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Conserved domains on  [gi|42570815|ref|NP_973481|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000098)

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

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
 111-349 2.37e-18

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 86.47  E-value: 2.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   111 ILKSQpNFRPGRSTFLILLShACrapdSSISNVHRVLNLMVNNGLE-----PDQVTTDIAVRSLCETGRVDEAKDLMKEL 185
Cdd:PLN03218  532 IMRSK-NVKPDRVVFNALIS-AC----GQSGAVDRAFDVLAEMKAEthpidPDHITVGALMKACANAGQVDRAKEVYQMI 605

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   186 TEKH--SPPDTYTynfLLKHLCKCK-DLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFK 262
Cdd:PLN03218  606 HEYNikGTPEVYT---IAVNSCSQKgDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK 681

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   263 PDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLM 342
Cdd:PLN03218  682 LGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL 761


                  ....*..
gi 42570815   343 NGMCRKG 349
Cdd:PLN03218  762 VASERKD 768
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 111-349 2.37e-18

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 86.47  E-value: 2.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   111 ILKSQpNFRPGRSTFLILLShACrapdSSISNVHRVLNLMVNNGLE-----PDQVTTDIAVRSLCETGRVDEAKDLMKEL 185
Cdd:PLN03218  532 IMRSK-NVKPDRVVFNALIS-AC----GQSGAVDRAFDVLAEMKAEthpidPDHITVGALMKACANAGQVDRAKEVYQMI 605

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   186 TEKH--SPPDTYTynfLLKHLCKCK-DLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFK 262
Cdd:PLN03218  606 HEYNikGTPEVYT---IAVNSCSQKgDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK 681

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   263 PDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLM 342
Cdd:PLN03218  682 LGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL 761


                  ....*..
gi 42570815   343 NGMCRKG 349
Cdd:PLN03218  762 VASERKD 768
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 298-347 6.78e-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: 65.08  E-value: 6.78e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 42570815   298 PDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCR 347
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 301-335 3.04e-07

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 46.29  E-value: 3.04e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42570815   301 ITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDT 335
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 111-349 2.37e-18

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 86.47  E-value: 2.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   111 ILKSQpNFRPGRSTFLILLShACrapdSSISNVHRVLNLMVNNGLE-----PDQVTTDIAVRSLCETGRVDEAKDLMKEL 185
Cdd:PLN03218  532 IMRSK-NVKPDRVVFNALIS-AC----GQSGAVDRAFDVLAEMKAEthpidPDHITVGALMKACANAGQVDRAKEVYQMI 605

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   186 TEKH--SPPDTYTynfLLKHLCKCK-DLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFK 262
Cdd:PLN03218  606 HEYNikGTPEVYT---IAVNSCSQKgDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK 681

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   263 PDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLM 342
Cdd:PLN03218  682 LGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL 761


                  ....*..
gi 42570815   343 NGMCRKG 349
Cdd:PLN03218  762 VASERKD 768
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 298-347 6.78e-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: 65.08  E-value: 6.78e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 42570815   298 PDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCR 347
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 164-346 1.36e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 71.83  E-value: 1.36e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   164 IAVRSLCETGRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCNS 243
Cdd:PLN03218  619 IAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQ-GIKLGTVSYSSLMGACSNA 697

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   244 KNLREAMYLVSKLGNAGFKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYL 323
Cdd:PLN03218  698 KNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLL 777

                         170       180
                  ....*....|....*....|...
gi 42570815   324 KTMVDAGYEPDTATYTSLMnGMC 346
Cdd:PLN03218  778 SQAKEDGIKPNLVMCRCIT-GLC 799
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 263-312 1.06e-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: 1.06e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 42570815   263 PDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSK 312
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 120-346 1.90e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 68.36  E-value: 1.90e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   120 PGRSTFLILLSHACRAPDssISNVHRVLNLMVNNGLEPDQV--TTDIavrSLC-ETGRVDEAKDLMKELTEKHSPPDTYT 196
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQD--IDGALRVLRLVQEAGLKADCKlyTTLI---STCaKSGKVDAMFEVFHEMVNAGVEANVHT 509

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   197 YNFLLKHLCKCKDLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAG--FKPDCFLYNTIMKG 274
Cdd:PLN03218  510 FGALIDGCARAGQVAKAFGAYGIMRSK-NVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKA 588

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   275 FCTLS-----------------KGSEAV------------------GVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEA 319
Cdd:PLN03218  589 CANAGqvdrakevyqmiheyniKGTPEVytiavnscsqkgdwdfalSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKA 668

                         250       260
                  ....*....|....*....|....*..
gi 42570815   320 RMYLKTMVDAGYEPDTATYTSLMnGMC 346
Cdd:PLN03218  669 FEILQDARKQGIKLGTVSYSSLM-GAC 694
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 107-349 7.84e-12

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 66.43  E-value: 7.84e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  107 LFQhILKSQPNFRPGRSTFLILLSHACRApdSSISNVHRVLNLMVNNGLEPDQVTTDIAVRSLCETGRVDEAKDLMKELT 186
Cdd:PLN03081 109 LFE-ILEAGCPFTLPASTYDALVEACIAL--KSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMP 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  187 EKhsppDTYTYNFLLKHLCKCKDLHVVYEFVDEMRDDFDvKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFKPDCF 266
Cdd:PLN03081 186 ER----NLASWGTIIGGLVDAGNYREAFALFREMWEDGS-DAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTF 260

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  267 L-------------------------------YNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGR 315
Cdd:PLN03081 261 VscalidmyskcgdiedarcvfdgmpekttvaWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLAL 340

                        250       260       270
                 ....*....|....*....|....*....|....
gi 42570815  316 VEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKG 349
Cdd:PLN03081 341 LEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWG 374
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 192-242 6.75e-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: 53.91  E-value: 6.75e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 42570815   192 PDTYTYNFLLKHLCKCKDLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCN 242
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKR-GVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 84-349 1.94e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 59.09  E-value: 1.94e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   84 DLKFHNSVLQSYGSIAVVNDTVKLFqhilkSQPNFRPGRS-TFLILLSHACRAPDSSISnvhrVLNLMVNNGLEPDQVTT 162
Cdd:PLN03077 322 DVSVCNSLIQMYLSLGSWGEAEKVF-----SRMETKDAVSwTAMISGYEKNGLPDKALE----TYALMEQDNVSPDEITI 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  163 dIAVRSLCET-GRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDLHVVYEFVDEMRDDfdvkpDLVSFTILIDNVC 241
Cdd:PLN03077 393 -ASVLSACAClGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK-----DVISWTSIIAGLR 466

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  242 NSKNLREAMY---------------LVSKL------------------------GNAGFKPDCFL--------------- 267
Cdd:PLN03077 467 LNNRCFEALIffrqmlltlkpnsvtLIAALsacarigalmcgkeihahvlrtgiGFDGFLPNALLdlyvrcgrmnyawnq 546

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  268 ----------YNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTM-VDAGYEPDTA 336
Cdd:PLN03077 547 fnshekdvvsWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMeEKYSITPNLK 626

                        330
                 ....*....|...
gi 42570815  337 TYTSLMNGMCRKG 349
Cdd:PLN03077 627 HYACVVDLLGRAG 639
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 157-206 1.87e-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: 50.05  E-value: 1.87e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 42570815   157 PDQVTTDIAVRSLCETGRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCK 206
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 192-349 2.54e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 55.65  E-value: 2.54e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   192 PDTYTYNFLLKHLCKCKDLHVVYEfVDEMRDDFDVKPDLVSFTILIdNVCNSKNLREAMYLV-SKLGNAGFKPDCFLYNT 270
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQDIDGALR-VLRLVQEAGLKADCKLYTTLI-STCAKSGKVDAMFEVfHEMVNAGVEANVHTFGA 512

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   271 IMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGY--EPDTATYTSLMNGMCRK 348
Cdd:PLN03218  513 LIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHpiDPDHITVGALMKACANA 592


                  .
gi 42570815   349 G 349
Cdd:PLN03218  593 G 593
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 294-327 4.00e-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: 48.50  E-value: 4.00e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 42570815   294 EGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMV 327
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 301-335 3.04e-07

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 46.29  E-value: 3.04e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42570815   301 ITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDT 335
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 266-299 2.68e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 43.60  E-value: 2.68e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 42570815   266 FLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPD 299
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 301-330 1.44e-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: 1.44e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 42570815   301 ITYNTLIFGLSKAGRVEEARMYLKTMVDAG 330
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 252-307 4.30e-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: 40.80  E-value: 4.30e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 42570815   252 LVSKLGNAGFKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLI 307
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 99-228 8.80e-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: 43.15  E-value: 8.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815    99 AVVNDTVKLFQHILksqpnfrpgrSTFLILLSHACRAPDS----SISNVHRVLNLMVNNGLEPDQVTTDIAVRSLCETGR 174
Cdd:pfam17177  36 AAKAEGVRLAQYHY----------NVLLYLCSKAADATDLkpqlAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGD 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 42570815   175 VDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDLHVVYEfVDEMRDDFDVKP 228
Cdd:pfam17177 106 GDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYE-VEEHMLAHGVEL 158
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 173-349 9.79e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 44.09  E-value: 9.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  173 GRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDL-HVVYEFVDEMRDDFDVkpDLVSFTILIDNVCNSKNLREAMY 251
Cdd:PLN03081 304 GYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLeHAKQAHAGLIRTGFPL--DIVANTALVDLYSKWGRMEDARN 381

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  252 LVSKLGnagfKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEA-RMYLKTMVDAG 330
Cdd:PLN03081 382 VFDRMP----RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGwEIFQSMSENHR 457

                        170
                 ....*....|....*....
gi 42570815  331 YEPDTATYTSLMNGMCRKG 349
Cdd:PLN03081 458 IKPRAMHYACMIELLGREG 476
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 266-296 1.50e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 38.60  E-value: 1.50e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 42570815   266 FLYNTIMKGFCTLSKGSEAVGVYKKMKEEGV 296
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 192-221 4.12e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 37.33  E-value: 4.12e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 42570815   192 PDTYTYNFLLKHLCKCKDLHVVYEFVDEMR 221
Cdd:pfam12854   5 PDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 217-275 4.17e-04

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 38.11  E-value: 4.17e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 42570815   217 VDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFKPDCFLYNTIMKGF 275
Cdd:pfam13812   3 LREMVRD-GIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 330-349 5.12e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 36.94  E-value: 5.12e-04
                          10        20
                  ....*....|....*....|
gi 42570815   330 GYEPDTATYTSLMNGMCRKG 349
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAG 21
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 284-341 6.76e-04

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 40.46  E-value: 6.76e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42570815   284 AVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYL---------KTMVDAGYEPDTATYTSL 341
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPQLaadrgfevfEAMKAQGVSPNEATYTAV 96
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 153-184 7.96e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 36.55  E-value: 7.96e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 42570815   153 NGLEPDQVTTDIAVRSLCETGRVDEAKDLMKE 184
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDE 32
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 260-292 9.70e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 36.17  E-value: 9.70e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42570815   260 GFKPDCFLYNTIMKGFCtlSKG--SEAVGVYKKMK 292
Cdd:pfam12854   2 GLKPDVVTYNTLINGLC--RAGrvDEAFELLDEME 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 287-349 1.82e-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: 39.30  E-value: 1.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42570815   287 VYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMNGMCRKG 349
Cdd:pfam17177  77 VFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAG 139
PLN03077 PLN03077
Protein ECB2; Provisional
 153-334 2.37e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 39.83  E-value: 2.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  153 NGLEPDQVTTDIAVRSLCETGRVDEAKDLMKELTEKHSPPDTYTYNFLLkhlCKCKDLHVV---YEFVDEMRDDFDVKPD 229
Cdd:PLN03077 548 NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLL---CACSRSGMVtqgLEYFHSMEEKYSITPN 624

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  230 LVSFTILIDNVCNSKNLREAMYLVSKLgnaGFKPDCFLYNTIMKGfCTLSKGSEAVGVYKKMKEEgVEPDQITYNTLIFG 309
Cdd:PLN03077 625 LKHYACVVDLLGRAGKLTEAYNFINKM---PITPDPAVWGALLNA-CRIHRHVELGELAAQHIFE-LDPNSVGYYILLCN 699

                        170       180
                 ....*....|....*....|....*.
gi 42570815  310 L-SKAGRVEEARMYLKTMVDAGYEPD 334
Cdd:PLN03077 700 LyADAGKWDEVARVRKTMRENGLTVD 725
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 287-343 2.60e-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: 2.60e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 42570815   287 VYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSLMN 343
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 195-229 2.90e-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: 34.74  E-value: 2.90e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42570815   195 YTYNFLLKHLCKCKDLHVVYEFVDEMRDDfDVKPD 229
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKER-GIEPD 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 195-341 4.16e-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: 38.15  E-value: 4.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   195 YTYNFLLkHLC----------KCKDLHVVYEFVDEMRDDfDVKPDLVSFTILIDNVCNSKNLREAMYLVSKLGNAGFKPD 264
Cdd:pfam17177  47 YHYNVLL-YLCskaadatdlkPQLAADRGFEVFEAMKAQ-GVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPR 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42570815   265 CFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLSKAGRVEEARMYLKTMVDAGYEPDTATYTSL 341
Cdd:pfam17177 125 LRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAYLHRLRDAVRQVSESTAGVL 201
PLN03077 PLN03077
Protein ECB2; Provisional
 5-342 6.63e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 38.29  E-value: 6.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815    5 PSSFRSMPANLLVRKTTPSP-PAPPRDFR-NRTAVGGDSAKLPQNTQAPREPSLRNPFKSPNLSDAKSLFNSIAATsRIP 82
Cdd:PLN03077   5 HFYLNPGKPNLFQLASHKAPnVLPYWNFHgRKRSRGLSVAASSSSSTHDSNSQLRALCSHGQLEQALKLLESMQEL-RVP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815   83 LDLKFHNSVLQSYGSIAVVNDTVKLFQHILKSQPNF--RPGRStfliLLSHACRAPDssISNVHRVLNLMVnnglEPDQV 160
Cdd:PLN03077  84 VDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLgvRLGNA----MLSMFVRFGE--LVHAWYVFGKMP----ERDLF 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  161 TTDIAVRSLCETGRVDEAKDLMKELTEKHSPPDTYTYNFLLKHLCKCKDL--------HVV-YEFvdemRDDFDVKPDLV 231
Cdd:PLN03077 154 SWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLargrevhaHVVrFGF----ELDVDVVNALI 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570815  232 SFTILIDNVCNSKNLREAMYlvsklgnagfKPDCFLYNTIMKGFCTLSKGSEAVGVYKKMKEEGVEPDQITYNTLIFGLS 311
Cdd:PLN03077 230 TMYVKCGDVVSARLVFDRMP----------RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACE 299

                        330       340       350
                 ....*....|....*....|....*....|.
gi 42570815  312 KAGRVEEARMYLKTMVDAGYEPDTATYTSLM 342
Cdd:PLN03077 300 LLGDERLGREMHGYVVKTGFAVDVSVCNSLI 330
 
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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