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Conserved domains on  [gi|15232243|ref|NP_191564|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1007939)

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
 152-435 8.81e-21

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 95.71  E-value: 8.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   152 YHLLMKIFAECGEYKAMWRLVDEMVQDGFPTTARTFNLLICSCGEAGLAKQAVVQF--MKSKtfNYRPFKHSYNAILNSL 229
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYgiMRSK--NVKPDRVVFNALISAC 552

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   230 LGVKQYKLIEWVYKQMLEDG--FSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGF--SPDSYTynILLHILGKGNKP 305
Cdd:PLN03218  553 GQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIkgTPEVYT--IAVNSCSQKGDW 630

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   306 LAALTTLNHMKEVGIDPSVLHYTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMITGYVVSGELDKAKEMFREM 385
Cdd:PLN03218  631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 15232243   386 TVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPNFVVYSTL 435
Cdd:PLN03218  711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSIL 760
PPR super family cl29710
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 423-456 9.36e-06

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.


The actual alignment was detected with superfamily member pfam12854:

Pssm-ID: 421891 [Multi-domain]  Cd Length: 34  Bit Score: 42.33  E-value: 9.36e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15232243   423 RGCNPNFVVYSTLVSYLRKAGKLSEARKVIREMV 456
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 152-435 8.81e-21

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 95.71  E-value: 8.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   152 YHLLMKIFAECGEYKAMWRLVDEMVQDGFPTTARTFNLLICSCGEAGLAKQAVVQF--MKSKtfNYRPFKHSYNAILNSL 229
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYgiMRSK--NVKPDRVVFNALISAC 552

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   230 LGVKQYKLIEWVYKQMLEDG--FSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGF--SPDSYTynILLHILGKGNKP 305
Cdd:PLN03218  553 GQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIkgTPEVYT--IAVNSCSQKGDW 630

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   306 LAALTTLNHMKEVGIDPSVLHYTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMITGYVVSGELDKAKEMFREM 385
Cdd:PLN03218  631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 15232243   386 TVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPNFVVYSTL 435
Cdd:PLN03218  711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSIL 760
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 357-405 2.26e-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: 70.08  E-value: 2.26e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15232243   357 PDVVCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMIRGLC 405
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 395-428 1.88e-08

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: 49.76  E-value: 1.88e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15232243   395 FTYNSMIRGLCMAGEFREACWLLKEMESRGCNPN 428
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 423-456 9.36e-06

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: 9.36e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15232243   423 RGCNPNFVVYSTLVSYLRKAGKLSEARKVIREMV 456
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 430-462 1.33e-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: 36.28  E-value: 1.33e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15232243   430 VVYSTLVSYLRKAGKLSEARKVIREMVKKGHYV 462
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 152-435 8.81e-21

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 95.71  E-value: 8.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   152 YHLLMKIFAECGEYKAMWRLVDEMVQDGFPTTARTFNLLICSCGEAGLAKQAVVQF--MKSKtfNYRPFKHSYNAILNSL 229
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYgiMRSK--NVKPDRVVFNALISAC 552

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   230 LGVKQYKLIEWVYKQMLEDG--FSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGF--SPDSYTynILLHILGKGNKP 305
Cdd:PLN03218  553 GQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIkgTPEVYT--IAVNSCSQKGDW 630

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   306 LAALTTLNHMKEVGIDPSVLHYTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMITGYVVSGELDKAKEMFREM 385
Cdd:PLN03218  631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 15232243   386 TVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPNFVVYSTL 435
Cdd:PLN03218  711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSIL 760
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 187-437 1.96e-18

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 88.78  E-value: 1.96e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   187 FNLLICSCGEAGLAKQA--VVQFMKSKTFNYRPFKHSYNAILNSLLGVKQYKLIEWVYKQMLEDGF--SPDVltYNILLW 262
Cdd:PLN03218  545 FNALISACGQSGAVDRAfdVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIkgTPEV--YTIAVN 622

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   263 TNYRLGKMDRFDRLFDEMARDGFSPDSYTYNILLHILGKGNKPLAALTTLNHMKEVGIDPSVLHYTTLIDGLSRAGNLEA 342
Cdd:PLN03218  623 SCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKK 702

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   343 CKYFLDEMVKAGCRPDVVCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEMES 422
Cdd:PLN03218  703 ALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKE 782

                         250
                  ....*....|....*
gi 15232243   423 RGCNPNFVVYSTLVS 437
Cdd:PLN03218  783 DGIKPNLVMCRCITG 797
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 357-405 2.26e-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: 70.08  E-value: 2.26e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15232243   357 PDVVCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMIRGLC 405
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 217-459 3.01e-15

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 78.37  E-value: 3.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  217 PFK---HSYNAILNSLLGVKQYKLIEWVYKQMLEDGFSPDVLTYNILLWTNYRLGKMDRFDRLFDEM-ARDGfspdsYTY 292
Cdd:PLN03081 118 PFTlpaSTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMpERNL-----ASW 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  293 NILLHILGKGNKPLAALTTLNHMKEVGIDPSVLHYTTLID-----GLSRAG-NLEACkyfldeMVKAGCRPDVVCYTVMI 366
Cdd:PLN03081 193 GTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRasaglGSARAGqQLHCC------VLKTGVVGDTFVSCALI 266

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  367 TGYVVSGELDKAKEMFREMTVKgqlpNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPNFVVYSTLVSYLRKAGKLS 446
Cdd:PLN03081 267 DMYSKCGDIEDARCVFDGMPEK----TTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLE 342

                        250
                 ....*....|...
gi 15232243  447 EARKVIREMVKKG 459
Cdd:PLN03081 343 HAKQAHAGLIRTG 355
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 291-459 1.93e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 69.91  E-value: 1.93e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   291 TYNILLHILGKGNKPLAALTTLNHMKEVGIDPSVLHYTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMITGYV 370
Cdd:PLN03218  439 TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCA 518

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   371 VSGELDKAKEMFREMTVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEM--ESRGCNPNFVVYSTLVSYLRKAGKLSEA 448
Cdd:PLN03218  519 RAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMkaETHPIDPDHITVGALMKACANAGQVDRA 598

                         170
                  ....*....|.
gi 15232243   449 RKVIREMVKKG 459
Cdd:PLN03218  599 KEVYQMIHEYN 609
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 392-437 1.83e-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: 58.91  E-value: 1.83e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15232243   392 PNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPNFVVYSTLVS 437
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 322-369 3.97e-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: 57.76  E-value: 3.97e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15232243   322 PSVLHYTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMITGY 369
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03077 PLN03077
Protein ECB2; Provisional
 355-455 4.01e-10

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 62.17  E-value: 4.01e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  355 CRPDVVCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEMESR-GCNPNFVVYS 433
Cdd:PLN03077 550 HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYA 629

                         90       100
                 ....*....|....*....|..
gi 15232243  434 TLVSYLRKAGKLSEARKVIREM 455
Cdd:PLN03077 630 CVVDLLGRAGKLTEAYNFINKM 651
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 252-297 7.32e-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: 54.29  E-value: 7.32e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15232243   252 PDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGFSPDSYTYNILLH 297
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 145-471 9.19e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 61.04  E-value: 9.19e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  145 FRHTVNSYHLLMKIFAECGEYKAMWRLVDEMVQDGFPTTARTFN---LLICSCGEAGLAKQAvvqfmksktFNYRPFKH- 220
Cdd:PLN03081 119 FTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNrvlLMHVKCGMLIDARRL---------FDEMPERNl 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  221 -SYNAILNSLLGVKQYKLIEWVYKQMLEDGFSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGFSPDSYTYNILLHIL 299
Cdd:PLN03081 190 aSWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMY 269

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  300 GKG---------------------NKPLA----------ALTTLNHMKEVGIDPSVLHYTTLIDGLSRAGNLEACKYFLD 348
Cdd:PLN03081 270 SKCgdiedarcvfdgmpekttvawNSMLAgyalhgyseeALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHA 349

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  349 EMVKAGCRPDVVCYTVMITGYVVSGELDKAKEMFREMTVKgqlpNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPN 428
Cdd:PLN03081 350 GLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPN 425

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 15232243  429 FVVYSTLVSYLRKAGkLSEARKVIREMVKKGHYVHlvPKMMKY 471
Cdd:PLN03081 426 HVTFLAVLSACRYSG-LSEQGWEIFQSMSENHRIK--PRAMHY 465
PLN03077 PLN03077
Protein ECB2; Provisional
 155-458 2.64e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 59.48  E-value: 2.64e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  155 LMKIFAECGEYKAMWRLVDEMVQ-DGFpttarTFNLLICSCGEAGLAKQAVVQFMKSKTFNYRPFKHSYNAILNSLLGVK 233
Cdd:PLN03077 127 MLSMFVRFGELVHAWYVFGKMPErDLF-----SWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIP 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  234 QYKLIEWVYKQMLEDGFSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDgfspDSYTYNILLHILGKGNKPLAALTTLN 313
Cdd:PLN03077 202 DLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGLELFF 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  314 HMKEVGIDPSVLHYTTLI--------DGLSR-----------AGNLEACKYFLDEMVKAGC------------RPDVVCY 362
Cdd:PLN03077 278 TMRELSVDPDLMTITSVIsacellgdERLGRemhgyvvktgfAVDVSVCNSLIQMYLSLGSwgeaekvfsrmeTKDAVSW 357

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  363 TVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPNFVVYSTLVSYLRKA 442
Cdd:PLN03077 358 TAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKC 437

                        330
                 ....*....|....*.
gi 15232243  443 GKLSEARKVIREMVKK 458
Cdd:PLN03077 438 KCIDKALEVFHNIPEK 453
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 151-453 3.25e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 59.11  E-value: 3.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  151 SYHLLMKIFAECGEYKAMWRLVDEMVQDGFPTTARTFNLLICSCGEAGLA-----------KQAVV--QF-------MKS 210
Cdd:PLN03081 191 SWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSAragqqlhccvlKTGVVgdTFvscalidMYS 270

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  211 K---------TFNYRPFKH--SYNAILN--SLLGVKQYKLIewVYKQMLEDGFSPDVLTYNILLWTNYRLGKMDRFDRLF 277
Cdd:PLN03081 271 KcgdiedarcVFDGMPEKTtvAWNSMLAgyALHGYSEEALC--LYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAH 348

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  278 DEMARDGFSPDsytynillhILGKgnkplaalttlnhmkevgidpsvlhyTTLIDGLSRAGNLEACKYFLDEMVkagcRP 357
Cdd:PLN03081 349 AGLIRTGFPLD---------IVAN--------------------------TALVDLYSKWGRMEDARNVFDRMP----RK 389

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  358 DVVCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMIRGLCMAGeFREACWLLKEMESR--GCNPNFVVYSTL 435
Cdd:PLN03081 390 NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSG-LSEQGWEIFQSMSEnhRIKPRAMHYACM 468

                        330
                 ....*....|....*...
gi 15232243  436 VSYLRKAGKLSEARKVIR 453
Cdd:PLN03081 469 IELLGREGLLDEAYAMIR 486
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 287-336 1.17e-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: 50.82  E-value: 1.17e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15232243   287 PDSYTYNILLHILGKGNKPLAALTTLNHMKEVGIDPSVLHYTTLIDGLSR 336
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 388-421 1.36e-08

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: 50.42  E-value: 1.36e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15232243   388 KGQLPNVFTYNSMIRGLCMAGEFREACWLLKEME 421
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 395-428 1.88e-08

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: 49.76  E-value: 1.88e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15232243   395 FTYNSMIRGLCMAGEFREACWLLKEMESRGCNPN 428
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 347-401 2.23e-08

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: 50.43  E-value: 2.23e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15232243   347 LDEMVKAGCRPDVVCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMI 401
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 275-331 2.34e-08

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: 50.43  E-value: 2.34e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15232243   275 RLFDEMARDGFSPDSYTYNILLHILGKGNKPLAALTTLNHMKEVGIDPSVLHYTTLI 331
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PLN03077 PLN03077
Protein ECB2; Provisional
 145-459 4.75e-08

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 55.63  E-value: 4.75e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  145 FRHTVNSYHLLMKIFAECGEYKAMWRLVDEMvqdgfPTTAR-TFNLLICSCGEAGLAKQAVVQFMKSKTFNYRPFKHSYN 223
Cdd:PLN03077 218 FELDVDVVNALITMYVKCGDVVSARLVFDRM-----PRRDCiSWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTIT 292

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  224 AILNSLLGVKQYKLIEWVYKQMLEDGFSPDVLTYNILLWTNYRLGKMDRFDRLFDEM-ARDGFS----PDSYTYNILlhi 298
Cdd:PLN03077 293 SVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMeTKDAVSwtamISGYEKNGL--- 369

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  299 lgkgnkPLAALTTLNHMKEVGIDPsvlhyttliDGLSRAGNLEACKYF--LDEMVK-------AGCRPDVVCYTVMITGY 369
Cdd:PLN03077 370 ------PDKALETYALMEQDNVSP---------DEITIASVLSACACLgdLDVGVKlhelaerKGLISYVVVANALIEMY 434

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  370 VVSGELDKAKEMFREMTVKgqlpNVFTYNSMIRGLCMAGEFREACWLLKEMESRgCNPNFVVYSTLVSYLRKAGKLSEAR 449
Cdd:PLN03077 435 SKCKCIDKALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIGALMCGK 509

                        330
                 ....*....|
gi 15232243  450 KVIREMVKKG 459
Cdd:PLN03077 510 EIHAHVLRTG 519
PLN03077 PLN03077
Protein ECB2; Provisional
 242-464 4.79e-08

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 55.63  E-value: 4.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  242 YKQMLEDgFSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGFSPDSYTYNILLHILGKGNKPLAALTTLN-HMKEVGi 320
Cdd:PLN03077 478 FRQMLLT-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNsHEKDVV- 555

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  321 dpsvlHYTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMITGYVVSGELDKAKEMFREMTVK-GQLPNVFTYNS 399
Cdd:PLN03077 556 -----SWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYAC 630

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15232243  400 MIRGLCMAGEFREACWLLKEMEsrgCNPNFVVYSTLVSYLR-----KAGKLseARKVIREMVKK--GHYVHL 464
Cdd:PLN03077 631 VVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACRihrhvELGEL--AAQHIFELDPNsvGYYILL 697
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 395-425 2.08e-07

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: 47.07  E-value: 2.08e-07
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15232243   395 FTYNSMIRGLCMAGEFREACWLLKEMESRGC 425
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 276-380 3.01e-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: 50.86  E-value: 3.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   276 LFDEMARDGFSPDSYTYNILLHILGKGNKPLAALTTLN---------HMKEVGIDPSVLHYTTLIDGLSRAGNLEACKYF 346
Cdd:pfam17177  33 LYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPQLAadrgfevfeAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDL 112

                          90       100       110
                  ....*....|....*....|....*....|....
gi 15232243   347 LDEMVKAGCRPDVVCYTVMITGYVVSGELDKAKE 380
Cdd:pfam17177 113 VKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYE 146
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 354-386 6.01e-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: 45.80  E-value: 6.01e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15232243   354 GCRPDVVCYTVMITGYVVSGELDKAKEMFREMT 386
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 327-359 1.84e-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: 44.37  E-value: 1.84e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15232243   327 YTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDV 359
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 221-261 3.41e-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: 43.89  E-value: 3.41e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 15232243   221 SYNAILNSLLGVKQYKLIEWVYKQMLEDGFSPDVLTYNILL 261
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILI 45
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 312-370 3.53e-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: 44.27  E-value: 3.53e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15232243   312 LNHMKEVGIDPSVLHYTTLIDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMITGYV 370
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 266-458 5.33e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 49.10  E-value: 5.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  266 RLGKMDRFDRLFD--EMARDG--FSPDSYTYNILLHILGKGNKPLAALTTLNHMKEVGIDPSVLHYTTLIDGLSRAGNLE 341
Cdd:PLN03081  96 KLVACGRHREALElfEILEAGcpFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLI 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243  342 ACKYFLDEMvkagcrPD--VVCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNVFTYNSMIR-----GLCMAGEFREAC 414
Cdd:PLN03081 176 DARRLFDEM------PErnLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRasaglGSARAGQQLHCC 249

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 15232243  415 WLlkemeSRGCNPNFVVYSTLVSYLRKAGKLSEARKVIREMVKK 458
Cdd:PLN03081 250 VL-----KTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEK 288
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 423-456 9.36e-06

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: 9.36e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15232243   423 RGCNPNFVVYSTLVSYLRKAGKLSEARKVIREMV 456
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 331-459 1.65e-05

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: 45.85  E-value: 1.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   331 IDGLSRAGNLEACKYFLDEMVKAGCRPDVVCYTVMItgYVVSG-----------ELDKAKEMFREMTVKGQLPNVFTYNS 399
Cdd:pfam17177  18 LDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLL--YLCSKaadatdlkpqlAADRGFEVFEAMKAQGVSPNEATYTA 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15232243   400 MIRgLCMA-GEFREACWLLKEMESRGCNPNFVVYSTLVSYLRKAGKLSEARKVIREMVKKG 459
Cdd:pfam17177  96 VAR-LAAAkGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHG 155
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 381-437 2.15e-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: 41.96  E-value: 2.15e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15232243   381 MFREMTVKGQLPNVFTYNSMIRGLCMAGEFREACWLLKEMESRGCNPNFVVYSTLVS 437
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 319-351 2.22e-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: 41.18  E-value: 2.22e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15232243   319 GIDPSVLHYTTLIDGLSRAGNL-EACKyFLDEMV 351
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVdEAFE-LLDEME 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 241-301 2.44e-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: 41.96  E-value: 2.44e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15232243   241 VYKQMLEDGFSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGFSPDSYTYNILLHILGK 301
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 360-389 3.39e-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: 40.53  E-value: 3.39e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 15232243   360 VCYTVMITGYVVSGELDKAKEMFREMTVKG 389
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 193-338 5.11e-05

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: 5.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   193 SCGEAGLAKQAVVQFMKSKTFNYRPFKHSYNAILN----------SLLGVKQYKLIEwVYKQMLEDGFSPDVLTYNILLw 262
Cdd:pfam17177  20 KCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYlcskaadatdLKPQLAADRGFE-VFEAMKAQGVSPNEATYTAVA- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   263 tnyRLGKMDR-FDRLFD---EMARDGFSPDSYTYNILLHILGKGNKPLAALTTLNHMKEVGIDPSVLHYTTLIDGLSRAG 338
Cdd:pfam17177  98 ---RLAAAKGdGDLAFDlvkEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAG 174
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 360-394 9.32e-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: 39.36  E-value: 9.32e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15232243   360 VCYTVMITGYVVSGELDKAKEMFREMTVKGQLPNV 394
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 171-288 4.70e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 42.94  E-value: 4.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232243   171 LVDEMVQDGFPTTARTFNLLICSCGEAGLAKQAVVQFMKSKTFNYRPFKHSYNAILNSLLGVKQY-KLIEwVYKQMLEDG 249
Cdd:PLN03218  671 ILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLpKALE-VLSEMKRLG 749

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 15232243   250 FSPDVLTYNILLWTNYRLGKMDRFDRLFDEMARDGFSPD 288
Cdd:PLN03218  750 LCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPN 788
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 327-355 8.75e-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: 36.67  E-value: 8.75e-04
                          10        20
                  ....*....|....*....|....*....
gi 15232243   327 YTTLIDGLSRAGNLEACKYFLDEMVKAGC 355
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 430-462 1.33e-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: 36.28  E-value: 1.33e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15232243   430 VVYSTLVSYLRKAGKLSEARKVIREMVKKGHYV 462
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 222-261 2.21e-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: 36.57  E-value: 2.21e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 15232243   222 YNAILNSLLGVKQYKLIEWVYKQMLEDGFSPDVLTYNILL 261
Cdd:pfam13812  18 YTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 220-254 2.83e-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: 35.12  E-value: 2.83e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15232243   220 HSYNAILNSLLGVKQYKLIEWVYKQMLEDGFSPDV 254
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 430-460 3.64e-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: 3.64e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15232243   430 VVYSTLVSYLRKAGKLSEARKVIREMVKKGH 460
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 148-194 4.26e-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: 35.03  E-value: 4.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15232243   148 TVNSYHLLMKIFAECGEYKAMWRLVDEMVQDGFPTTARTFNLLICSC 194
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 427-459 4.43e-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: 35.03  E-value: 4.43e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15232243   427 PNFVVYSTLVSYLRKAGKLSEARKVIREMVKKG 459
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRG 33
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 290-324 7.21e-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: 34.35  E-value: 7.21e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15232243   290 YTYNILLHILGKGNKPLAALTTLNHMKEVGIDPSV 324
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
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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