NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1063699304|ref|NP_850342|]
View 

pentatricopeptide (PPR) repeat 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

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
 9-650 4.38e-150

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: 450.48  E-value: 4.38e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304   9 VRPLSVDPATAIATLCSKGNLREAFQRFRL----NIFT-NTSLFTPFIQSCTTRQSLPSGKQLHCLLVVSGFSSDKFICN 83
Cdd:PLN03081   83 IRKSGVSLCSQIEKLVACGRHREALELFEIleagCPFTlPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  84 HLMSMYsklgdfpsavavygrmrkknymssnilingyVRAGDLVNARKVFDEMPDRKLTTWNAMIAGLIQFEFNEEGLSL 163
Cdd:PLN03081  163 RVLLMH-------------------------------VKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFAL 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 164 FREMHGLGFSPDEYTLGSVFSGSAGLRSVSIGQQIHGYTIKYGLELDLVVNSSLAHMYMRNGKLQDGEIVIRSMPVRNLV 243
Cdd:PLN03081  212 FREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTV 291

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 244 AWNTLIMGNAQNGCPETVLYLYKMMKISGCRPNKITFVTVLSSCSDLAIRGQGQQIHAEAIKIGASSVVAVVSSLISMYS 323
Cdd:PLN03081  292 AWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYS 371

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 324 KCGCLGDAAKAFSEREDEDEVMWSSMISAYGFHGQGDEAIELFNTMAEQtNMEINEVAFLNLLYACSHSGLKDKGLELFD 403
Cdd:PLN03081  372 KWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAE-GVAPNHVTFLAVLSACRYSGLSEQGWEIFQ 450

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 404 MMVEKYGFKPGLKHYTCVVDLLGRAGCLDQAEAIIRSMPIKTDIVIWKTLLSACNIHKNAEMAQRVFKEILQIDPNDSAC 483
Cdd:PLN03081  451 SMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNN 530

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 484 YVLLANVHASAKRWRDVSEVRKSMRDKNVKKEAGISWFEHKGEVHQFKMGDRSQSKSKEIYSYLKELTLEMKLKGYKPDT 563
Cdd:PLN03081  531 YVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEE 610

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 564 ASVLHDMDEEEKESDLVQHSEKLAVAFALMILPEGAPIRIIKNLRVCSDCHVAFKYISVIKNREITLRDGSRFHHFINGK 643
Cdd:PLN03081  611 NELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGK 690


                  ....*..
gi 1063699304 644 CSCGDYW 650
Cdd:PLN03081  691 CSCGDYW 697
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 9-650 4.38e-150

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 450.48  E-value: 4.38e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304   9 VRPLSVDPATAIATLCSKGNLREAFQRFRL----NIFT-NTSLFTPFIQSCTTRQSLPSGKQLHCLLVVSGFSSDKFICN 83
Cdd:PLN03081   83 IRKSGVSLCSQIEKLVACGRHREALELFEIleagCPFTlPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  84 HLMSMYsklgdfpsavavygrmrkknymssnilingyVRAGDLVNARKVFDEMPDRKLTTWNAMIAGLIQFEFNEEGLSL 163
Cdd:PLN03081  163 RVLLMH-------------------------------VKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFAL 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 164 FREMHGLGFSPDEYTLGSVFSGSAGLRSVSIGQQIHGYTIKYGLELDLVVNSSLAHMYMRNGKLQDGEIVIRSMPVRNLV 243
Cdd:PLN03081  212 FREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTV 291

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 244 AWNTLIMGNAQNGCPETVLYLYKMMKISGCRPNKITFVTVLSSCSDLAIRGQGQQIHAEAIKIGASSVVAVVSSLISMYS 323
Cdd:PLN03081  292 AWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYS 371

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 324 KCGCLGDAAKAFSEREDEDEVMWSSMISAYGFHGQGDEAIELFNTMAEQtNMEINEVAFLNLLYACSHSGLKDKGLELFD 403
Cdd:PLN03081  372 KWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAE-GVAPNHVTFLAVLSACRYSGLSEQGWEIFQ 450

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 404 MMVEKYGFKPGLKHYTCVVDLLGRAGCLDQAEAIIRSMPIKTDIVIWKTLLSACNIHKNAEMAQRVFKEILQIDPNDSAC 483
Cdd:PLN03081  451 SMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNN 530

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 484 YVLLANVHASAKRWRDVSEVRKSMRDKNVKKEAGISWFEHKGEVHQFKMGDRSQSKSKEIYSYLKELTLEMKLKGYKPDT 563
Cdd:PLN03081  531 YVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEE 610

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 564 ASVLHDMDEEEKESDLVQHSEKLAVAFALMILPEGAPIRIIKNLRVCSDCHVAFKYISVIKNREITLRDGSRFHHFINGK 643
Cdd:PLN03081  611 NELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGK 690


                  ....*..
gi 1063699304 644 CSCGDYW 650
Cdd:PLN03081  691 CSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 558-650 1.20e-46

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: 159.51  E-value: 1.20e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 558 GYKPDTASVLHDMDEEEKESDLVQHSEKLAVAFALMILPEGAPIRIIKNLRVCSDCHVAFKYISVIKNREITLRDGSRFH 637
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 1063699304 638 HFINGKCSCGDYW 650
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 357-499 6.95e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 48.19  E-value: 6.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 357 GQGDEAIELFNTMAEQTnmEINEVAFLNLLYACSHSGLKDKGLELFDMMVEKYGFKPglKHYTCVVDLLGRAG----CLD 432
Cdd:COG2956    56 GEYDRAIRIHQKLLERD--PDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDA--EALRLLAEIYEQEGdwekAIE 131

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063699304 433 QAEAIIRSMPikTDIVIWKTLLSACNIHKNAEMAQRVFKEILQIDPNDSACYVLLANVHASAKRWRD 499
Cdd:COG2956   132 VLERLLKLGP--ENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEE 196
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 114-141 3.18e-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: 35.51  E-value: 3.18e-03
                          10        20
                  ....*....|....*....|....*...
gi 1063699304 114 NILINGYVRAGDLVNARKVFDEMPDRKL 141
Cdd:TIGR00756   4 NTLIDGLCKAGRVEEALELFKEMKERGI 31
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 9-650 4.38e-150

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 450.48  E-value: 4.38e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304   9 VRPLSVDPATAIATLCSKGNLREAFQRFRL----NIFT-NTSLFTPFIQSCTTRQSLPSGKQLHCLLVVSGFSSDKFICN 83
Cdd:PLN03081   83 IRKSGVSLCSQIEKLVACGRHREALELFEIleagCPFTlPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  84 HLMSMYsklgdfpsavavygrmrkknymssnilingyVRAGDLVNARKVFDEMPDRKLTTWNAMIAGLIQFEFNEEGLSL 163
Cdd:PLN03081  163 RVLLMH-------------------------------VKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFAL 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 164 FREMHGLGFSPDEYTLGSVFSGSAGLRSVSIGQQIHGYTIKYGLELDLVVNSSLAHMYMRNGKLQDGEIVIRSMPVRNLV 243
Cdd:PLN03081  212 FREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTV 291

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 244 AWNTLIMGNAQNGCPETVLYLYKMMKISGCRPNKITFVTVLSSCSDLAIRGQGQQIHAEAIKIGASSVVAVVSSLISMYS 323
Cdd:PLN03081  292 AWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYS 371

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 324 KCGCLGDAAKAFSEREDEDEVMWSSMISAYGFHGQGDEAIELFNTMAEQtNMEINEVAFLNLLYACSHSGLKDKGLELFD 403
Cdd:PLN03081  372 KWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAE-GVAPNHVTFLAVLSACRYSGLSEQGWEIFQ 450

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 404 MMVEKYGFKPGLKHYTCVVDLLGRAGCLDQAEAIIRSMPIKTDIVIWKTLLSACNIHKNAEMAQRVFKEILQIDPNDSAC 483
Cdd:PLN03081  451 SMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNN 530

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 484 YVLLANVHASAKRWRDVSEVRKSMRDKNVKKEAGISWFEHKGEVHQFKMGDRSQSKSKEIYSYLKELTLEMKLKGYKPDT 563
Cdd:PLN03081  531 YVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEE 610

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 564 ASVLHDMDEEEKESDLVQHSEKLAVAFALMILPEGAPIRIIKNLRVCSDCHVAFKYISVIKNREITLRDGSRFHHFINGK 643
Cdd:PLN03081  611 NELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGK 690


                  ....*..
gi 1063699304 644 CSCGDYW 650
Cdd:PLN03081  691 CSCGDYW 697
PLN03077 PLN03077
Protein ECB2; Provisional
 2-648 8.91e-142

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 434.28  E-value: 8.91e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304   2 RCSVSSVVRPLSVDPATAIATLCSKGNLREAFQRF----RLNIFTNTSLFTPFIQSCTTRQSLPSGKQLHCLLVVSGFSS 77
Cdd:PLN03077   40 GLSVAASSSSSTHDSNSQLRALCSHGQLEQALKLLesmqELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSL 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  78 DKFICNHLMSMYSKLGDFPSAVAVYGRMRKKNYMSSNILING-------------------------------------- 119
Cdd:PLN03077  120 GVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGyakagyfdealclyhrmlwagvrpdvytfpcvlrtcgg 199

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 120 --------------------------------YVRAGDLVNARKVFDEMPDRKLTTWNAMIAGLIQFEFNEEGLSLFREM 167
Cdd:PLN03077  200 ipdlargrevhahvvrfgfeldvdvvnalitmYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTM 279

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 168 HGLGFSPDEYTLGSVFSGSAGLRSVSIGQQIHGYTIKYGLELDLVVNSSLAHMYMRNGKLQDGEIVIRSMPVRNLVAWNT 247
Cdd:PLN03077  280 RELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTA 359

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 248 LIMGNAQNGCPETVLYLYKMMKISGCRPNKITFVTVLSSCSDLAIRGQGQQIHAEAIKIGASSVVAVVSSLISMYSKCGC 327
Cdd:PLN03077  360 MISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKC 439

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 328 LGDAAKAFSEREDEDEVMWSSMI--------------------------------------------------------- 350
Cdd:PLN03077  440 IDKALEVFHNIPEKDVISWTSIIaglrlnnrcfealiffrqmlltlkpnsvtliaalsacarigalmcgkeihahvlrtg 519

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 351 ------------------------------------------SAYGFHGQGDEAIELFNTMAEqtnMEIN--EVAFLNLL 386
Cdd:PLN03077  520 igfdgflpnalldlyvrcgrmnyawnqfnshekdvvswnillTGYVAHGKGSMAVELFNRMVE---SGVNpdEVTFISLL 596

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 387 YACSHSGLKDKGLELFDMMVEKYGFKPGLKHYTCVVDLLGRAGCLDQAEAIIRSMPIKTDIVIWKTLLSACNIHKNAEMA 466
Cdd:PLN03077  597 CACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELG 676

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 467 QRVFKEILQIDPNDSACYVLLANVHASAKRWRDVSEVRKSMRDKNVKKEAGISWFEHKGEVHQFKMGDRSQSKSKEIYSY 546
Cdd:PLN03077  677 ELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTV 756

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 547 LKELTLEMKLKGYkpdTASVLHDMDEEEKESD--LVQHSEKLAVAFALMILPEGAPIRIIKNLRVCSDCHVAFKYISVIK 624
Cdd:PLN03077  757 LEGFYEKMKASGL---AGSESSSMDEIEVSKDdiFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIV 833

                         810       820
                  ....*....|....*....|....
gi 1063699304 625 NREITLRDGSRFHHFINGKCSCGD 648
Cdd:PLN03077  834 RREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 558-650 1.20e-46

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: 159.51  E-value: 1.20e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 558 GYKPDTASVLHDMDEEEKESDLVQHSEKLAVAFALMILPEGAPIRIIKNLRVCSDCHVAFKYISVIKNREITLRDGSRFH 637
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 1063699304 638 HFINGKCSCGDYW 650
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 460-522 8.97e-15

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: 69.11  E-value: 8.97e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063699304 460 HKNAEMAQRVFKEILQIDPNDSACYVLLANVHASAKRWRDVSEVRKSMRDKNVKKEAGISWFE 522
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 211-473 1.84e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 61.05  E-value: 1.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  211 LVVNSSLAHMYM-----RNGKLQDGEI-VIRSMPVRNLVA----WNTLIMGNAQNGCPETVLYLYKMMKISGCRPNKITF 280
Cdd:PLN03218   431 LIRNPTLSTFNMlmsvcASSQDIDGALrVLRLVQEAGLKAdcklYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTF 510

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  281 VTVLSSCsdlAIRGQ-GQQIHAEAIKIGASSV--VAVVSSLIsmySKCGCLGDAAKAF-------SERE--DEDEVMWSS 348
Cdd:PLN03218   511 GALIDGC---ARAGQvAKAFGAYGIMRSKNVKpdRVVFNALI---SACGQSGAVDRAFdvlaemkAETHpiDPDHITVGA 584

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  349 MISAYGFHGQGDEAIELFNtMAEQTNMEINEVAFLNLLYACSHSGLKDKGLELFDMMVEKyGFKPGLKHYTCVVDLLGRA 428
Cdd:PLN03218   585 LMKACANAGQVDRAKEVYQ-MIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHA 662

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 1063699304  429 GCLDQAEAII---RSMPIKTDIVIWKTLLSACNIHKNAEMAQRVFKEI 473
Cdd:PLN03218   663 GDLDKAFEILqdaRKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 163-483 2.89e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 53.73  E-value: 2.89e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  163 LFREMHGLGFSPDEYTLGSVFSGSAGLRSVSIGQQIHGYTIKYGLELDLVVNSSLAHMYMRNGKLQDGEIVIRSM----- 237
Cdd:PLN03218   494 VFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMkaeth 573

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  238 PVR-NLVAWNTLIMGNAQNGCPETVLYLYKMMKISGCRPNKITFVTVLSSCSDLAIRGQGQQIHAEAIKIGASsvvavvs 316
Cdd:PLN03218   574 PIDpDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVK------- 646

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  317 slismyskcgclgdaakafseredEDEVMWSSMISAYGFHGQGDEAIELFNTMAEQtNMEINEVAFLNLLYACSHSGLKD 396
Cdd:PLN03218   647 ------------------------PDEVFFSALVDVAGHAGDLDKAFEILQDARKQ-GIKLGTVSYSSLMGACSNAKNWK 701

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  397 KGLELFDmMVEKYGFKPGLKHYTCVVDLLGRAGCLDQAEAI---IRSMPIKTDIVIWKTLLSACNIHKNAEMAQRVFKEI 473
Cdd:PLN03218   702 KALELYE-DIKSIKLRPTVSTMNALITALCEGNQLPKALEVlseMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQA 780

                          330
                   ....*....|..
gi 1063699304  474 LQ--IDPNDSAC 483
Cdd:PLN03218   781 KEdgIKPNLVMC 792
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 385-593 8.33e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 52.57  E-value: 8.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  385 LLYACSHSGLKDKGLELFDMMVEKyGFKPGLKHYTCVVDLLGRAGCLDQA---EAIIRSMPIKTDIVIWKTLLSACNihk 461
Cdd:PLN03218   478 LISTCAKSGKVDAMFEVFHEMVNA-GVEANVHTFGALIDGCARAGQVAKAfgaYGIMRSKNVKPDRVVFNALISACG--- 553

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304  462 NAEMAQRVF-------KEILQIDPnDSACYVLLANVHASAKRWRDVSEVRKSMRDKNVkkeagiswfehKGEVHQFKMGD 534
Cdd:PLN03218   554 QSGAVDRAFdvlaemkAETHPIDP-DHITVGALMKACANAGQVDRAKEVYQMIHEYNI-----------KGTPEVYTIAV 621

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063699304  535 RSQSKSKEiYSYLKELTLEMKLKGYKPDTA--SVLhdmdeeekeSDLVQHSEKLAVAFALM 593
Cdd:PLN03218   622 NSCSQKGD-WDFALSIYDDMKKKGVKPDEVffSAL---------VDVAGHAGDLDKAFEIL 672
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 240-289 2.16e-06

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 45.05  E-value: 2.16e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063699304 240 RNLVAWNTLIMGNAQNGCPETVLYLYKMMKISGCRPNKITFVTVLSSCSD 289
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 357-499 6.95e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 48.19  E-value: 6.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 357 GQGDEAIELFNTMAEQTnmEINEVAFLNLLYACSHSGLKDKGLELFDMMVEKYGFKPglKHYTCVVDLLGRAG----CLD 432
Cdd:COG2956    56 GEYDRAIRIHQKLLERD--PDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDA--EALRLLAEIYEQEGdwekAIE 131

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063699304 433 QAEAIIRSMPikTDIVIWKTLLSACNIHKNAEMAQRVFKEILQIDPNDSACYVLLANVHASAKRWRD 499
Cdd:COG2956   132 VLERLLKLGP--ENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEE 196
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 114-151 2.86e-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: 41.58  E-value: 2.86e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063699304 114 NILINGYVRAGDLVNARKVFDEMPDRKLT----TWNAMIAGL 151
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKKRGVKpnvyTYTILINGL 48
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 328-497 1.37e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 44.33  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 328 LGDAAKAFS------EREDEDEVMWSSMISAYGFHGQGDEAIELFNTMAEQTnmEINEVAFLNLLYACSHSGLKDKGLEL 401
Cdd:COG2956    55 RGEYDRAIRihqkllERDPDRAEALLELAQDYLKAGLLDRAEELLEKLLELD--PDDAEALRLLAEIYEQEGDWEKAIEV 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063699304 402 FDMMVEKygfKPGLKHYTC-VVDLLGRAGCLDQAEAIIRSMpIKTDIVIWKTLLSACNIH---KNAEMAQRVFKEILQID 477
Cdd:COG2956   133 LERLLKL---GPENAHAYCeLAELYLEQGDYDEAIEALEKA-LKLDPDCARALLLLAELYleqGDYEEAIAALERALEQD 208

                         170       180
                  ....*....|....*....|
gi 1063699304 478 PNDSACYVLLANVHASAKRW 497
Cdd:COG2956   209 PDYLPALPRLAELYEKLGDP 228
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 143-185 1.85e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.27  E-value: 1.85e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063699304 143 TWNAMIAGLIQFEFNEEGLSLFREMHGLGFSPDEYTLGSVFSG 185
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 114-136 2.21e-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: 38.87  E-value: 2.21e-04
                          10        20
                  ....*....|....*....|...
gi 1063699304 114 NILINGYVRAGDLVNARKVFDEM 136
Cdd:pfam12854  11 NTLINGLCRAGRVDEAFELLDEM 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 342-391 2.52e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 38.88  E-value: 2.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063699304 342 DEVMWSSMISAYGFHGQGDEAIELFNTMaEQTNMEINEVAFLNLLYACSH 391
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEM-KKRGVKPNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 344-369 3.08e-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: 38.22  E-value: 3.08e-04
                          10        20
                  ....*....|....*....|....*.
gi 1063699304 344 VMWSSMISAYGFHGQGDEAIELFNTM 369
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEM 26
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 80-122 6.28e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 38.11  E-value: 6.28e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063699304  80 FICNHLMSMYSKLGDFPSAVAVYGRMRKKNYMSS----NILINGYVR 122
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNvytyTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 243-273 1.33e-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: 36.67  E-value: 1.33e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063699304 243 VAWNTLIMGNAQNGCPETVLYLYKMMKISGC 273
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 114-141 1.96e-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: 35.90  E-value: 1.96e-03
                          10        20
                  ....*....|....*....|....*...
gi 1063699304 114 NILINGYVRAGDLVNARKVFDEMPDRKL 141
Cdd:pfam01535   4 NSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 114-141 3.18e-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: 35.51  E-value: 3.18e-03
                          10        20
                  ....*....|....*....|....*...
gi 1063699304 114 NILINGYVRAGDLVNARKVFDEMPDRKL 141
Cdd:TIGR00756   4 NTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 143-172 4.30e-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: 35.13  E-value: 4.30e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1063699304 143 TWNAMIAGLIQFEFNEEGLSLFREMHGLGF 172
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH