NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15229194|ref|NP_190540|]
View 

Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000585)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
 78-719 1.74e-161

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 487.82  E-value: 1.74e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   78 NVIVKAYAKDSKIHIARQLFDEIPQPDTVSYNTLISGYADARETFAAMVLFKRMRKLGFEVDGFTLSGLIAAC--CDRVD 155
Cdd:PLN03077 226 NALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACelLGDER 305

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  156 LIKQLHCFSVSGGFDSYSSVNNAFVTYYSKGGLLREAVSVFYGMdELRDEVSWNSMIVAYGQHKEGAKALALYKEMIFKG 235
Cdd:PLN03077 306 LGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRM-ETKDAVSWTAMISGYEKNGLPDKALETYALMEQDN 384

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  236 FKIDMFTLASVLNALTSLDHLIGGRQFHGKLIKAGFHQNSHVGSGLIDFYSKCGGCDGMYDsekVFQEILSPDLVVWNTM 315
Cdd:PLN03077 385 VSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALE---VFHNIPEKDVISWTSI 461

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  316 ISGYSMNEElSEEAVKSFRQMqrIGH-RPDDCSFVCVTSACSNLSSPSQCKQIHGLAIKSHIPSNRIsVNNALISLYYKS 394
Cdd:PLN03077 462 IAGLRLNNR-CFEALIFFRQM--LLTlKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGF-LPNALLDLYVRC 537

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  395 GNLQDArWVFDRMPELNAVSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPNKITFVAVLSACAHCGKVDEGQEYFNTMK 474
Cdd:PLN03077 538 GRMNYA-WNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSME 616

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  475 ETFKIEPEAEHYSCMIDLLGRAGKLEEAERFIDAMPYKPGSVAWAALLGACRKHKNMALAERAANELMVMQPLAATPYVM 554
Cdd:PLN03077 617 EKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYIL 696

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  555 LANMYADARKWEEMASVRKSMRGKRIRKKPGCSWIEVKKKKHVFVAEDWSHPMIREVNEYLEEMMKKMKKVGYVMDKKWA 634
Cdd:PLN03077 697 LCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSS 776

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  635 MVKEDEAGEGDeemrLGHHSEKLAVAFGLMSTRDGEELVVVKNLRICGDCHNAIKFMSAVAGREIIVRDNLRFHCFKDGK 714
Cdd:PLN03077 777 MDEIEVSKDDI----FCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGE 852


                 ....*
gi 15229194  715 CSCGD 719
Cdd:PLN03077 853 CSCGD 857
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 78-719 1.74e-161

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 487.82  E-value: 1.74e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   78 NVIVKAYAKDSKIHIARQLFDEIPQPDTVSYNTLISGYADARETFAAMVLFKRMRKLGFEVDGFTLSGLIAAC--CDRVD 155
Cdd:PLN03077 226 NALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACelLGDER 305

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  156 LIKQLHCFSVSGGFDSYSSVNNAFVTYYSKGGLLREAVSVFYGMdELRDEVSWNSMIVAYGQHKEGAKALALYKEMIFKG 235
Cdd:PLN03077 306 LGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRM-ETKDAVSWTAMISGYEKNGLPDKALETYALMEQDN 384

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  236 FKIDMFTLASVLNALTSLDHLIGGRQFHGKLIKAGFHQNSHVGSGLIDFYSKCGGCDGMYDsekVFQEILSPDLVVWNTM 315
Cdd:PLN03077 385 VSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALE---VFHNIPEKDVISWTSI 461

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  316 ISGYSMNEElSEEAVKSFRQMqrIGH-RPDDCSFVCVTSACSNLSSPSQCKQIHGLAIKSHIPSNRIsVNNALISLYYKS 394
Cdd:PLN03077 462 IAGLRLNNR-CFEALIFFRQM--LLTlKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGF-LPNALLDLYVRC 537

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  395 GNLQDArWVFDRMPELNAVSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPNKITFVAVLSACAHCGKVDEGQEYFNTMK 474
Cdd:PLN03077 538 GRMNYA-WNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSME 616

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  475 ETFKIEPEAEHYSCMIDLLGRAGKLEEAERFIDAMPYKPGSVAWAALLGACRKHKNMALAERAANELMVMQPLAATPYVM 554
Cdd:PLN03077 617 EKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYIL 696

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  555 LANMYADARKWEEMASVRKSMRGKRIRKKPGCSWIEVKKKKHVFVAEDWSHPMIREVNEYLEEMMKKMKKVGYVMDKKWA 634
Cdd:PLN03077 697 LCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSS 776

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  635 MVKEDEAGEGDeemrLGHHSEKLAVAFGLMSTRDGEELVVVKNLRICGDCHNAIKFMSAVAGREIIVRDNLRFHCFKDGK 714
Cdd:PLN03077 777 MDEIEVSKDDI----FCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGE 852


                 ....*
gi 15229194  715 CSCGD 719
Cdd:PLN03077 853 CSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 626-721 2.66e-34

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: 126.00  E-value: 2.66e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   626 GYVMDKKWAMVKEDEAGEGDEEMRlghHSEKLAVAFGLMSTRDGEELVVVKNLRICGDCHNAIKFMSAVAGREIIVRDNL 705
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCG---HSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDAS 77

                          90
                  ....*....|....*.
gi 15229194   706 RFHCFKDGKCSCGDYW 721
Cdd:pfam14432  78 RFHHFKNGLCSCGDFW 93
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 371-571 1.48e-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: 50.50  E-value: 1.48e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 371 AIKSH-----IPSNRISVNNALISLYYKSGNLQDARWVFDRMPEL---NAVSFNCMIKGYAQHGHGTEALLLYQRMLDsg 442
Cdd:COG2956  61 AIRIHqklleRDPDRAEALLELAQDYLKAGLLDRAEELLEKLLELdpdDAEALRLLAEIYEQEGDWEKAIEVLERLLK-- 138

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 443 IAPNKITFVAVLSACA-HCGKVDEGQEYFntmKETFKIEPEAEHYSCMI-DLLGRAGKLEEAERFI-DAMPYKPGSVAWA 519
Cdd:COG2956 139 LGPENAHAYCELAELYlEQGDYDEAIEAL---EKALKLDPDCARALLLLaELYLEQGDYEEAIAALeRALEQDPDYLPAL 215

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|...
gi 15229194 520 ALLGAC-RKHKNMALAERAANELMVMQPlAATPYVMLANMYADARKWEEMASV 571
Cdd:COG2956 216 PRLAELyEKLGDPEEALELLRKALELDP-SDDLLLALADLLERKEGLEAALAL 267
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 413-446 1.14e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 42.44  E-value: 1.14e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15229194   413 VSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPN 446
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 78-719 1.74e-161

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 487.82  E-value: 1.74e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   78 NVIVKAYAKDSKIHIARQLFDEIPQPDTVSYNTLISGYADARETFAAMVLFKRMRKLGFEVDGFTLSGLIAAC--CDRVD 155
Cdd:PLN03077 226 NALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACelLGDER 305

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  156 LIKQLHCFSVSGGFDSYSSVNNAFVTYYSKGGLLREAVSVFYGMdELRDEVSWNSMIVAYGQHKEGAKALALYKEMIFKG 235
Cdd:PLN03077 306 LGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRM-ETKDAVSWTAMISGYEKNGLPDKALETYALMEQDN 384

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  236 FKIDMFTLASVLNALTSLDHLIGGRQFHGKLIKAGFHQNSHVGSGLIDFYSKCGGCDGMYDsekVFQEILSPDLVVWNTM 315
Cdd:PLN03077 385 VSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALE---VFHNIPEKDVISWTSI 461

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  316 ISGYSMNEElSEEAVKSFRQMqrIGH-RPDDCSFVCVTSACSNLSSPSQCKQIHGLAIKSHIPSNRIsVNNALISLYYKS 394
Cdd:PLN03077 462 IAGLRLNNR-CFEALIFFRQM--LLTlKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGF-LPNALLDLYVRC 537

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  395 GNLQDArWVFDRMPELNAVSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPNKITFVAVLSACAHCGKVDEGQEYFNTMK 474
Cdd:PLN03077 538 GRMNYA-WNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSME 616

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  475 ETFKIEPEAEHYSCMIDLLGRAGKLEEAERFIDAMPYKPGSVAWAALLGACRKHKNMALAERAANELMVMQPLAATPYVM 554
Cdd:PLN03077 617 EKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYIL 696

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  555 LANMYADARKWEEMASVRKSMRGKRIRKKPGCSWIEVKKKKHVFVAEDWSHPMIREVNEYLEEMMKKMKKVGYVMDKKWA 634
Cdd:PLN03077 697 LCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSS 776

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  635 MVKEDEAGEGDeemrLGHHSEKLAVAFGLMSTRDGEELVVVKNLRICGDCHNAIKFMSAVAGREIIVRDNLRFHCFKDGK 714
Cdd:PLN03077 777 MDEIEVSKDDI----FCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGE 852


                 ....*
gi 15229194  715 CSCGD 719
Cdd:PLN03077 853 CSCGD 857
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 115-721 6.16e-160

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 478.60  E-value: 6.16e-160
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  115 YADARETFaamvlfkRMRKLG--FEVDGFTLSGLIAACC--DRVDLIKQLHCFSVSGGFDSYSSVNNAFVTYYSKGGLLR 190
Cdd:PLN03081 103 HREALELF-------EILEAGcpFTLPASTYDALVEACIalKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLI 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  191 EAVSVFYGMDElRDEVSWNSMI---VAYGQHKEgakALALYKEMIFKGFKIDMFTLASVLNALTSLDHLIGGRQFHGKLI 267
Cdd:PLN03081 176 DARRLFDEMPE-RNLASWGTIIgglVDAGNYRE---AFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVL 251

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  268 KAGFHQNSHVGSGLIDFYSKCGGCDgmyDSEKVFQEILSPDLVVWNTMISGYSMNEeLSEEAVKSFRQMQRIGHRPDDCS 347
Cdd:PLN03081 252 KTGVVGDTFVSCALIDMYSKCGDIE---DARCVFDGMPEKTTVAWNSMLAGYALHG-YSEEALCLYYEMRDSGVSIDQFT 327

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  348 FVCVTSACSNLSSPSQCKQIHGLAIKSHIPSNrISVNNALISLYYKSGNLQDARWVFDRMPELNAVSFNCMIKGYAQHGH 427
Cdd:PLN03081 328 FSIMIRIFSRLALLEHAKQAHAGLIRTGFPLD-IVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGR 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  428 GTEALLLYQRMLDSGIAPNKITFVAVLSACAHCGKVDEGQEYFNTMKETFKIEPEAEHYSCMIDLLGRAGKLEEAERFID 507
Cdd:PLN03081 407 GTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIR 486

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  508 AMPYKPGSVAWAALLGACRKHKNMALAERAANELMVMQPLAATPYVMLANMYADARKWEEMASVRKSMRGKRIRKKPGCS 587
Cdd:PLN03081 487 RAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACT 566

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  588 WIEVKKKKHVFVAEDWSHPMIREVNEYLEEMMKKMKKVGYVMDKKWAMVKEDEAGEGDEEMrlgHHSEKLAVAFGLMSTR 667
Cdd:PLN03081 567 WIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGR---YHSEKLAIAFGLINTS 643

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15229194  668 DGEELVVVKNLRICGDCHNAIKFMSAVAGREIIVRDNLRFHCFKDGKCSCGDYW 721
Cdd:PLN03081 644 EWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 626-721 2.66e-34

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: 126.00  E-value: 2.66e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   626 GYVMDKKWAMVKEDEAGEGDEEMRlghHSEKLAVAFGLMSTRDGEELVVVKNLRICGDCHNAIKFMSAVAGREIIVRDNL 705
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCG---HSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDAS 77

                          90
                  ....*....|....*.
gi 15229194   706 RFHCFKDGKCSCGDYW 721
Cdd:pfam14432  78 RFHHFKNGLCSCGDFW 93
PLN03077 PLN03077
Protein ECB2; Provisional
 294-528 3.49e-26

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 114.95  E-value: 3.49e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  294 MYDSEKVFQEILSPDLVVWNTMISGYSmNEELSEEAVKSFRQMQRIGHRPDDCSFVCVTSACSNLSSPSQCKQIHGLAIK 373
Cdd:PLN03077 137 LVHAWYVFGKMPERDLFSWNVLVGGYA-KAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVR 215

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  374 SHIPSNrISVNNALISLYYKSGNLQDARWVFDRMPELNAVSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPNKITFVAV 453
Cdd:PLN03077 216 FGFELD-VDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSV 294

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15229194  454 LSACAHCGKVDEGQEYFN-TMKETFKIepEAEHYSCMIDLLGRAGKLEEAERFIDAMPYKpGSVAWAALLGACRKH 528
Cdd:PLN03077 295 ISACELLGDERLGREMHGyVVKTGFAV--DVSVCNSLIQMYLSLGSWGEAEKVFSRMETK-DAVSWTAMISGYEKN 367
PLN03077 PLN03077
Protein ECB2; Provisional
 327-522 8.31e-20

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 94.53  E-value: 8.31e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  327 EEAVKSFRQMQRIGHRPDDCSFVCVTSACSNLSSPSQCKQIHGLAIKSHiPSNRISVNNALISLYYKSGNLQDARWVFDR 406
Cdd:PLN03077  68 EQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSH-PSLGVRLGNAMLSMFVRFGELVHAWYVFGK 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194  407 MPELNAVSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPNKITFVAVLSACAHCGKVDEGQE-YFNTMKetFKIEPEAEH 485
Cdd:PLN03077 147 MPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREvHAHVVR--FGFELDVDV 224

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 15229194  486 YSCMIDLLGRAGKLEEAERFIDAMPYKpGSVAWAALL 522
Cdd:PLN03077 225 VNALITMYVKCGDVVSARLVFDRMPRR-DCISWNAMI 260
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 528-590 4.94e-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: 69.88  E-value: 4.94e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15229194   528 HKNMALAERAANELMVMQPLAATPYVMLANMYADARKWEEMASVRKSMRGKRIRKKPGCSWIE 590
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 411-459 5.81e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 55.06  E-value: 5.81e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15229194   411 NAVSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPNKITFVAVLSACAH 459
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 212-530 9.54e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 62.20  E-value: 9.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   212 IVAYGQHKEGA-KALALYKEmifKGFKID-MF--TLASVLNALTSLDHLIggRQFHgKLIKAGFHQNSHVGSGLIDFYSK 287
Cdd:PLN03218  446 VCASSQDIDGAlRVLRLVQE---AGLKADcKLytTLISTCAKSGKVDAMF--EVFH-EMVNAGVEANVHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   288 CG------GCDGMYDSEKVfqeilSPDLVVWNTMIsgysmneelseeavksfrqmqrighrpddcsfvcvtSACSnlssp 361
Cdd:PLN03218  520 AGqvakafGAYGIMRSKNV-----KPDRVVFNALI------------------------------------SACG----- 553

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   362 sqckqihglaikshipsnrisvnnalislyyKSGNLQDArwvFDRMPELNA---------VSFNCMIKGYAQHGHGTEAL 432
Cdd:PLN03218  554 -------------------------------QSGAVDRA---FDVLAEMKAethpidpdhITVGALMKACANAGQVDRAK 599

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   433 LLYQRMLDSGIAPNKITFVAVLSACAHCGKVDEGQEYFNTMKETfKIEPEAEHYSCMIDLLGRAGKLEEAERFIDAMP-- 510
Cdd:PLN03218  600 EVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARkq 678

                         330       340
                  ....*....|....*....|.
gi 15229194   511 -YKPGSVAWAALLGACRKHKN 530
Cdd:PLN03218  679 gIKLGTVSYSSLMGACSNAKN 699
PLN03077 PLN03077
Protein ECB2; Provisional
 24-131 2.61e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 60.63  E-value: 2.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194   24 LFTGKSLHALYVKSIVASSTYLSNHFVNLYSKCGRLSYARAAFySTEEPNVFSYNVIVKAYAKDSKIHIARQLFDEIPQ- 102
Cdd:PLN03077 505 LMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVEs 583

                         90       100       110
                 ....*....|....*....|....*....|..
gi 15229194  103 ---PDTVSYNTLISGYADARETFAAMVLFKRM 131
Cdd:PLN03077 584 gvnPDEVTFISLLCACSRSGMVTQGLEYFHSM 615
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 103-152 3.04e-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: 53.14  E-value: 3.04e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15229194   103 PDTVSYNTLISGYADARETFAAMVLFKRMRKLGFEVDGFTLSGLIAACCD 152
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 72-117 1.75e-08

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 50.82  E-value: 1.75e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15229194    72 PNVFSYNVIVKAYAKDSKIHIARQLFDEIP----QPDTVSYNTLISGYAD 117
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKkrgvKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 203-250 4.67e-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: 46.97  E-value: 4.67e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15229194   203 RDEVSWNSMIVAYGQHKEGAKALALYKEMIFKGFKIDMFTLASVLNAL 250
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 371-571 1.48e-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: 50.50  E-value: 1.48e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 371 AIKSH-----IPSNRISVNNALISLYYKSGNLQDARWVFDRMPEL---NAVSFNCMIKGYAQHGHGTEALLLYQRMLDsg 442
Cdd:COG2956  61 AIRIHqklleRDPDRAEALLELAQDYLKAGLLDRAEELLEKLLELdpdDAEALRLLAEIYEQEGDWEKAIEVLERLLK-- 138

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 443 IAPNKITFVAVLSACA-HCGKVDEGQEYFntmKETFKIEPEAEHYSCMI-DLLGRAGKLEEAERFI-DAMPYKPGSVAWA 519
Cdd:COG2956 139 LGPENAHAYCELAELYlEQGDYDEAIEAL---EKALKLDPDCARALLLLaELYLEQGDYEEAIAALeRALEQDPDYLPAL 215

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|...
gi 15229194 520 ALLGAC-RKHKNMALAERAANELMVMQPlAATPYVMLANMYADARKWEEMASV 571
Cdd:COG2956 216 PRLAELyEKLGDPEEALELLRKALELDP-SDDLLLALADLLERKEGLEAALAL 267
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 413-446 1.14e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 42.44  E-value: 1.14e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15229194   413 VSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPN 446
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
Eplus_motif pfam20430
E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins ...
 596-622 1.74e-05

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: 41.87  E-value: 1.74e-05
                          10        20
                  ....*....|....*....|....*..
gi 15229194   596 HVFVAEDWSHPMIREVNEYLEEMMKKM 622
Cdd:pfam20430   2 YTFFAGDKSHPESKQIYEKLSDLTQRI 28
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 461-567 2.09e-05

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 44.80  E-value: 2.09e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 461 GKVDEGQEYFNTMKETFKIEPEAehYSCMIDLLGRAGKLEEAERFID-AMPYKPGSVAWAALLG-ACRKHKNMALAERAA 538
Cdd:COG4783  18 GDYDEAEALLEKALELDPDNPEA--FALLGEILLQLGDLDEAIVLLHeALELDPDEPEARLNLGlALLKAGDYDEALALL 95

                        90       100
                ....*....|....*....|....*....
gi 15229194 539 NELMVMQPLAATPYVMLANMYADARKWEE 567
Cdd:COG4783  96 EKALKLDPEHPEAYLRLARAYRALGRPDE 124
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 307-357 2.25e-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: 41.97  E-value: 2.25e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15229194   307 PDLVVWNTMISGYSMNEELsEEAVKSFRQMQRIGHRPDDCSFVCVTSACSN 357
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKV-EEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 413-443 7.31e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 40.14  E-value: 7.31e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15229194   413 VSFNCMIKGYAQHGHGTEALLLYQRMLDSGI 443
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 376-545 7.49e-05

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: 45.11  E-value: 7.49e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 376 IPSNRISVNNALISLYYKSGNLQDARWVFDRMPELNAVS--FNCMI-KGYAQHGHGTEALLLYQRMLDsgIAPNkitFVA 452
Cdd:COG2956 105 LDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENahAYCELaELYLEQGDYDEAIEALEKALK--LDPD---CAR 179

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 453 VLSACAHC----GKVDEGQEYFntmKETFKIEPE-AEHYSCMIDLLGRAGKLEEAERFID-AMPYKPGSVAWAALLGACR 526
Cdd:COG2956 180 ALLLLAELyleqGDYEEAIAAL---ERALEQDPDyLPALPRLAELYEKLGDPEEALELLRkALELDPSDDLLLALADLLE 256

                       170
                ....*....|....*....
gi 15229194 527 KHKNMALAERAANELMVMQ 545
Cdd:COG2956 257 RKEGLEAALALLERQLRRH 275
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 106-139 1.13e-04

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 39.75  E-value: 1.13e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15229194   106 VSYNTLISGYADARETFAAMVLFKRMRKLGFEVD 139
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 206-239 1.30e-04

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 39.75  E-value: 1.30e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15229194   206 VSWNSMIVAYGQHKEGAKALALYKEMIFKGFKID 239
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 102-132 2.40e-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: 2.40e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15229194   102 QPDTVSYNTLISGYADARETFAAMVLFKRMR 132
Cdd:pfam12854   4 KPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 206-236 2.47e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 38.60  E-value: 2.47e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15229194   206 VSWNSMIVAYGQHKEGAKALALYKEMIFKGF 236
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 ...
 106-136 2.52e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 38.60  E-value: 2.52e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15229194   106 VSYNTLISGYADARETFAAMVLFKRMRKLGF 136
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 390-567 5.11e-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: 42.41  E-value: 5.11e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 390 LYYKSGNLQDARWVFDRMPELNAVSFNCMI---KGYAQHGHGTEALLLYQRMLDsgIAPNKITFVAVLSACAHC-GKVDE 465
Cdd:COG2956  17 NYLLNGQPDKAIDLLEEALELDPETVEAHLalgNLYRRRGEYDRAIRIHQKLLE--RDPDRAEALLELAQDYLKaGLLDR 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 466 GQEYFNTMKETFKIEPEAehYSCMIDLLGRAGKLEEAERFID-AMPYKPGSVAWAALLGAC-RKHKNMALAERAANELMV 543
Cdd:COG2956  95 AEELLEKLLELDPDDAEA--LRLLAEIYEQEGDWEKAIEVLErLLKLGPENAHAYCELAELyLEQGDYDEAIEALEKALK 172

                       170       180
                ....*....|....*....|....
gi 15229194 544 MQPLAATPYVMLANMYADARKWEE 567
Cdd:COG2956 173 LDPDCARALLLLAELYLEQGDYEE 196
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
422-567 6.25e-04

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 42.30  E-value: 6.25e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229194 422 YAQHGHGTEALLLYQRMLDsgIAPNkitFVAVLSACAHC----GKVDEGQEYFntmKETFKIEPE-AEHYSCMIDLLGRA 496
Cdd:COG0457  18 YRRLGRYEEAIEDYEKALE--LDPD---DAEALYNLGLAylrlGRYEEALADY---EQALELDPDdAEALNNLGLALQAL 89

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15229194 497 GKLEEAERFID-AMPYKPGSV-AWAALLGACRKHKNMALAERAANELMVMQPLAATPYVMLANMYADARKWEE 567
Cdd:COG0457  90 GRYEEALEDYDkALELDPDDAeALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEE 162
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 385-424 1.08e-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: 37.34  E-value: 1.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15229194   385 NALISLYYKSGNLQDARWVFDRMP----ELNAVSFNCMIKGYAQ 424
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKkrgvKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 102-153 1.19e-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: 37.72  E-value: 1.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15229194   102 QPDTVSYNTLISGYADARETFAAMVLFKRMRKLGFEVDGFTLSGLIAACCDR 153
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 310-341 3.34e-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: 35.52  E-value: 3.34e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15229194   310 VVWNTMISGYSMNEELsEEAVKSFRQMQRIGH 341
Cdd:pfam01535   1 VTYNSLISGYCKNGKL-EEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 433-494 5.86e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 35.80  E-value: 5.86e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229194   433 LLYQRMLDSGIAPNKITFVAVLSACAHCGKVDEGQEYFNTMKETfKIEPEAEHYSCMIDLLG 494
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKK-GIKPTLDTYNAILGVIG 61
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 71-99 5.93e-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: 35.01  E-value: 5.93e-03
                          10        20
                  ....*....|....*....|....*....
gi 15229194    71 EPNVFSYNVIVKAYAKDSKIHIARQLFDE 99
Cdd:pfam12854   4 KPDVVTYNTLINGLCRAGRVDEAFELLDE 32
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 409-457 7.00e-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: 35.41  E-value: 7.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15229194   409 ELNAVSFNCMIKGYAQHGHGTEALLLYQRMLDSGIAPNKITFVAVLSAC 457
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 479-509 8.29e-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: 34.63  E-value: 8.29e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15229194   479 IEPEAEHYSCMIDLLGRAGKLEEAERFIDAM 509
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 305-336 9.05e-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: 9.05e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15229194   305 LSPDLVVWNTMISGYSMNEELsEEAVKSFRQM 336
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRV-DEAFELLDEM 33
 
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