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Conserved domains on  [gi|15234984|ref|NP_194257|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000225)

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

Gene Ontology:  GO:0003723|GO:0009451
PubMed:  24471833|19004664

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
 59-525 8.57e-102

pentatricopeptide (PPR) repeat-containing protein; Provisional


The actual alignment was detected with superfamily member PLN03081:

Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 321.43  E-value: 8.57e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   59 IEKQSIHRTQLEALDsvitdLETSAQKGISLTEP-EIFASLLETCYSLRAIDHGVRVHHLIPPYLLRNNLGISSKLVRLY 137
Cdd:PLN03081  94 IEKLVACGRHREALE-----LFEILEAGCPFTLPaSTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMH 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  138 ASCGYAEVAHEVFDRMSKRdsSPFAWNSLISGYAELGQYEDAMALYFQMAEDGVKPDRFTFPRVLKACGGIGSVQIGEAI 217
Cdd:PLN03081 169 VKCGMLIDARRLFDEMPER--NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQL 246

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  218 HRDLVKEGFGYDVYVLNALVVMYAKCGDIVKARNVFDMIPHKDYVSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPDKV 297
Cdd:PLN03081 247 HCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQF 326

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  298 AISSVL---ARVLSFKHGRQLHGWVIRRGMEWELSVANALIVLYSKRGQLGQACFIFDQMLERDTVSWNAIISA---HSK 371
Cdd:PLN03081 327 TFSIMIrifSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGygnHGR 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  372 NSNGLKYFEQMHRANAKPDGITFVSVLSLCANTGMVEDGERLFSLMSKEYGIDPKMEHYACMVNLYGRAGMMEEAYSMIv 451
Cdd:PLN03081 407 GTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMI- 485

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15234984  452 QEMGLEAGPTVWGALLYACYLHGNTDIGEVAAQRLFELEPDNEHNFELLIRIYSKAKRAEDVERVRQMMVDRGL 525
Cdd:PLN03081 486 RRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGL 559
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 59-525 8.57e-102

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 321.43  E-value: 8.57e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   59 IEKQSIHRTQLEALDsvitdLETSAQKGISLTEP-EIFASLLETCYSLRAIDHGVRVHHLIPPYLLRNNLGISSKLVRLY 137
Cdd:PLN03081  94 IEKLVACGRHREALE-----LFEILEAGCPFTLPaSTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMH 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  138 ASCGYAEVAHEVFDRMSKRdsSPFAWNSLISGYAELGQYEDAMALYFQMAEDGVKPDRFTFPRVLKACGGIGSVQIGEAI 217
Cdd:PLN03081 169 VKCGMLIDARRLFDEMPER--NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQL 246

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  218 HRDLVKEGFGYDVYVLNALVVMYAKCGDIVKARNVFDMIPHKDYVSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPDKV 297
Cdd:PLN03081 247 HCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQF 326

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  298 AISSVL---ARVLSFKHGRQLHGWVIRRGMEWELSVANALIVLYSKRGQLGQACFIFDQMLERDTVSWNAIISA---HSK 371
Cdd:PLN03081 327 TFSIMIrifSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGygnHGR 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  372 NSNGLKYFEQMHRANAKPDGITFVSVLSLCANTGMVEDGERLFSLMSKEYGIDPKMEHYACMVNLYGRAGMMEEAYSMIv 451
Cdd:PLN03081 407 GTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMI- 485

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15234984  452 QEMGLEAGPTVWGALLYACYLHGNTDIGEVAAQRLFELEPDNEHNFELLIRIYSKAKRAEDVERVRQMMVDRGL 525
Cdd:PLN03081 486 RRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGL 559
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 473-526 3.04e-10

E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466580 [Multi-domain]  Cd Length: 63  Bit Score: 56.01  E-value: 3.04e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15234984   473 HGNTDIGEVAAQRLFELEPDNEHNFELLIRIYSKAKRAEDVERVRQMMVDRGLE 526
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIK 54
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 262-295 3.87e-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: 3.87e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15234984   262 VSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPD 295
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 59-525 8.57e-102

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 321.43  E-value: 8.57e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   59 IEKQSIHRTQLEALDsvitdLETSAQKGISLTEP-EIFASLLETCYSLRAIDHGVRVHHLIPPYLLRNNLGISSKLVRLY 137
Cdd:PLN03081  94 IEKLVACGRHREALE-----LFEILEAGCPFTLPaSTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMH 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  138 ASCGYAEVAHEVFDRMSKRdsSPFAWNSLISGYAELGQYEDAMALYFQMAEDGVKPDRFTFPRVLKACGGIGSVQIGEAI 217
Cdd:PLN03081 169 VKCGMLIDARRLFDEMPER--NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQL 246

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  218 HRDLVKEGFGYDVYVLNALVVMYAKCGDIVKARNVFDMIPHKDYVSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPDKV 297
Cdd:PLN03081 247 HCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQF 326

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  298 AISSVL---ARVLSFKHGRQLHGWVIRRGMEWELSVANALIVLYSKRGQLGQACFIFDQMLERDTVSWNAIISA---HSK 371
Cdd:PLN03081 327 TFSIMIrifSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGygnHGR 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  372 NSNGLKYFEQMHRANAKPDGITFVSVLSLCANTGMVEDGERLFSLMSKEYGIDPKMEHYACMVNLYGRAGMMEEAYSMIv 451
Cdd:PLN03081 407 GTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMI- 485

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15234984  452 QEMGLEAGPTVWGALLYACYLHGNTDIGEVAAQRLFELEPDNEHNFELLIRIYSKAKRAEDVERVRQMMVDRGL 525
Cdd:PLN03081 486 RRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGL 559
PLN03077 PLN03077
Protein ECB2; Provisional
 97-526 1.17e-95

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 309.09  E-value: 1.17e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   97 SLLETCYSLRAIDHGVRVHHLIPPYLLRNNLGISSKLVRLYASCGYAEVAHEVFDRMSKRDSspFAWNSLISGYAELGQY 176
Cdd:PLN03077 293 SVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDA--VSWTAMISGYEKNGLP 370

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  177 EDAMALYFQMAEDGVKPDRFTFPRVLKACGGIGSVQIGEAIHRDLVKEGFGYDVYVLNALVVMYAKCGDIVKARNVFDMI 256
Cdd:PLN03077 371 DKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNI 450

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  257 PHKDYVSWNSMLTGYLHHGLLHEALDIFRLMVQNgIEPDKVAISSVL---ARVLSFKHGRQLHGWVIRRGMEWELSVANA 333
Cdd:PLN03077 451 PEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALsacARIGALMCGKEIHAHVLRTGIGFDGFLPNA 529

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  334 LIVLYSKRGQLGQACFIFDQMlERDTVSWNAIISAHSKNSNG---LKYFEQMHRANAKPDGITFVSVLSLCANTGMVEDG 410
Cdd:PLN03077 530 LLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGsmaVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQG 608

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  411 ERLFSLMSKEYGIDPKMEHYACMVNLYGRAGMMEEAYSMIvQEMGLEAGPTVWGALLYACYLHGNTDIGEVAAQRLFELE 490
Cdd:PLN03077 609 LEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFI-NKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELD 687

                        410       420       430
                 ....*....|....*....|....*....|....*.
gi 15234984  491 PDNEHNFELLIRIYSKAKRAEDVERVRQMMVDRGLE 526
Cdd:PLN03077 688 PNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLT 723
PLN03077 PLN03077
Protein ECB2; Provisional
 164-446 2.15e-40

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 156.16  E-value: 2.15e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  164 NSLISGYAELGQYEDAMALYFQMAEDGVKPDRFTFPRVLKACGGIGSVQIGEAIHRDLVKEGFGYDVYVLNALVVMYAKC 243
Cdd:PLN03077  55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRF 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  244 GDIVKARNVFDMIPHKDYVSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPDKVAISSVL---ARVLSFKHGRQLHGWVI 320
Cdd:PLN03077 135 GELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLrtcGGIPDLARGREVHAHVV 214

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984  321 RRGMEWELSVANALIVLYSKRGQLGQACFIFDQMLERDTVSWNAIISAHSKNS---NGLKYFEQMHRANAKPDGITFVSV 397
Cdd:PLN03077 215 RFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGeclEGLELFFTMRELSVDPDLMTITSV 294

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 15234984  398 LSLCANTGMVEDGERLFSLMSKEyGIDPKMEHYACMVNLYGRAGMMEEA 446
Cdd:PLN03077 295 ISACELLGDERLGREMHGYVVKT-GFAVDVSVCNSLIQMYLSLGSWGEA 342
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 95-436 3.17e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.60  E-value: 3.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984    95 FASLLETCYSLRAIDHGVRVHHLIPPYLLRNNLGISSKLVRLYASCGYAEVAHEVFDRMSKRDSSP--FAWNSLISGYAE 172
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEAnvHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   173 LGQYEDAMALYFQMAEDGVKPDRFTFPRVLKACGGIGSVQIGEAIHRDLVKEG--FGYDVYVLNALVVMYAKCGDIVKAR 250
Cdd:PLN03218  520 AGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAK 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   251 NVFDMIPHKDYVSWNSMLTGYLHH----GLLHEALDIFRLMVQNGIEPDKVAISsvlARVLSFKHGRQLH-GWVI----- 320
Cdd:PLN03218  600 EVYQMIHEYNIKGTPEVYTIAVNScsqkGDWDFALSIYDDMKKKGVKPDEVFFS---ALVDVAGHAGDLDkAFEIlqdar 676

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   321 RRGMEWELSVANALIVLYSKRGQLGQACFIFDQ---MLERDTVS-WNAIISAHSKNSNGLKYFE---QMHRANAKPDGIT 393
Cdd:PLN03218  677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDiksIKLRPTVStMNALITALCEGNQLPKALEvlsEMKRLGLCPNTIT 756

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 15234984   394 FVSVLSLCANTGMVEDGERLFSlMSKEYGIDPKMEHYACMVNL 436
Cdd:PLN03218  757 YSILLVASERKDDADVGLDLLS-QAKEDGIKPNLVMCRCITGL 798
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 473-526 3.04e-10

E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466580 [Multi-domain]  Cd Length: 63  Bit Score: 56.01  E-value: 3.04e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15234984   473 HGNTDIGEVAAQRLFELEPDNEHNFELLIRIYSKAKRAEDVERVRQMMVDRGLE 526
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIK 54
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 259-303 3.08e-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: 49.67  E-value: 3.08e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 15234984   259 KDYVSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPDKVAISSVL 303
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILI 45
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 161-198 1.18e-07

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: 48.13  E-value: 1.18e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 15234984   161 FAWNSLISGYAELGQYEDAMALYFQMAEDGVKPDRFTF 198
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 262-295 3.87e-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: 3.87e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15234984   262 VSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPD 295
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 ...
 262-292 1.16e-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.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 44.76  E-value: 1.16e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15234984   262 VSWNSMLTGYLHHGLLHEALDIFRLMVQNGI 292
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 161-194 3.00e-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: 43.98  E-value: 3.00e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15234984   161 FAWNSLISGYAELGQYEDAMALYFQMAEDGVKPD 194
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 339-447 3.04e-06

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: 48.16  E-value: 3.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   339 SKRGQLGQACFIFDQMLERDTV----SWNAIISAHSKNS------------NGLKYFEQMHRANAKPDGITFVSVLSLCA 402
Cdd:pfam17177  22 SKHADATGALALYDAAKAEGVRlaqyHYNVLLYLCSKAAdatdlkpqlaadRGFEVFEAMKAQGVSPNEATYTAVARLAA 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 15234984   403 NTGmveDGERLFSLMS--KEYGIDPKMEHYACMVNLYGRAGMMEEAY 447
Cdd:pfam17177 102 AKG---DGDLAFDLVKemEAAGVSPRLRSYSPALHAYCEAGDADKAY 145
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 161-191 2.20e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 41.30  E-value: 2.20e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15234984   161 FAWNSLISGYAELGQYEDAMALYFQMAEDGV 191
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 379-438 4.29e-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: 41.57  E-value: 4.29e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   379 FEQMHRANAKPDGITFVSVLSLCANTGMVEDGERLFSLMsKEYGIDPKMEHYACMVNLYG 438
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERM-KKKGIKPTLDTYNAILGVIG 61
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 357-403 4.84e-05

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.81  E-value: 4.84e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15234984   357 RDTVSWNAIISAHSKNSNG---LKYFEQMHRANAKPDGITFVSVLSLCAN 403
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVeeaFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 149-207 6.18e-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: 6.18e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15234984   149 VFDRMSKRDSSP--FAWNSLISGYAELGQYEDAMALYFQMAEDGVKPDRFTFPRVLKACGG 207
Cdd:pfam13812   2 ILREMVRDGIQLnvNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 104-470 6.31e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 46.02  E-value: 6.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   104 SLRAIDHGVRVHHLIPPYLLRNNLGISSKLVRLYASCGYAEVAHEVFDRMSKRDSSPFAWNSL-ISGYAEL---GQYEDA 179
Cdd:PLN03218  310 NVKGLRKGVSSATNSLSLDKKNNGVKDAELPGQSSGQAASDVEEENSLAAYNGGVSGKRKSPEyIDAYNRLlrdGRIKDC 389

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   180 MALYFQMAEDG-VKPDRFTFPRVLKACGGIGSVqigeaihrdlvKEGFGYDVYVLNA-------LVVMYAKCGDIVKARN 251
Cdd:PLN03218  390 IDLLEDMEKRGlLDMDKIYHAKFFKACKKQRAV-----------KEAFRFAKLIRNPtlstfnmLMSVCASSQDIDGALR 458

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   252 VFDMIPHK----DYVSWNSMLTGYLHHGLLHEALDIFRLMVQNGIEPDkvaissvlarvlsfkhgrqLHGWvirrgmewe 327
Cdd:PLN03218  459 VLRLVQEAglkaDCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEAN-------------------VHTF--------- 510

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   328 lsvaNALIVLYSKRGQLGQACFIFDQMLER----DTVSWNAIISAHSKNSNGLKYFEQMHRANA-----KPDGITFVSVL 398
Cdd:PLN03218  511 ----GALIDGCARAGQVAKAFGAYGIMRSKnvkpDRVVFNALISACGQSGAVDRAFDVLAEMKAethpiDPDHITVGALM 586

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234984   399 SLCANTGMVEDGERLFSLMsKEYGIDPKMEHY-----AC------------------------------MVNLYGRAGMM 443
Cdd:PLN03218  587 KACANAGQVDRAKEVYQMI-HEYNIKGTPEVYtiavnSCsqkgdwdfalsiyddmkkkgvkpdevffsaLVDVAGHAGDL 665

                         410       420       430
                  ....*....|....*....|....*....|
gi 15234984   444 EEAYSmIVQEM---GLEAGPTVWGALLYAC 470
Cdd:PLN03218  666 DKAFE-ILQDArkqGIKLGTVSYSSLMGAC 694
 
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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