Cdd:PLN03218   750 LCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT 796
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 119-165 4.97e-08

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 49.28  E-value: 4.97e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063712016 119 PNVFTYTILIDGFLIAGRVDEALKQLEMMRVRKLNPNEATIRTFVHG 165
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 377-490 8.27e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 55.27  E-value: 8.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  377 CRA-KEIKDAFDCFKEMLEwgiePNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNATIQSFCKMRKVKKA 455
Cdd:PLN03218   416 CKKqRAVKEAFRFAKLIRN----PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAM 491

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1063712016  456 EELLKTMLRIGLKPDNFTYSTLIKALSESGRESEA 490
Cdd:PLN03218   492 FEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKA 526
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 285-419 1.05e-07

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: 52.40  E-value: 1.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 285 KQMGVDGLLSSVYSYNAVIDcLCKARRIENAAMFLTEMQD----------RGISPNLVTFNTFLSGYSVRGDVKKVHGVL 354
Cdd:pfam17177  35 DAAKAEGVRLAQYHYNVLLY-LCSKAADATDLKPQLAADRgfevfeamkaQGVSPNEATYTAVARLAAAKGDGDLAFDLV 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1063712016 355 EKLLVHGFKPDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDR 419
Cdd:pfam17177 114 KEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADK 178
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 360-392 1.09e-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: 47.73  E-value: 1.09e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063712016 360 HGFKPDVITFSLIINCLCRAKEIKDAFDCFKEM 392
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 367-401 1.20e-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: 47.84  E-value: 1.20e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063712016 367 ITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNE 401
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 119-148 1.98e-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: 46.96  E-value: 1.98e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 1063712016 119 PNVFTYTILIDGFLIAGRVDEALKQLEMMR 148
Cdd:pfam12854   5 PDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 353-411 2.10e-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: 2.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063712016 353 VLEKLLVHGFKPDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSC 411
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 395-428 2.53e-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: 46.96  E-value: 2.53e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063712016 395 WGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMK 428
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 19-480 4.29e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 52.93  E-value: 4.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  19 MCVLIGSWGRLGLAKYCNDVFAQISFLGMKPSTRLYNAVIDALVKSNSLDLAYLKFQQMRsdgCKpDRFTYNILIHGVCK 98
Cdd:PLN03077  291 ITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME---TK-DAVSWTAMISGYEK 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  99 KGVVDEAIRLVKQMEQEGNRPNVFTYTILIDGFLIAGRVDEALKQLEMMRVRKLNPNEATIRTFVHGIFRCLPPCKAFEV 178
Cdd:PLN03077  367 NGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEV 446

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 179 LVGFMEKDSnlqrVGYDAVLYCLSNNSMAKETGQFLRKIgERGYIPDSSTFNAAMSCLLKGHDLVETCRIFDGFVSRGVk 258
Cdd:PLN03077  447 FHNIPEKDV----ISWTSIIAGLRLNNRCFEALIFFRQM-LLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGI- 520

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 259 pGFNGYLVlvqallnaqrfsegdrylkqmgvdgllssvysyNAVIDCLCKARRIENA-AMFLTEMQDrgispnLVTFNTF 337
Cdd:PLN03077  521 -GFDGFLP---------------------------------NALLDLYVRCGRMNYAwNQFNSHEKD------VVSWNIL 560

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 338 LSGYSVRGdvkkvhgvlekllvhgfKPDVitfsliinclcrakeikdAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDT 417
Cdd:PLN03077  561 LTGYVAHG-----------------KGSM------------------AVELFNRMVESGVNPDEVTFISLLCACSRSGMV 605

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063712016 418 DRSVKLFAKMKEN-GLSPDLYAYNATIQSFCKMRKVKKAEELLKTMlriGLKPDNFTYSTLIKA 480
Cdd:PLN03077  606 TQGLEYFHSMEEKySITPNLKHYACVVDLLGRAGKLTEAYNFINKM---PITPDPAVWGALLNA 666
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 402-435 7.08e-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: 7.08e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063712016 402 ITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPD 435
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 319-374 1.13e-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: 45.81  E-value: 1.13e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1063712016 319 LTEMQDRGISPNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVHGFKPDVITFSLIIN 374
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 297-330 1.21e-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: 1.21e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063712016 297 YSYNAVIDCLCKARRIENAAMFLTEMQDRGISPN 330
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 128-508 1.89e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 50.64  E-value: 1.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 128 IDGFLIAGRVDEALKQLEMMRVRklNPNEATIRTFVHGIFRC--LPPCKAFEVLVGFMEKDS-NLQRVGYDAVLYCLSNN 204
Cdd:PLN03081   94 IEKLVACGRHREALELFEILEAG--CPFTLPASTYDALVEACiaLKSIRCVKAVYWHVESSGfEPDQYMMNRVLLMHVKC 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 205 SMAKETGQFLRKIGERgyipDSSTFNAAMSCLLKGHDLVETCRIFDGFVSRGVKPGFNGYLVLVQALLNAQRFSEGdryl 284
Cdd:PLN03081  172 GMLIDARRLFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAG---- 243

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 285 KQMGV----DGLLSSVYSYNAVIDCLCKARRIENAAMFLTEMQDRGIspnlVTFNTFLSGYSVrgdvkkvHGVLEkllvh 360
Cdd:PLN03081  244 QQLHCcvlkTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTT----VAWNSMLAGYAL-------HGYSE----- 307

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 361 gfkpdvitfsliinclcrakeikDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYN 440
Cdd:PLN03081  308 -----------------------EALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANT 364

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063712016 441 ATIQSFCKMRKVKKAEELLKTMLRIGLkpdnFTYSTLIKALSESGRESEAREMFSSIERHGCVPDSYT 508
Cdd:PLN03081  365 ALVDLYSKWGRMEDARNVFDRMPRKNL----ISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVT 428
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 378-504 2.71e-06

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 48.55  E-value: 2.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 378 RAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDT---------DRSVKLFAKMKENGLSPDLYAYNATIQSFCK 448
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADAtdlkpqlaaDRGFEVFEAMKAQGVSPNEATYTAVARLAAA 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1063712016 449 MRKVKKAEELLKTMLRIGLKPDNFTYSTLIKALSESGRESEAREMFSSIERHGCVP 504
Cdd:pfam17177 103 KGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 87-121 3.71e-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: 43.60  E-value: 3.71e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063712016  87 FTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNV 121
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 46-157 4.87e-06

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 47.78  E-value: 4.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  46 GMKPSTRLYNAVI---------DALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEG 116
Cdd:pfam17177  41 GVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAG 120

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1063712016 117 NRPNVFTYTILIDGFLIAGRVDEALKQLEMMRVRKLNPNEA 157
Cdd:pfam17177 121 VSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEP 161
PLN03077 PLN03077
Protein ECB2; Provisional
 214-505 4.90e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 49.46  E-value: 4.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 214 LRKIGERGYIPDSSTF-NAAMSCLLKGHDLVETCRIFDGFVSRGVKPGFNGYLVLVQALLNAQRFSEGDRYLKQMgvdgl 292
Cdd:PLN03077   38 SRGLSVAASSSSSTHDsNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRA----- 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 293 LSSVYSY-----NAVIDCLCKARRIENAAMFLTEMQDRgispNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVHGFKPDVI 367
Cdd:PLN03077  113 LSSHPSLgvrlgNAMLSMFVRFGELVHAWYVFGKMPER----DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVY 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 368 TFSLII-NC-----LCRAKEIKdafdcfKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENglspDLYAYNA 441
Cdd:PLN03077  189 TFPCVLrTCggipdLARGREVH------AHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNA 258

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063712016 442 TIQSFCKMRKVKKAEELLKTMLRIGLKPDNFTYSTLIKALSESGRESEAREMFSSIERHGCVPD 505
Cdd:PLN03077  259 MISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVD 322
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 20-158 6.01e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 49.11  E-value: 6.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016   20 CVLIGSWGrlglakYCNDVFAQISFLGMKPSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIhGVC-- 97
Cdd:PLN03218   624 CSQKGDWD------FALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM-GACsn 696

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063712016   98 ----KKGV-VDEAIRLVKQmeqegnRPNVFTYTILIDGFLIAGRVDEALKQLEMMRVRKLNPNEAT 158
Cdd:PLN03218   697 aknwKKALeLYEDIKSIKL------RPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTIT 756
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 469-508 6.13e-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: 6.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063712016 469 PDNFTYSTLIKALSESGRESEAREMFSSIERHGCVPDSYT 508
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
PLN03077 PLN03077
Protein ECB2; Provisional
 230-508 9.76e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 48.31  E-value: 9.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 230 NAAMSCLLKGHDLVETCRIFDGFVSRGVkpgFNgYLVLVQALLNAQRFSEG-DRYLKQMGVdGLLSSVYSYNAVI-DC-- 305
Cdd:PLN03077  125 NAMLSMFVRFGELVHAWYVFGKMPERDL---FS-WNVLVGGYAKAGYFDEAlCLYHRMLWA-GVRPDVYTFPCVLrTCgg 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 306 ---LCKARRIENAAMFLtemqdrGISPNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVHgfkpDVITFSLIINCLCRAKEI 382
Cdd:PLN03077  200 ipdLARGREVHAHVVRF------GFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGEC 269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 383 KDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNATIQSFCKMRKVKKAEELLKTM 462
Cdd:PLN03077  270 LEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRM 349

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1063712016 463 LRiglkPDNFTYSTLIKALSESGRESEAREMFSSIERHGCVPDSYT 508
Cdd:PLN03077  350 ET----KDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEIT 391
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 241-364 9.95e-06

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 46.62  E-value: 9.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 241 DLVETCRIFDGFVSRGVKPGFNGYLVLVQALLNAQRFSEGDRYL---------KQMGVDGLLSSVYSYNAVIDCLCKARR 311
Cdd:pfam17177  26 DATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPQLaadrgfevfEAMKAQGVSPNEATYTAVARLAAAKGD 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063712016 312 IENAAMFLTEMQDRGISPNLVTFNTFLSGYSVRGDVKKVHGVLEKLLVHGFKP 364
Cdd:pfam17177 106 GDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 472-506 1.10e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 42.06  E-value: 1.10e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063712016 472 FTYSTLIKALSESGRESEAREMFSSIERHGCVPDS 506
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 430-462 1.12e-05

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 42.33  E-value: 1.12e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063712016 430 NGLSPDLYAYNATIQSFCKMRKVKKAEELLKTM 462
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 402-432 1.54e-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: 41.68  E-value: 1.54e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063712016 402 ITYNILIRSCCSTGDTDRSVKLFAKMKENGL 432
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 74-128 1.68e-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: 42.73  E-value: 1.68e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063712016  74 FQQMRSDGCKPDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNVFTYTILI 128
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 422-480 2.28e-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: 42.35  E-value: 2.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063712016 422 KLFAKMKENGLSPDLYAYNATIQSFCKMRKVKKAEELLKTMLRIGLKPDNFTYSTLIKA 480
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 1-154 4.64e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 46.02  E-value: 4.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016   1 MELLKEIRDSGYRISDELMCVLIGSWGRLGLAKYCNDVFAQISFLGMKPSTRLYNAVIDALVKSNSLDLAYLKFQQMrsd 80
Cdd:PLN03081  310 LCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRM--- 386

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063712016  81 gckPDR--FTYNILIHGVCKKGVVDEAIRLVKQMEQEGNRPNVFTYTILIDGFLIAGRVDEALKQLEMM-RVRKLNP 154
Cdd:PLN03081  387 ---PRKnlISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMsENHRIKP 460
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 87-116 7.04e-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: 39.76  E-value: 7.04e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1063712016  87 FTYNILIHGVCKKGVVDEAIRLVKQMEQEG 116
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 367-397 1.86e-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: 38.60  E-value: 1.86e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063712016 367 ITFSLIINCLCRAKEIKDAFDCFKEMLEWGI 397
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 290-322 1.95e-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: 38.87  E-value: 1.95e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063712016 290 DGLLSSVYSYNAVIDCLCKARRIENAAMFLTEM 322
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 52-85 2.93e-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: 38.21  E-value: 2.93e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063712016  52 RLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPD 85
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 45-97 4.44e-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: 4.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063712016  45 LGMKPSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIhGVC 97
Cdd:pfam13812   9 DGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL-GVI 60
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 38-159 4.45e-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: 41.61  E-value: 4.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016  38 VFAQISFLGMKPSTRLYNAVIDALVKSNSLDLAYLKFQQMRSDGCKPDRFTYNILIHGVCKKGVVDEAIRLVKQMEQEGN 117
Cdd:pfam17177  77 VFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGV 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1063712016 118 RPNVFTYTILIDGFLIAGRVDEALKQLEMMR--VRKLNPNEATI 159
Cdd:pfam17177 157 ELEEPELAALLKVSAKAGRADKVYAYLHRLRdaVRQVSESTAGV 200
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 297-327 4.50e-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: 4.50e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063712016 297 YSYNAVIDCLCKARRIENAAMFLTEMQDRGI 327
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 282-344 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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063712016 282 RYLKQMGVDGLLSSVYSYNAVIDCLCKARRIENAAMFLTEMQDRGISPNLVTFNTFLSGYSVR 344
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 466-494 9.69e-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: 36.55  E-value: 9.69e-04
                          10        20
                  ....*....|....*....|....*....
gi 1063712016 466 GLKPDNFTYSTLIKALSESGRESEAREMF 494
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELL 30
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 107-155 1.00e-03

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: 37.72  E-value: 1.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063712016 107 RLVKQMEQEGNRPNVFTYTILIDGFLIAGRVDEALKQLEMMRVRKLNPN 155
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPT 49
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 332-366 1.12e-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: 36.66  E-value: 1.12e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063712016 332 VTFNTFLSGYSVRGDVKKVHGVLEKLLVHGFKPDV 366
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 122-156 1.86e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.89  E-value: 1.86e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063712016 122 FTYTILIDGFLIAGRVDEALKQLEMMRVRKLNPNE 156
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03077 PLN03077
Protein ECB2; Provisional
 280-508 1.94e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.99  E-value: 1.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 280 GDRYLKQMGVDGLLSSVYSY-NAVIDCLCKARRIENAAMFLTEMQDRGISPNLVTF------------------------ 334
Cdd:PLN03077   34 GRKRSRGLSVAASSSSSTHDsNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYvalfrlcewkraveegsrvcsral 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 335 -----------NTFLSGYSVRGDVKKVHGVLEKLLvhgfKPDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEIT 403
Cdd:PLN03077  114 sshpslgvrlgNAMLSMFVRFGELVHAWYVFGKMP----ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYT 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063712016 404 YNILIRSCCSTGDTDRSVKLFAKMKENGLSPDLYAYNATIQSFCKMRKVKKAEELLKTMLRIglkpDNFTYSTLIKALSE 483
Cdd:PLN03077  190 FPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFE 265

                         250       260
                  ....*....|....*....|....*
gi 1063712016 484 SGRESEAREMFSSIERHGCVPDSYT 508
Cdd:PLN03077  266 NGECLEGLELFFTMRELSVDPDLMT 290
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 472-502 2.30e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 35.52  E-value: 2.30e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063712016 472 FTYSTLIKALSESGRESEAREMFSSIERHGC 502
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 ...
 437-467 3.84e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 35.13  E-value: 3.84e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063712016 437 YAYNATIQSFCKMRKVKKAEELLKTMLRIGL 467
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 ...
 122-152 4.19e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 34.75  E-value: 4.19e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063712016 122 FTYTILIDGFLIAGRVDEALKQLEMMRVRKL 152
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
 
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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