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Conserved domains on  [gi|2217324858|ref|XP_047298765|]
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leucine-rich PPR motif-containing protein, mitochondrial isoform X2 [Homo sapiens]

Protein Classification

lipopolysaccharide assembly protein LapB( domain architecture ID 11459274)

lipopolysaccharide assembly protein LapB is a tetratricopeptide repeat (TPR) protein that modulates cellular lipopolysaccharide (LPS) levels by regulating LpxC, which is involved in lipid A biosynthesis

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
 102-242 3.76e-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: 3.76e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  102 EFAHRIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFM 181
Cdd:PLN03218   631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2217324858  182 KTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDID 242
Cdd:PLN03218   711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDAD 771
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1004-1269 7.81e-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: 52.42  E-value: 7.81e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1004 NQKKGAYDIFLNAKEQNiVFNAETYSNLIKLLMSEDYFTQAMEVkafAETHIKGFTLNDAANSRLIITQVRRDYLKEAVT 1083
Cdd:COG2956     22 GQPDKAIDLLEEALELD-PETVEAHLALGNLYRRRGEYDRAIRI---HQKLLERDPDRAEALLELAQDYLKAGLLDRAEE 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1084 TLKTVLDQQQTpSRLAVTRVIQALAMKGDVEN-IEVVQKMLNgledsIGLSKMVFINNIALAQIKNNNIDAAIENIENML 1162
Cdd:COG2956     98 LLEKLLELDPD-DAEALRLLAEIYEQEGDWEKaIEVLERLLK-----LGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1163 TSENKVIEPqYFGLAYLFRKviEEQLEPAVEKISIMAERLANQFAIYKPVTDFFLQLvdaGKVDDARALLQRCGAIAEQT 1242
Cdd:COG2956    172 KLDPDCARA-LLLLAELYLE--QGDYEEAIAALERALEQDPDYLPALPRLAELYEKL---GDPEEALELLRKALELDPSD 245

                          250       260
                   ....*....|....*....|....*..
gi 2217324858 1243 PILLLFLLRNSRKQGKASTVKSVLELI 1269
Cdd:COG2956    246 DLLLALADLLERKEGLEAALALLERQL 272
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 102-242 3.76e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.88  E-value: 3.76e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  102 EFAHRIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFM 181
Cdd:PLN03218   631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2217324858  182 KTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDID 242
Cdd:PLN03218   711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDAD 771
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 181-287 3.85e-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: 3.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  181 MKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHLMD 260
Cdd:pfam17177   81 MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEE 160

                           90       100
                   ....*....|....*....|....*..
gi 2217324858  261 RDLLQIIFSFSKAGYPQYVSEILEKVT 287
Cdd:pfam17177  161 PELAALLKVSAKAGRADKVYAYLHRLR 187
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1004-1269 7.81e-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: 52.42  E-value: 7.81e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1004 NQKKGAYDIFLNAKEQNiVFNAETYSNLIKLLMSEDYFTQAMEVkafAETHIKGFTLNDAANSRLIITQVRRDYLKEAVT 1083
Cdd:COG2956     22 GQPDKAIDLLEEALELD-PETVEAHLALGNLYRRRGEYDRAIRI---HQKLLERDPDRAEALLELAQDYLKAGLLDRAEE 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1084 TLKTVLDQQQTpSRLAVTRVIQALAMKGDVEN-IEVVQKMLNgledsIGLSKMVFINNIALAQIKNNNIDAAIENIENML 1162
Cdd:COG2956     98 LLEKLLELDPD-DAEALRLLAEIYEQEGDWEKaIEVLERLLK-----LGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1163 TSENKVIEPqYFGLAYLFRKviEEQLEPAVEKISIMAERLANQFAIYKPVTDFFLQLvdaGKVDDARALLQRCGAIAEQT 1242
Cdd:COG2956    172 KLDPDCARA-LLLLAELYLE--QGDYEEAIAALERALEQDPDYLPALPRLAELYEKL---GDPEEALELLRKALELDPSD 245

                          250       260
                   ....*....|....*....|....*..
gi 2217324858 1243 PILLLFLLRNSRKQGKASTVKSVLELI 1269
Cdd:COG2956    246 DLLLALADLLERKEGLEAALALLERQL 272
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 102-242 3.76e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.88  E-value: 3.76e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  102 EFAHRIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFM 181
Cdd:PLN03218   631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2217324858  182 KTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDID 242
Cdd:PLN03218   711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDAD 771
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 181-287 3.85e-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: 3.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  181 MKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHLMD 260
Cdd:pfam17177   81 MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEE 160

                           90       100
                   ....*....|....*....|....*..
gi 2217324858  261 RDLLQIIFSFSKAGYPQYVSEILEKVT 287
Cdd:pfam17177  161 PELAALLKVSAKAGRADKVYAYLHRLR 187
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1004-1269 7.81e-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: 52.42  E-value: 7.81e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1004 NQKKGAYDIFLNAKEQNiVFNAETYSNLIKLLMSEDYFTQAMEVkafAETHIKGFTLNDAANSRLIITQVRRDYLKEAVT 1083
Cdd:COG2956     22 GQPDKAIDLLEEALELD-PETVEAHLALGNLYRRRGEYDRAIRI---HQKLLERDPDRAEALLELAQDYLKAGLLDRAEE 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1084 TLKTVLDQQQTpSRLAVTRVIQALAMKGDVEN-IEVVQKMLNgledsIGLSKMVFINNIALAQIKNNNIDAAIENIENML 1162
Cdd:COG2956     98 LLEKLLELDPD-DAEALRLLAEIYEQEGDWEKaIEVLERLLK-----LGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1163 TSENKVIEPqYFGLAYLFRKviEEQLEPAVEKISIMAERLANQFAIYKPVTDFFLQLvdaGKVDDARALLQRCGAIAEQT 1242
Cdd:COG2956    172 KLDPDCARA-LLLLAELYLE--QGDYEEAIAALERALEQDPDYLPALPRLAELYEKL---GDPEEALELLRKALELDPSD 245

                          250       260
                   ....*....|....*....|....*..
gi 2217324858 1243 PILLLFLLRNSRKQGKASTVKSVLELI 1269
Cdd:COG2956    246 DLLLALADLLERKEGLEAALALLERQL 272
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 141-258 3.04e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 51.80  E-value: 3.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  141 DFLAKM--EEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRD 218
Cdd:PLN03218   563 DVLAEMkaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKK 642

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2217324858  219 AGIEPGPDTYLALLNAYAEKGDIDHVKQTLEKVEKSELHL 258
Cdd:PLN03218   643 KGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKL 682
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 146-256 1.18e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 49.88  E-value: 1.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  146 MEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGP 225
Cdd:PLN03218   605 IHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGT 684

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2217324858  226 DTYLALLNAYAEKGDIDHVKQTLEKVEKSEL 256
Cdd:PLN03218   685 VSYSSLMGACSNAKNWKKALELYEDIKSIKL 715
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 145-254 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 2217324858  145 KMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAG--IE 222
Cdd:PLN03218   497 EMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEThpID 576

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2217324858  223 PGPDTYLALLNAYAEKGDIDHVKQTLEKVEKS 254
Cdd:PLN03218   577 PDHITVGALMKACANAGQVDRAKEVYQMIHEY 608
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1142-1306 3.18e-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: 47.42  E-value: 3.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1142 ALAQIKNNNIDAAIENIENMLTSENKVIEPqYFGLAYLFRKviEEQLEPAVEK----ISIMAERLANQFAIYKpvtDFFl 1217
Cdd:COG2956     15 GLNYLLNGQPDKAIDLLEEALELDPETVEA-HLALGNLYRR--RGEYDRAIRIhqklLERDPDRAEALLELAQ---DYL- 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858 1218 qlvDAGKVDDARALLQRCGAIAEQTPILLLFLLRNSRKQGKASTVKSVLELIPELN-EKEEAYNSLMKSYVSEKDVTSAK 1296
Cdd:COG2956     88 ---KAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGpENAHAYCELAELYLEQGDYDEAI 164

                          170
                   ....*....|
gi 2217324858 1297 ALYEHLTAKN 1306
Cdd:COG2956    165 EALEKALKLD 174
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 141-227 1.94e-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: 1.94e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  141 DFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAG 220
Cdd:pfam17177  111 DLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAYLHRLRDAV 190


                   ....*..
gi 2217324858  221 IEPGPDT 227
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 ...
 153-202 1.99e-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: 1.99e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2217324858  153 PNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHAR 202
Cdd:pfam13041    1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 93-250 2.78e-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: 2.78e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858   93 PELKLEERTEFAHRIWDTLQKLgAVYDVS----------HYNALLKVYLQNEYKFSPTDFLA---------KMEEANIQP 153
Cdd:pfam17177   10 PESELRFQLDKCSKHADATGAL-ALYDAAkaegvrlaqyHYNVLLYLCSKAADATDLKPQLAadrgfevfeAMKAQGVSP 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  154 NRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLN 233
Cdd:pfam17177   89 NEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLK 168

                          170
                   ....*....|....*..
gi 2217324858  234 AYAEKGDIDHVKQTLEK 250
Cdd:pfam17177  169 VSAKAGRADKVYAYLHR 185
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 176-235 4.32e-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: 39.65  E-value: 4.32e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  176 KILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAY 235
Cdd:pfam13812    1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 106-167 1.11e-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: 38.49  E-value: 1.11e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217324858  106 RIWDTLQKLGAVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCN 167
Cdd:pfam13812    1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 143-197 1.16e-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: 38.49  E-value: 1.16e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2217324858  143 LAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALV 197
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 ...
 193-236 1.87e-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: 1.87e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2217324858  193 FSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALLNAYA 236
Cdd:pfam13041    6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 150-182 7.33e-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: 7.33e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2217324858  150 NIQPNRVTYQRLIASYCNVGDIEGASKILGFMK 182
Cdd:pfam12854    2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 153-241 7.62e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 40.63  E-value: 7.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  153 PNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSALVTGHARAGDMENAENILTVMRDAGIEPGPDTYLALL 232
Cdd:PLN03218   435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514


                   ....*....
gi 2217324858  233 NAYAEKGDI 241
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 ...
 119-167 9.35e-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: 35.42  E-value: 9.35e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2217324858  119 DVSHYNALLKVYLQNEyKFSPT-DFLAKMEEANIQPNRVTYQRLIASYCN 167
Cdd:pfam13041    2 DVVTYNTLINGYCKKG-KVEEAfKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 116-219 9.38e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 9.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217324858  116 AVYDVSHYNALLKVYLQNEYKFSPTDFLAKMEEANIQPNRVTYQRLIASYCNVGDIEGASKILGFMKTKDLPVTEAVFSA 195
Cdd:PLN03077   249 PRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNS 328

                           90       100
                   ....*....|....*....|....*.
gi 2217324858  196 LVTGHARAGDMENAENILTVM--RDA 219
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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