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Conserved domains on  [gi|1002314181|ref|XP_015620468|]
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pentatricopeptide repeat-containing protein At2g15980 [Oryza sativa Japonica Group]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13329789)

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_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 248-295 2.86e-14

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: 66.62  E-value: 2.86e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002314181 248 NVCTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMISGYC 295
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 217-447 1.98e-13

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.60  E-value: 1.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  217 FNSLLLAFYREGKCDVFKVVLQEMDRYScvHNV----CTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMIS 292
Cdd:PLN03218   545 FNALISACGQSGAVDRAFDVLAEMKAET--HPIdpdhITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVN 622

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  293 GYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLV--RGHcrVGDIDAAMLVRADMSRRGFQMAAEVVEEVVNVLCQKKRV 370
Cdd:PLN03218   623 SCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVdvAGH--AGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNW 700

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002314181  371 KEALGVLkEEMRKEEFVPSRECYEVLIRELCEQGEVEVAMRLQAEMAGMGFKVGSEVYCAFVCAYEKAEDYEMAEKL 447
Cdd:PLN03218   701 KKALELY-EDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDL 776
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 248-295 2.86e-14

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: 66.62  E-value: 2.86e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002314181 248 NVCTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMISGYC 295
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 217-447 1.98e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.60  E-value: 1.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  217 FNSLLLAFYREGKCDVFKVVLQEMDRYScvHNV----CTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMIS 292
Cdd:PLN03218   545 FNALISACGQSGAVDRAFDVLAEMKAET--HPIdpdhITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVN 622

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  293 GYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLV--RGHcrVGDIDAAMLVRADMSRRGFQMAAEVVEEVVNVLCQKKRV 370
Cdd:PLN03218   623 SCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVdvAGH--AGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNW 700

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002314181  371 KEALGVLkEEMRKEEFVPSRECYEVLIRELCEQGEVEVAMRLQAEMAGMGFKVGSEVYCAFVCAYEKAEDYEMAEKL 447
Cdd:PLN03218   701 KKALELY-EDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDL 776
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 282-331 1.40e-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: 62.00  E-value: 1.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002314181 282 PDVPAYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLVRGHCR 331
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 250-284 1.22e-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: 44.75  E-value: 1.22e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002314181 250 CTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDV 284
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 286-319 4.40e-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: 43.21  E-value: 4.40e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1002314181 286 AYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSV 319
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 248-295 2.86e-14

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: 66.62  E-value: 2.86e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002314181 248 NVCTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMISGYC 295
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 217-447 1.98e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.60  E-value: 1.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  217 FNSLLLAFYREGKCDVFKVVLQEMDRYScvHNV----CTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMIS 292
Cdd:PLN03218   545 FNALISACGQSGAVDRAFDVLAEMKAET--HPIdpdhITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVN 622

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  293 GYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLV--RGHcrVGDIDAAMLVRADMSRRGFQMAAEVVEEVVNVLCQKKRV 370
Cdd:PLN03218   623 SCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVdvAGH--AGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNW 700

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002314181  371 KEALGVLkEEMRKEEFVPSRECYEVLIRELCEQGEVEVAMRLQAEMAGMGFKVGSEVYCAFVCAYEKAEDYEMAEKL 447
Cdd:PLN03218   701 KKALELY-EDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDL 776
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 282-331 1.40e-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: 62.00  E-value: 1.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002314181 282 PDVPAYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLVRGHCR 331
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 199-457 6.36e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 64.90  E-value: 6.36e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  199 YTRPSSRINSqLLPTVHTFNSLLlafyREGKCDVFKVVLQEMDR----------YSCVHNVC------------------ 250
Cdd:PLN03218   360 YNGGVSGKRK-SPEYIDAYNRLL----RDGRIKDCIDLLEDMEKrglldmdkiyHAKFFKACkkqravkeafrfaklirn 434

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  251 ----TYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLV 326
Cdd:PLN03218   435 ptlsTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  327 RGHCRVGDIDAAMLVRADMSRRGFQMAAEVVEEVVNVLCQKKRVKEALGVLKeEMRKEE--FVPSRECYEVLIRELCEQG 404
Cdd:PLN03218   515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLA-EMKAEThpIDPDHITVGALMKACANAG 593

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1002314181  405 EVEVAMRLQAEMAGMGFKVGSEVYCAFVCAYEKAEDYEMAEKLRKELSVISIQ 457
Cdd:PLN03218   594 QVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVK 646
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 217-457 1.82e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 56.81  E-value: 1.82e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  217 FNSLLLAFYREGKCDVFKVVLQEMDRYSCVHNVCTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMISGyCG 296
Cdd:PLN03218   475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISA-CG 553

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  297 -VGEVGMAEEMFKDM--EMGGIDPSVTTFEWLVRGHCRVGDIDAAMLVRADMSRRGFQMAAEVVEEVVNVLCQKKRVKEA 373
Cdd:PLN03218   554 qSGAVDRAFDVLAEMkaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFA 633

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  374 LGVLKeEMRKEEFVPSRECYEVLIRELCEQGEVEVAMRLQAEMAGMGFKVGSEVYCAFVCAYEKAEDYEMAEKLRKELSV 453
Cdd:PLN03218   634 LSIYD-DMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKS 712


                   ....
gi 1002314181  454 ISIQ 457
Cdd:PLN03218   713 IKLR 716
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 279-311 1.27e-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: 47.34  E-value: 1.27e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1002314181 279 GIQPDVPAYNTMISGYCGVGEVGMAEEMFKDME 311
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 271-326 3.16e-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: 47.35  E-value: 3.16e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002314181 271 LWDEMVEGGIQPDVPAYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLV 326
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 250-284 1.22e-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: 44.75  E-value: 1.22e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002314181 250 CTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDV 284
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 286-319 4.40e-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: 43.21  E-value: 4.40e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1002314181 286 AYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSV 319
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 286-315 2.25e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 41.30  E-value: 2.25e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1002314181 286 AYNTMISGYCGVGEVGMAEEMFKDMEMGGI 315
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 212-261 1.75e-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: 38.88  E-value: 1.75e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1002314181 212 PTVHTFNSLLLAFYREGK----CDVFKvvlqEMDRYSCVHNVCTYNIRMAAYCD 261
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKveeaFKLFN----EMKKRGVKPNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 251-280 4.95e-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: 4.95e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1002314181 251 TYNIRMAAYCDSKEVEKARGLWDEMVEGGI 280
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 243-351 1.12e-03

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 40.07  E-value: 1.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181 243 YSCVHNVCTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSVTTF 322
Cdd:pfam17177  49 YNVLLYLCSKAADATDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSY 128

                          90       100
                  ....*....|....*....|....*....
gi 1002314181 323 EWLVRGHCRVGDIDAAMLVRADMSRRGFQ 351
Cdd:pfam17177 129 SPALHAYCEAGDADKAYEVEEHMLAHGVE 157
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 191-300 1.60e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 41.02  E-value: 1.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181  191 ALDMYREIYTrpssrinSQLLPTVHTFNSLLLAFyregkCDVFKV-----VLQEMDRYSCVHNVCTYNIRMAAYCDSKEV 265
Cdd:PLN03218   703 ALELYEDIKS-------IKLRPTVSTMNALITAL-----CEGNQLpkaleVLSEMKRLGLCPNTITYSILLVASERKDDA 770

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1002314181  266 EKARGLWDEMVEGGIQPDVPAYNTMIS-------GYCGVGEV 300
Cdd:PLN03218   771 DVGLDLLSQAKEDGIKPNLVMCRCITGlclrrfeKACALGEP 812
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 212-259 3.64e-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: 35.80  E-value: 3.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002314181 212 PTVHTFNSLLLAFYREGKCDVFKVVLQEMDRYSCVHNVCTYNIRMAAY 259
Cdd:pfam13812  13 LNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 254-383 4.46e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 39.47  E-value: 4.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002314181 254 IRMAAYCDSkeVEKARGLWDEMVEggiqPDVPAYNTMISGYCGVGEVGMAEEMFKDMEMGGIDPSVTTFEWLVRGHCRVG 333
Cdd:PLN03081  266 IDMYSKCGD--IEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLA 339

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002314181 334 DIDAAMLVRADMSRRGFQMAAEVVEEVVNVLCQKKRVKEALGVLKEEMRK 383
Cdd:PLN03081  340 LLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRK 389
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 235-296 4.85e-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: 35.41  E-value: 4.85e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002314181 235 VVLQEMDRYSCVHNVCTYNIRMAAYCDSKEVEKARGLWDEMVEGGIQPDVPAYNTMISGYCG 296
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 248-276 7.77e-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: 33.86  E-value: 7.77e-03
                          10        20
                  ....*....|....*....|....*....
gi 1002314181 248 NVCTYNIRMAAYCDSKEVEKARGLWDEMV 276
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEME 34
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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