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Conserved domains on  [gi|578802651|ref|XP_006711978|]
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leucine-rich PPR motif-containing protein, mitochondrial isoform X1 [Homo sapiens]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1051123)

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
PPR_long super family cl38513
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 197-303 3.62e-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.


The actual alignment was detected with superfamily member pfam17177:

Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 52.40  E-value: 3.62e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651   197 MKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHLMD 276
Cdd:pfam17177   81 MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEE 160

                           90       100
                   ....*....|....*....|....*..
gi 578802651   277 RDLLQIIFSFSKAGYPQYVSEILEKVT 303
Cdd:pfam17177  161 PELAALLKVSAKAGRADKVYAYLHRLR 187
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 118-258 3.69e-07

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.88  E-value: 3.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  118 EFAHRIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFM 197
Cdd:PLN03218  631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 578802651  198 KTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDID 258
Cdd:PLN03218  711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDAD 771
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1020-1285 5.27e-07

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 52.81  E-value: 5.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1020 NQKKGAYDIFLNAKEQNiVFNAETYSNLIKLLMSEDYFTQAMEVkafAETHIKGFTLNDAANSRLIITQVRRDYLKEAVT 1099
Cdd:COG2956    22 GQPDKAIDLLEEALELD-PETVEAHLALGNLYRRRGEYDRAIRI---HQKLLERDPDRAEALLELAQDYLKAGLLDRAEE 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1100 TLKTVLDQQQTpSRLAVTRVIQALAMKGDVEN-IEVVQKMLNgledsIGLSKMVFINNIALAQIKNNNIDAAIENIENML 1178
Cdd:COG2956    98 LLEKLLELDPD-DAEALRLLAEIYEQEGDWEKaIEVLERLLK-----LGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1179 TSENKVIEPqYFGLAYLFRKviEEQLEPAVEKISIMAERLANQFAIYKPVTDFFLQLvdaGKVDDARALLQRCGAIAEQT 1258
Cdd:COG2956   172 KLDPDCARA-LLLLAELYLE--QGDYEEAIAALERALEQDPDYLPALPRLAELYEKL---GDPEEALELLRKALELDPSD 245

                         250       260
                  ....*....|....*....|....*..
gi 578802651 1259 PILLLFLLRNSRKQGKASTVKSVLELI 1285
Cdd:COG2956   246 DLLLALADLLERKEGLEAALALLERQL 272
 
Name Accession Description Interval E-value
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 197-303 3.62e-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: 3.62e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651   197 MKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHLMD 276
Cdd:pfam17177   81 MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEE 160

                           90       100
                   ....*....|....*....|....*..
gi 578802651   277 RDLLQIIFSFSKAGYPQYVSEILEKVT 303
Cdd:pfam17177  161 PELAALLKVSAKAGRADKVYAYLHRLR 187
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 118-258 3.69e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.88  E-value: 3.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  118 EFAHRIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFM 197
Cdd:PLN03218  631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 578802651  198 KTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDID 258
Cdd:PLN03218  711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDAD 771
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1020-1285 5.27e-07

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 52.81  E-value: 5.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1020 NQKKGAYDIFLNAKEQNiVFNAETYSNLIKLLMSEDYFTQAMEVkafAETHIKGFTLNDAANSRLIITQVRRDYLKEAVT 1099
Cdd:COG2956    22 GQPDKAIDLLEEALELD-PETVEAHLALGNLYRRRGEYDRAIRI---HQKLLERDPDRAEALLELAQDYLKAGLLDRAEE 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1100 TLKTVLDQQQTpSRLAVTRVIQALAMKGDVEN-IEVVQKMLNgledsIGLSKMVFINNIALAQIKNNNIDAAIENIENML 1178
Cdd:COG2956    98 LLEKLLELDPD-DAEALRLLAEIYEQEGDWEKaIEVLERLLK-----LGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1179 TSENKVIEPqYFGLAYLFRKviEEQLEPAVEKISIMAERLANQFAIYKPVTDFFLQLvdaGKVDDARALLQRCGAIAEQT 1258
Cdd:COG2956   172 KLDPDCARA-LLLLAELYLE--QGDYEEAIAALERALEQDPDYLPALPRLAELYEKL---GDPEEALELLRKALELDPSD 245

                         250       260
                  ....*....|....*....|....*..
gi 578802651 1259 PILLLFLLRNSRKQGKASTVKSVLELI 1285
Cdd:COG2956   246 DLLLALADLLERKEGLEAALALLERQL 272
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 157-274 3.06e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 51.80  E-value: 3.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  157 DFLAKM--EEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRD 234
Cdd:PLN03218  563 DVLAEMkaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKK 642

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 578802651  235 AGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHL 274
Cdd:PLN03218  643 KGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKL 682
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 169-218 1.84e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.42  E-value: 1.84e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 578802651   169 PNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHAR 218
Cdd:pfam13041    1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
 
Name Accession Description Interval E-value
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 197-303 3.62e-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: 3.62e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651   197 MKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHLMD 276
Cdd:pfam17177   81 MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEE 160

                           90       100
                   ....*....|....*....|....*..
gi 578802651   277 RDLLQIIFSFSKAGYPQYVSEILEKVT 303
Cdd:pfam17177  161 PELAALLKVSAKAGRADKVYAYLHRLR 187
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 118-258 3.69e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.88  E-value: 3.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  118 EFAHRIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFM 197
Cdd:PLN03218  631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 578802651  198 KTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDID 258
Cdd:PLN03218  711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDAD 771
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1020-1285 5.27e-07

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 52.81  E-value: 5.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1020 NQKKGAYDIFLNAKEQNiVFNAETYSNLIKLLMSEDYFTQAMEVkafAETHIKGFTLNDAANSRLIITQVRRDYLKEAVT 1099
Cdd:COG2956    22 GQPDKAIDLLEEALELD-PETVEAHLALGNLYRRRGEYDRAIRI---HQKLLERDPDRAEALLELAQDYLKAGLLDRAEE 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1100 TLKTVLDQQQTpSRLAVTRVIQALAMKGDVEN-IEVVQKMLNgledsIGLSKMVFINNIALAQIKNNNIDAAIENIENML 1178
Cdd:COG2956    98 LLEKLLELDPD-DAEALRLLAEIYEQEGDWEKaIEVLERLLK-----LGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1179 TSENKVIEPqYFGLAYLFRKviEEQLEPAVEKISIMAERLANQFAIYKPVTDFFLQLvdaGKVDDARALLQRCGAIAEQT 1258
Cdd:COG2956   172 KLDPDCARA-LLLLAELYLE--QGDYEEAIAALERALEQDPDYLPALPRLAELYEKL---GDPEEALELLRKALELDPSD 245

                         250       260
                  ....*....|....*....|....*..
gi 578802651 1259 PILLLFLLRNSRKQGKASTVKSVLELI 1285
Cdd:COG2956   246 DLLLALADLLERKEGLEAALALLERQL 272
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 157-274 3.06e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 51.80  E-value: 3.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  157 DFLAKM--EEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRD 234
Cdd:PLN03218  563 DVLAEMkaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKK 642

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 578802651  235 AGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHL 274
Cdd:PLN03218  643 KGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKL 682
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 162-272 1.15e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 49.88  E-value: 1.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  162 MEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGP 241
Cdd:PLN03218  605 IHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGT 684

                          90       100       110
                  ....*....|....*....|....*....|.
gi 578802651  242 DTYLALLNAYAEKGDIDHVKQTLEKVEKSEL 272
Cdd:PLN03218  685 VSYSSLMGACSNAKNWKKALELYEDIKSIKL 715
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 161-270 1.35e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 49.88  E-value: 1.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  161 KMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAG--IE 238
Cdd:PLN03218  497 EMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEThpID 576

                          90       100       110
                  ....*....|....*....|....*....|..
gi 578802651  239 PGPDTYLALLNAYAEKGDIDHVKQTLEKVEKS 270
Cdd:PLN03218  577 PDHITVGALMKACANAGQVDRAKEVYQMIHEY 608
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1158-1322 2.23e-05

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.80  E-value: 2.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1158 ALAQIKNNNIDAAIENIENMLTSENKVIEPqYFGLAYLFRKviEEQLEPAVEK----ISIMAERLANQFAIYKpvtDFFl 1233
Cdd:COG2956    15 GLNYLLNGQPDKAIDLLEEALELDPETVEA-HLALGNLYRR--RGEYDRAIRIhqklLERDPDRAEALLELAQ---DYL- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651 1234 qlvDAGKVDDARALLQRCGAIAEQTPILLLFLLRNSRKQGKASTVKSVLELIPELN-EKEEAYNSLMKSYVSEKDVTSAK 1312
Cdd:COG2956    88 ---KAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGpENAHAYCELAELYLEQGDYDEAI 164

                         170
                  ....*....|
gi 578802651 1313 ALYEHLTAKN 1322
Cdd:COG2956   165 EALEKALKLD 174
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 157-243 1.76e-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: 44.31  E-value: 1.76e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651   157 DFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAG 236
Cdd:pfam17177  111 DLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAYLHRLRDAV 190


                   ....*..
gi 578802651   237 IEPGPDT 243
Cdd:pfam17177  191 RQVSEST 197
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 169-218 1.84e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.42  E-value: 1.84e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 578802651   169 PNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHAR 218
Cdd:pfam13041    1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 109-266 2.57e-04

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 43.92  E-value: 2.57e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651   109 PELKLEERTEFAHRIWDTLQKLgAVYDVS----------HYNALLKVYLQNEYKFSPTDFLA---------KMEEANIQP 169
Cdd:pfam17177   10 PESELRFQLDKCSKHADATGAL-ALYDAAkaegvrlaqyHYNVLLYLCSKAADATDLKPQLAadrgfevfeAMKAQGVSP 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651   170 NRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLN 249
Cdd:pfam17177   89 NEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLK 168

                          170
                   ....*....|....*..
gi 578802651   250 AYAEKGDIDHVKQTLEK 266
Cdd:pfam17177  169 VSAKAGRADKVYAYLHR 185
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 192-251 3.78e-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: 40.03  E-value: 3.78e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651   192 KILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAY 251
Cdd:pfam13812    1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 122-183 1.03e-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: 38.88  E-value: 1.03e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578802651   122 RIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCN 183
Cdd:pfam13812    1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 159-213 1.04e-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: 38.88  E-value: 1.04e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 578802651   159 LAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALV 213
Cdd:pfam13812    3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 209-252 1.86e-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: 37.34  E-value: 1.86e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 578802651   209 FSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYA 252
Cdd:pfam13041    6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 166-198 7.06e-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: 35.40  E-value: 7.06e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 578802651   166 NIQPNRVTYQRLIASYCNVGDIEGASKILGFMK 198
Cdd:pfam12854    2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 169-257 7.53e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 41.02  E-value: 7.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  169 PNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALL 248
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514


                  ....*....
gi 578802651  249 NAYAEKGDI 257
Cdd:PLN03218  515 DGCARAGQV 523
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 135-183 8.91e-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: 35.80  E-value: 8.91e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 578802651   135 DVSHYNALLKVYLQNEyKFSPT-DFLAKMEEANIQPNRVTYQRLIASYCN 183
Cdd:pfam13041    2 DVVTYNTLINGYCKKG-KVEEAfKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 132-235 9.50e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 9.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578802651  132 AVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSA 211
Cdd:PLN03077  249 PRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNS 328

                          90       100
                  ....*....|....*....|....*.
gi 578802651  212 LVTGHARAGDMENAENILTVM--RDA 235
Cdd:PLN03077  329 LIQMYLSLGSWGEAEKVFSRMetKDA 354
 
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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