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Conserved domains on  [gi|1039010071|gb|ANM60058|]
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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

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
 69-534 1.72e-116

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: 359.57  E-value: 1.72e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  69 LKACARALCSSAMDQLHCQINRRGLSADSLLCTTLLDAYSKNGDLISAYKLFDEMPVRDVASWNALIAGLVSGNRASEAM 148
Cdd:PLN03081  231 LRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEAL 310

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 149 ELYKRMETEGIRRSEVTVVAALGACSHLGDVKEGEN-----IFHGYSNDnvIVSNAA-IDMYSKCGFVDKAYQVFEQFTg 222
Cdd:PLN03081  311 CLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQahaglIRTGFPLD--IVANTAlVDLYSKWGRMEDARNVFDRMP- 387

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 223 KKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNMA-CKGVERNMKHYGC 301
Cdd:PLN03081  388 RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSeNHRIKPRAMHYAC 467

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 302 VVDLLSRAGRLREAHDIICSMSMIPDPVLWQSLLGASEIYSDVEMAEIASREIKEMGVNNDGDFVLLSNVYAAQGRWKDV 381
Cdd:PLN03081  468 MIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEA 547

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 382 GRVRDDMESKQVKKIPGLSYIEAKGTIHEFYNSDKSHEQWREIYEKIDEIRFKIREDGYVAQTGLVLHDIGEEEKENALC 461
Cdd:PLN03081  548 AKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGR 627

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039010071 462 YHSEKLAVAYGLMmmdGADEESPVRVINNLRICGDCHVVFKHISKIYKREIIVRDRVRFHRFKDGSCSCRDFW 534
Cdd:PLN03081  628 YHSEKLAIAFGLI---NTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 69-534 1.72e-116

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 359.57  E-value: 1.72e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  69 LKACARALCSSAMDQLHCQINRRGLSADSLLCTTLLDAYSKNGDLISAYKLFDEMPVRDVASWNALIAGLVSGNRASEAM 148
Cdd:PLN03081  231 LRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEAL 310

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 149 ELYKRMETEGIRRSEVTVVAALGACSHLGDVKEGEN-----IFHGYSNDnvIVSNAA-IDMYSKCGFVDKAYQVFEQFTg 222
Cdd:PLN03081  311 CLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQahaglIRTGFPLD--IVANTAlVDLYSKWGRMEDARNVFDRMP- 387

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 223 KKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNMA-CKGVERNMKHYGC 301
Cdd:PLN03081  388 RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSeNHRIKPRAMHYAC 467

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 302 VVDLLSRAGRLREAHDIICSMSMIPDPVLWQSLLGASEIYSDVEMAEIASREIKEMGVNNDGDFVLLSNVYAAQGRWKDV 381
Cdd:PLN03081  468 MIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEA 547

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 382 GRVRDDMESKQVKKIPGLSYIEAKGTIHEFYNSDKSHEQWREIYEKIDEIRFKIREDGYVAQTGLVLHDIGEEEKENALC 461
Cdd:PLN03081  548 AKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGR 627

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039010071 462 YHSEKLAVAYGLMmmdGADEESPVRVINNLRICGDCHVVFKHISKIYKREIIVRDRVRFHRFKDGSCSCRDFW 534
Cdd:PLN03081  628 YHSEKLAIAFGLI---NTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 439-534 1.88e-40

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 141.41  E-value: 1.88e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 439 GYVAQTGLVLHDIGEEEKENALCYHSEKLAVAYGLMMM-DGAdeesPVRVINNLRICGDCHVVFKHISKIYKREIIVRDR 517
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTpDGA----TIRITKNLRVCGDCHTAFKYISKIRGREIVVRDA 76

                          90
                  ....*....|....*..
gi 1039010071 518 VRFHRFKDGSCSCRDFW 534
Cdd:pfam14432  77 SRFHHFKNGLCSCGDFW 93
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 227-261 8.69e-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: 42.44  E-value: 8.69e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1039010071 227 VTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDD 261
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 69-534 1.72e-116

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 359.57  E-value: 1.72e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  69 LKACARALCSSAMDQLHCQINRRGLSADSLLCTTLLDAYSKNGDLISAYKLFDEMPVRDVASWNALIAGLVSGNRASEAM 148
Cdd:PLN03081  231 LRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEAL 310

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 149 ELYKRMETEGIRRSEVTVVAALGACSHLGDVKEGEN-----IFHGYSNDnvIVSNAA-IDMYSKCGFVDKAYQVFEQFTg 222
Cdd:PLN03081  311 CLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQahaglIRTGFPLD--IVANTAlVDLYSKWGRMEDARNVFDRMP- 387

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 223 KKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNMA-CKGVERNMKHYGC 301
Cdd:PLN03081  388 RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSeNHRIKPRAMHYAC 467

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 302 VVDLLSRAGRLREAHDIICSMSMIPDPVLWQSLLGASEIYSDVEMAEIASREIKEMGVNNDGDFVLLSNVYAAQGRWKDV 381
Cdd:PLN03081  468 MIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEA 547

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 382 GRVRDDMESKQVKKIPGLSYIEAKGTIHEFYNSDKSHEQWREIYEKIDEIRFKIREDGYVAQTGLVLHDIGEEEKENALC 461
Cdd:PLN03081  548 AKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGR 627

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039010071 462 YHSEKLAVAYGLMmmdGADEESPVRVINNLRICGDCHVVFKHISKIYKREIIVRDRVRFHRFKDGSCSCRDFW 534
Cdd:PLN03081  628 YHSEKLAIAFGLI---NTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
PLN03077 PLN03077
Protein ECB2; Provisional
 61-532 9.45e-111

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 349.15  E-value: 9.45e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  61 DALTCSFTLKACAralCSSAMD---QLHCQINRRGLSADSLLCTTLLDAYSKNGDLISAYKLFDEMPVRDVASWNALIAG 137
Cdd:PLN03077  388 DEITIASVLSACA---CLGDLDvgvKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAG 464

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 138 LVSGNRASEAMELYKRMETEgIRRSEVTVVAALGACSHLGDVKEGENI----------FHGYsndnviVSNAAIDMYSKC 207
Cdd:PLN03077  465 LRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIGALMCGKEIhahvlrtgigFDGF------LPNALLDLYVRC 537

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 208 GFVDKAYQVFEqfTGKKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNM 287
Cdd:PLN03077  538 GRMNYAWNQFN--SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSM 615

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 288 ACK-GVERNMKHYGCVVDLLSRAGRLREAHDIICSMSMIPDPVLWQSLLGASEIYSDVEMAEIASREIKEMGVNNDGDFV 366
Cdd:PLN03077  616 EEKySITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYI 695

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 367 LLSNVYAAQGRWKDVGRVRDDMESKQVKKIPGLSYIEAKGTIHEFYNSDKSHEQWREIYEKIDEIRFKIREDGYVAQTGL 446
Cdd:PLN03077  696 LLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESS 775

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 447 VLHDIgEEEKENALCYHSEKLAVAYGLMmmdGADEESPVRVINNLRICGDCHVVFKHISKIYKREIIVRDRVRFHRFKDG 526
Cdd:PLN03077  776 SMDEI-EVSKDDIFCGHSERLAIAFGLI---NTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDG 851


                  ....*.
gi 1039010071 527 SCSCRD 532
Cdd:PLN03077  852 ECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 439-534 1.88e-40

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 141.41  E-value: 1.88e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 439 GYVAQTGLVLHDIGEEEKENALCYHSEKLAVAYGLMMM-DGAdeesPVRVINNLRICGDCHVVFKHISKIYKREIIVRDR 517
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTpDGA----TIRITKNLRVCGDCHTAFKYISKIRGREIVVRDA 76

                          90
                  ....*....|....*..
gi 1039010071 518 VRFHRFKDGSCSCRDFW 534
Cdd:pfam14432  77 SRFHHFKNGLCSCGDFW 93
PLN03077 PLN03077
Protein ECB2; Provisional
 7-339 1.73e-27

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 117.26  E-value: 1.73e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071   7 NQTTPISLP---HRRPFPIFLSPFSSSRTLRNLTIRRPFLRRTNFPqSSSSSAICRVDALTCSFTLKACARAL------- 76
Cdd:PLN03077    9 NPGKPNLFQlasHKAPNVLPYWNFHGRKRSRGLSVAASSSSSTHDS-NSQLRALCSHGQLEQALKLLESMQELrvpvded 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  77 CSSAMDQLhCQiNRRGLSADSLLCT---------------TLLDAYSKNGDLISAYKLFDEMPVRDVASWNALIAGLVSG 141
Cdd:PLN03077   88 AYVALFRL-CE-WKRAVEEGSRVCSralsshpslgvrlgnAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKA 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 142 NRASEAMELYKRMETEGIRRSEVTVVAALGACSHLGDVKEGENIF-----HGYSNDnVIVSNAAIDMYSKCGFVDKAYQV 216
Cdd:PLN03077  166 GYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHahvvrFGFELD-VDVVNALITMYVKCGDVVSARLV 244

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 217 FEQFTgKKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNMACKGVERNM 296
Cdd:PLN03077  245 FDRMP-RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDV 323

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 1039010071 297 KHYGCVVDLLSRAGRLREAHDIICSMSMiPDPVLWQSLLGASE 339
Cdd:PLN03077  324 SVCNSLIQMYLSLGSWGEAEKVFSRMET-KDAVSWTAMISGYE 365
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 341-403 4.47e-20

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: 83.75  E-value: 4.47e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039010071 341 YSDVEMAEIASREIKEMGVNNDGDFVLLSNVYAAQGRWKDVGRVRDDMESKQVKKIPGLSYIE 403
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 75-360 1.17e-18

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 89.94  E-value: 1.17e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071   75 ALCSSAMD-----QLHCQINRRGLSADSLLCTTLLDAYSKNGDLISAYKLFDEMPVR----DVASWNALIAGLVSGNRAS 145
Cdd:PLN03218   445 SVCASSQDidgalRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAgveaNVHTFGALIDGCARAGQVA 524

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  146 EAMELYkrmeteGIRRSEvtvvaalgacshlgDVKEGENIFhgysndnvivsNAAIDMYSKCGFVDKAYQVFEQFTG--- 222
Cdd:PLN03218   525 KAFGAY------GIMRSK--------------NVKPDRVVF-----------NALISACGQSGAVDRAFDVLAEMKAeth 573

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  223 --KKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNMACKGVERNMKHYG 300
Cdd:PLN03218   574 piDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFS 653

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039010071  301 CVVDLLSRAGRLREAHDIICSM---SMIPDPVLWQSLLGASEIYSDVEMAEIASREIKEMGVN 360
Cdd:PLN03218   654 ALVDVAGHAGDLDKAFEILQDArkqGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLR 716
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 61-308 1.54e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 73.76  E-value: 1.54e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071   61 DALTCSFTLKACARALCSSAMDQLHCQINRRGLSADSLLCTTLLDAYSKNGDLISAYKLFDEMPVRDVAS----WNALIA 136
Cdd:PLN03218   578 DHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPdevfFSALVD 657

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  137 GLVSGNRASEAMELYKRMETEGIRRSEVTVVAALGACSHLGDVKegenifhgysndnvivsnaaidmyskcgfvdKAYQV 216
Cdd:PLN03218   658 VAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWK-------------------------------KALEL 706

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071  217 FEQFTGKK---SVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNMACKGVE 293
Cdd:PLN03218   707 YEDIKSIKlrpTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIK 786

                          250
                   ....*....|....*
gi 1039010071  294 RNMKHYGCVVDLLSR 308
Cdd:PLN03218   787 PNLVMCRCITGLCLR 801
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 224-271 6.40e-09

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: 51.98  E-value: 6.40e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1039010071 224 KSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTAC 271
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 223-271 3.85e-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: 3.85e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1039010071 223 KKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTAC 271
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 227-261 8.69e-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: 42.44  E-value: 8.69e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1039010071 227 VTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDD 261
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 ...
 227-257 1.53e-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: 41.68  E-value: 1.53e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1039010071 227 VTWNTMITGFAVHGEAHRALEIFDKLEDNGI 257
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 ...
 96-138 5.00e-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: 5.00e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1039010071  96 DSLLCTTLLDAYSKNGDLISAYKLFDEMPVR----DVASWNALIAGL 138
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 ...
 126-165 8.85e-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: 40.04  E-value: 8.85e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1039010071 126 RDVASWNALIAGLVSGNRASEAMELYKRMETEGIRRSEVT 165
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 130-159 3.25e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.83  E-value: 3.25e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1039010071 130 SWNALIAGLVSGNRASEAMELYKRMETEGI 159
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 239-322 8.01e-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: 40.84  E-value: 8.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 239 HGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGL---------VEYGLSVFNNMACKGVERNMKHYGCVVDLLSRA 309
Cdd:pfam17177  24 HADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADatdlkpqlaADRGFEVFEAMKAQGVSPNEATYTAVARLAAAK 103

                          90
                  ....*....|...
gi 1039010071 310 GRLREAHDIICSM 322
Cdd:pfam17177 104 GDGDLAFDLVKEM 116
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 100-128 1.31e-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: 36.29  E-value: 1.31e-03
                          10        20
                  ....*....|....*....|....*....
gi 1039010071 100 CTTLLDAYSKNGDLISAYKLFDEMPVRDV 128
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 104-218 1.98e-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: 39.69  E-value: 1.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039010071 104 LDAYSKNGDLISAYKLFDEMPVRDVA----SWNALIAGLVSGNRASEAM---------ELYKRMETEGIRRSEVTVVAAL 170
Cdd:pfam17177  18 LDKCSKHADATGALALYDAAKAEGVRlaqyHYNVLLYLCSKAADATDLKpqlaadrgfEVFEAMKAQGVSPNEATYTAVA 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1039010071 171 GACSHLGDVKEGENIFHGYSNDNV---IVSNA-AIDMYSKCGFVDKAYQVFE 218
Cdd:pfam17177  98 RLAAAKGDGDLAFDLVKEMEAAGVsprLRSYSpALHAYCEAGDADKAYEVEE 149
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 130-163 2.05e-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: 35.89  E-value: 2.05e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1039010071 130 SWNALIAGLVSGNRASEAMELYKRMETEGIRRSE 163
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
Eplus_motif pfam20430
E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins ...
 408-431 3.52e-03

E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins which contain a C-terminal 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 th RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466579 [Multi-domain]  Cd Length: 28  Bit Score: 34.94  E-value: 3.52e-03
                          10        20
                  ....*....|....*....|....
gi 1039010071 408 IHEFYNSDKSHEQWREIYEKIDEI 431
Cdd:pfam20430   1 TYTFFAGDKSHPESKQIYEKLSDL 24
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 193-237 4.87e-03

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 35.03  E-value: 4.87e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1039010071 193 NVIVSNAAIDMYSKCGFVDKAYQVFEQFTGKK---SVVTWNTMITGFA 237
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGvkpNVYTYTILINGLC 49
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 91-123 6.46e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 34.24  E-value: 6.46e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1039010071  91 RGLSADSLLCTTLLDAYSKNGDLISAYKLFDEM 123
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 248-299 8.41e-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: 35.03  E-value: 8.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1039010071 248 IFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLSVFNNMACKGVERNMKHY 299
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTY 53
 
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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