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Conserved domains on  [gi|42567862|ref|NP_197034|]
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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

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List of domain hits

 Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
 29-523 1.60e-99

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 320.26  E-value: 1.60e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   29 KQIHASMVVNGLMSNLSVVGELIysaSLSVP-GALKYAHKLFDEIPKPDVSICNHVLRGSAQSMKPEKTVSLYTEMEKRG 107
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALI---TMYVKcGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELS 283

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  108 VSPDRYTFTFVLKACSKLEWRSNGFAFHGKVVRHGFVLNEYVKNALILFHANCGDLGIASELFDDSAKAHKVAWSSMTSG 187
Cdd:PLN03077 284 VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG 363

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  188 YAKRGKIDEAMRLFDEMPYKDQVAWNVMITGCL---------------------------------------KCKEMDSA 228
Cdd:PLN03077 364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLsacaclgdldvgvklhelaerkglisyvvvanaliemysKCKCIDKA 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  229 RELFDRFTEKDVVTWNAMISGYVNCGYPKEALGIFKEMRdAGEHPDVVTILSLLSACAVLGDLETGKRLHIYILETAsVS 308
Cdd:PLN03077 444 LEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTG-IG 521

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  309 SSIYVGtpiwNALIDMYAKCGSIDRAIEVFrGVKDRDLSTWNTLIVGLAlHHAEGSI--EMFEEMQRLKVWPNEVTFIGV 386
Cdd:PLN03077 522 FDGFLP----NALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYV-AHGKGSMavELFNRMVESGVNPDEVTFISL 595

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  387 ILACSHSGRVDEGRKYFSLMRDMYNIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMKIEPNAIVWRTLLGACKIYGNVEL 466
Cdd:PLN03077 596 LCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVEL 675

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 42567862  467 GKYANEKLLSMRKDESGDYVLLSNIYASTGQWDGVQKVRKMFDDTRVKKPTGVSLIE 523
Cdd:PLN03077 676 GELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVE 732
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 29-523 1.60e-99

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 320.26  E-value: 1.60e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   29 KQIHASMVVNGLMSNLSVVGELIysaSLSVP-GALKYAHKLFDEIPKPDVSICNHVLRGSAQSMKPEKTVSLYTEMEKRG 107
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALI---TMYVKcGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELS 283

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  108 VSPDRYTFTFVLKACSKLEWRSNGFAFHGKVVRHGFVLNEYVKNALILFHANCGDLGIASELFDDSAKAHKVAWSSMTSG 187
Cdd:PLN03077 284 VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG 363

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  188 YAKRGKIDEAMRLFDEMPYKDQVAWNVMITGCL---------------------------------------KCKEMDSA 228
Cdd:PLN03077 364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLsacaclgdldvgvklhelaerkglisyvvvanaliemysKCKCIDKA 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  229 RELFDRFTEKDVVTWNAMISGYVNCGYPKEALGIFKEMRdAGEHPDVVTILSLLSACAVLGDLETGKRLHIYILETAsVS 308
Cdd:PLN03077 444 LEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTG-IG 521

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  309 SSIYVGtpiwNALIDMYAKCGSIDRAIEVFrGVKDRDLSTWNTLIVGLAlHHAEGSI--EMFEEMQRLKVWPNEVTFIGV 386
Cdd:PLN03077 522 FDGFLP----NALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYV-AHGKGSMavELFNRMVESGVNPDEVTFISL 595

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  387 ILACSHSGRVDEGRKYFSLMRDMYNIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMKIEPNAIVWRTLLGACKIYGNVEL 466
Cdd:PLN03077 596 LCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVEL 675

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 42567862  467 GKYANEKLLSMRKDESGDYVLLSNIYASTGQWDGVQKVRKMFDDTRVKKPTGVSLIE 523
Cdd:PLN03077 676 GELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVE 732
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 461-523 4.07e-14

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: 67.18  E-value: 4.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42567862   461 YGNVELGKYANEKLLSMRKDESGDYVLLSNIYASTGQWDGVQKVRKMFDDTRVKKPTGVSLIE 523
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 241-275 1.02e-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: 45.14  E-value: 1.02e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42567862   241 VTWNAMISGYVNCGYPKEALGIFKEMRDAGEHPDV 275
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 393-499 1.35e-04

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: 42.10  E-value: 1.35e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862 393 SGRVDEGRKyfsLMRDMYNIEP-NIKHYGCMVDMLGRAGQLEEAF-MFVESMKIEPNAIVWRTLLGACKIygnvELGKYA 470
Cdd:COG4783  17 AGDYDEAEA---LLEKALELDPdNPEAFALLGEILLQLGDLDEAIvLLHEALELDPDEPEARLNLGLALL----KAGDYD 89

                        90       100       110
                ....*....|....*....|....*....|....
gi 42567862 471 N-----EKLLSMRKDESGDYVLLSNIYASTGQWD 499
Cdd:COG4783  90 EalallEKALKLDPEHPEAYLRLARAYRALGRPD 123
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 29-523 1.60e-99

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 320.26  E-value: 1.60e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   29 KQIHASMVVNGLMSNLSVVGELIysaSLSVP-GALKYAHKLFDEIPKPDVSICNHVLRGSAQSMKPEKTVSLYTEMEKRG 107
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALI---TMYVKcGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELS 283

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  108 VSPDRYTFTFVLKACSKLEWRSNGFAFHGKVVRHGFVLNEYVKNALILFHANCGDLGIASELFDDSAKAHKVAWSSMTSG 187
Cdd:PLN03077 284 VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG 363

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  188 YAKRGKIDEAMRLFDEMPYKDQVAWNVMITGCL---------------------------------------KCKEMDSA 228
Cdd:PLN03077 364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLsacaclgdldvgvklhelaerkglisyvvvanaliemysKCKCIDKA 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  229 RELFDRFTEKDVVTWNAMISGYVNCGYPKEALGIFKEMRdAGEHPDVVTILSLLSACAVLGDLETGKRLHIYILETAsVS 308
Cdd:PLN03077 444 LEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTG-IG 521

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  309 SSIYVGtpiwNALIDMYAKCGSIDRAIEVFrGVKDRDLSTWNTLIVGLAlHHAEGSI--EMFEEMQRLKVWPNEVTFIGV 386
Cdd:PLN03077 522 FDGFLP----NALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYV-AHGKGSMavELFNRMVESGVNPDEVTFISL 595

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  387 ILACSHSGRVDEGRKYFSLMRDMYNIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMKIEPNAIVWRTLLGACKIYGNVEL 466
Cdd:PLN03077 596 LCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVEL 675

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 42567862  467 GKYANEKLLSMRKDESGDYVLLSNIYASTGQWDGVQKVRKMFDDTRVKKPTGVSLIE 523
Cdd:PLN03077 676 GELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVE 732
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 53-504 9.64e-81

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 266.74  E-value: 9.64e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   53 SASLSVPGALKYAHKLFDEIPKPDVSICNHVLRGSAQSMKPekTVSLYTEMEKRgVSPDRY------------------- 113
Cdd:PLN03081  46 ISCSSVEQGLKPRPRLKPEPIRIEVSESKDARLDDTQIRKS--GVSLCSQIEKL-VACGRHrealelfeileagcpftlp 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  114 --TFTFVLKACSKLewRSNGFA--FHGKVVRHGFVLNEYVKNALILFHANCGDLGIASELFDDSAKAHKVAWSSMTSGYA 189
Cdd:PLN03081 123 asTYDALVEACIAL--KSIRCVkaVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLV 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  190 KRGKIDEAMRLFDEM----------------------------------PYKDQVAWNVMITGCL-----KCKEMDSARE 230
Cdd:PLN03081 201 DAGNYREAFALFREMwedgsdaeprtfvvmlrasaglgsaragqqlhccVLKTGVVGDTFVSCALidmysKCGDIEDARC 280

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  231 LFDRFTEKDVVTWNAMISGYVNCGYPKEALGIFKEMRDAGEHPDVVTILSLLSACAVLGDLETGKRLHIYILETAsVSSS 310
Cdd:PLN03081 281 VFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTG-FPLD 359

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  311 IYVGTpiwnALIDMYAKCGSIDRAIEVFRGVKDRDLSTWNTLIVGLALH-HAEGSIEMFEEMQRLKVWPNEVTFIGVILA 389
Cdd:PLN03081 360 IVANT----ALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHgRGTKAVEMFERMIAEGVAPNHVTFLAVLSA 435

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  390 CSHSGRVDEGRKYFSLMRDMYNIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMKIEPNAIVWRTLLGACKIYGNVELGKY 469
Cdd:PLN03081 436 CRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRL 515

                        490       500       510
                 ....*....|....*....|....*....|....*
gi 42567862  470 ANEKLLSMRKDESGDYVLLSNIYASTGQWDGVQKV 504
Cdd:PLN03081 516 AAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKV 550
PLN03077 PLN03077
Protein ECB2; Provisional
 213-458 1.51e-26

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 114.56  E-value: 1.51e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  213 NVMITGCLKCKEMDSARELFDRFTEKDVVTWNAMISGYVNCGYPKEALGIFKEMRDAGEHPDVVTILSLLSACAVLGDLE 292
Cdd:PLN03077 125 NAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLA 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  293 TGKRLHIYILETASVSSsiyvgTPIWNALIDMYAKCGSIDRAIEVFRGVKDRDLSTWNTLIVG-LALHHAEGSIEMFEEM 371
Cdd:PLN03077 205 RGREVHAHVVRFGFELD-----VDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGyFENGECLEGLELFFTM 279

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  372 QRLKVWPNEVTFIGVILACSHSGRVDEGRKYFSL-MRDMYNIepNIKHYGCMVDMLGRAGQLEEAFMFVESMKIEpNAIV 450
Cdd:PLN03077 280 RELSVDPDLMTITSVISACELLGDERLGREMHGYvVKTGFAV--DVSVCNSLIQMYLSLGSWGEAEKVFSRMETK-DAVS 356


                 ....*...
gi 42567862  451 WRTLLGAC 458
Cdd:PLN03077 357 WTAMISGY 364
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 190-478 1.32e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 77.22  E-value: 1.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   190 KRGKIDEAMRLFDEMPYKDQVAWNVMITGCLKCKEMDSARELFDRFTEK----DVVTWNAMISGYVNCGYPKEALGIFKE 265
Cdd:PLN03218  418 KQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAglkaDCKLYTTLISTCAKSGKVDAMFEVFHE 497

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   266 MRDAGEHPDVVTILSLLSACAVLGDLetGKRLHIY-ILETASVSSSIYVgtpiWNALIDMYAKCGSIDRAIEVFRGVK-- 342
Cdd:PLN03218  498 MVNAGVEANVHTFGALIDGCARAGQV--AKAFGAYgIMRSKNVKPDRVV----FNALISACGQSGAVDRAFDVLAEMKae 571

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   343 ----DRDLSTWNTLIVGLA-LHHAEGSIEMFEEMQRLKVWPNEVTFIGVILACSHSGRVDEGRK-YFSLMRDmyNIEPNI 416
Cdd:PLN03218  572 thpiDPDHITVGALMKACAnAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSiYDDMKKK--GVKPDE 649

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42567862   417 KHYGCMVDMLGRAGQLEEAFMFVESMK---IEPNAIVWRTLLGACKIYGNVELGKYANEKLLSMR 478
Cdd:PLN03218  650 VFFSALVDVAGHAGDLDKAFEILQDARkqgIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 57-425 2.04e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 76.45  E-value: 2.04e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862    57 SVPGALKYAhKLfdeIPKPDVSICNHVLRGSAQSMKPEKTVSLYTEMEKRGVSPDRYTFTFVLKACSKLEWRSNGF-AFH 135
Cdd:PLN03218  421 AVKEAFRFA-KL---IRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFeVFH 496

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   136 gKVVRHGFVLNEYVKNALILFHANCGDL-------GIaseLFDDSAKAHKVAWSSMTSGYAKRGKIDEAMRLFDEM---- 204
Cdd:PLN03218  497 -EMVNAGVEANVHTFGALIDGCARAGQVakafgayGI---MRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMkaet 572

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   205 -PYK-DQVAWNVMITGCLKCKEMDSARELFDRFTEKDVVTWNAMISGYVN-C---GYPKEALGIFKEMRDAGEHPDVVTI 278
Cdd:PLN03218  573 hPIDpDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNsCsqkGDWDFALSIYDDMKKKGVKPDEVFF 652

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   279 LSLLSACAVLGDLETGkrlhIYILETASvSSSIYVGTPIWNALIDMYAKCGSIDRAIEVFRGVKDRDL----STWNTLIV 354
Cdd:PLN03218  653 SALVDVAGHAGDLDKA----FEILQDAR-KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLrptvSTMNALIT 727

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42567862   355 GLAlhhaEG-----SIEMFEEMQRLKVWPNEVTFIGVILACSHSGRVDEGRKYFSLMRDmYNIEPNIKHYGCMVDM 425
Cdd:PLN03218  728 ALC----EGnqlpkALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKE-DGIKPNLVMCRCITGL 798
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 461-523 4.07e-14

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: 67.18  E-value: 4.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42567862   461 YGNVELGKYANEKLLSMRKDESGDYVLLSNIYASTGQWDGVQKVRKMFDDTRVKKPTGVSLIE 523
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 196-482 4.99e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 75.30  E-value: 4.99e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   196 EAMRLFDEMPYK-DQVAWNVMITGCLKCKEMDSARELFDRFT----EKDVVTWNAMISGYVNCGYPKEALGIFKEMRDAG 270
Cdd:PLN03218  458 RVLRLVQEAGLKaDCKLYTTLISTCAKSGKVDAMFEVFHEMVnagvEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKN 537

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   271 EHPDVVTILSLLSACA----------VLGDLETgkrlhiyilETASVSSS-IYVGtpiwnALIDMYAKCGSIDRAIEVFR 339
Cdd:PLN03218  538 VKPDRVVFNALISACGqsgavdrafdVLAEMKA---------ETHPIDPDhITVG-----ALMKACANAGQVDRAKEVYQ 603

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   340 GVKDRDL-STWNTLIVGLALHHAEGSIE----MFEEMQRLKVWPNEVTFIGVILACSHSGRVD-------EGRK------ 401
Cdd:PLN03218  604 MIHEYNIkGTPEVYTIAVNSCSQKGDWDfalsIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDkafeilqDARKqgiklg 683

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   402 ---YFSLMRDMYN------------------IEPNIKHYGCMVDMLGRAGQLEEAFMFVESMK---IEPNAIVWRTLLGA 457
Cdd:PLN03218  684 tvsYSSLMGACSNaknwkkalelyediksikLRPTVSTMNALITALCEGNQLPKALEVLSEMKrlgLCPNTITYSILLVA 763

                         330       340
                  ....*....|....*....|....*
gi 42567862   458 CKIYGNVELGkyanEKLLSMRKDES 482
Cdd:PLN03218  764 SERKDDADVG----LDLLSQAKEDG 784
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 97-459 5.25e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 75.30  E-value: 5.25e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862    97 VSLYTEMEKRG-VSPDRYTFTFVLKACSKLEWRSNGFAFhGKVVRHGfVLNEYvkNALILFHANCGD----LGIASELFD 171
Cdd:PLN03218  390 IDLLEDMEKRGlLDMDKIYHAKFFKACKKQRAVKEAFRF-AKLIRNP-TLSTF--NMLMSVCASSQDidgaLRVLRLVQE 465

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   172 DSAKAHKVAWSSMTSGYAKRGKIDEAMRLFDEMPyKDQVAWNV-----MITGCLKCKEMDSARELFDRFTEKDV----VT 242
Cdd:PLN03218  466 AGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMV-NAGVEANVhtfgaLIDGCARAGQVAKAFGAYGIMRSKNVkpdrVV 544

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   243 WNAMISGYVNCGYPKEALGIFKEMRdAGEHP---DVVTILSLLSACAVLGD----LETGKRLHIYILE------TASVSS 309
Cdd:PLN03218  545 FNALISACGQSGAVDRAFDVLAEMK-AETHPidpDHITVGALMKACANAGQvdraKEVYQMIHEYNIKgtpevyTIAVNS 623

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   310 -----------SIYVG------TP---IWNALIDMYAKCGSIDRAIEVFRGVKDRDLS----TWNTLI-VGLALHHAEGS 364
Cdd:PLN03218  624 csqkgdwdfalSIYDDmkkkgvKPdevFFSALVDVAGHAGDLDKAFEILQDARKQGIKlgtvSYSSLMgACSNAKNWKKA 703

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   365 IEMFEEMQRLKVWPNEVTFIGVILACSHSGRVDEGRKYFSLMRDMyNIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMKI 444
Cdd:PLN03218  704 LELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRL-GLCPNTITYSILLVASERKDDADVGLDLLSQAKE 782

                         410
                  ....*....|....*...
gi 42567862   445 E---PNAIVWRTLLGACK 459
Cdd:PLN03218  783 DgikPNLVMCRCITGLCL 800
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 238-286 9.09e-12

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 60.07  E-value: 9.09e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 42567862   238 KDVVTWNAMISGYVNCGYPKEALGIFKEMRDAGEHPDVVTILSLLSACA 286
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 336-514 1.84e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 60.66  E-value: 1.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   336 EVFRGVK---DRDLSTWNTLI-VGLALHHAEGSIEMFEEMQRLKVWPNEVTFIGVILACSHSGRVDegrKYFSLMRDMYN 411
Cdd:PLN03218  424 EAFRFAKlirNPTLSTFNMLMsVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVD---AMFEVFHEMVN 500

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   412 --IEPNIKHYGCMVDMLGRAGQLEEAF---MFVESMKIEPNAIVWRTLLGACKIYGNVElgkYANEKLLSMRKDES---G 483
Cdd:PLN03218  501 agVEANVHTFGALIDGCARAGQVAKAFgayGIMRSKNVKPDRVVFNALISACGQSGAVD---RAFDVLAEMKAETHpidP 577

                         170       180       190
                  ....*....|....*....|....*....|....
gi 42567862   484 DYVL---LSNIYASTGQWDGVQKVRKMFDDTRVK 514
Cdd:PLN03218  578 DHITvgaLMKACANAGQVDRAKEVYQMIHEYNIK 611
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 75-124 2.78e-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: 52.75  E-value: 2.78e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 42567862    75 PDVSICNHVLRGSAQSMKPEKTVSLYTEMEKRGVSPDRYTFTFVLKACSK 124
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 241-270 2.62e-07

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: 46.69  E-value: 2.62e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 42567862   241 VTWNAMISGYVNCGYPKEALGIFKEMRDAG 270
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 179-221 8.90e-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: 45.82  E-value: 8.90e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 42567862   179 VAWSSMTSGYAKRGKIDEAMRLFDEMPYK----DQVAWNVMITGCLK 221
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 241-275 1.02e-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: 45.14  E-value: 1.02e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42567862   241 VTWNAMISGYVNCGYPKEALGIFKEMRDAGEHPDV 275
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 207-252 1.10e-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: 45.43  E-value: 1.10e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 42567862   207 KDQVAWNVMITGCLKCKEMDSARELFDRFTEK----DVVTWNAMISGYVN 252
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 244-504 2.09e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 50.62  E-value: 2.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  244 NAMISGYVNCGYPKEALGIFKEMRDAGEHPDVVTILSLLSACAVLGDLETGKRLHIYILetasvSSSIYVGTPIWNALID 323
Cdd:PLN03077  55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRAL-----SSHPSLGVRLGNAMLS 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  324 MYAKCGSIDRAIEVFRGVKDRDLSTWNTLIVGLA-LHHAEGSIEMFEEMQRLKVWPNEVTFIGVILACS----------- 391
Cdd:PLN03077 130 MFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAkAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGgipdlargrev 209

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  392 HS------------------------GRVDEGRKYFSLMRDMYNIEPNIKHYGCMVDMLGRAGqLEEAFMFVEsMKIEPN 447
Cdd:PLN03077 210 HAhvvrfgfeldvdvvnalitmyvkcGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEG-LELFFTMRE-LSVDPD 287

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862  448 AIVWRTLLGACKIYGNVELGKYANEklLSMRKDESGDYVL---LSNIYASTGQWDGVQKV 504
Cdd:PLN03077 288 LMTITSVISACELLGDERLGREMHG--YVVKTGFAVDVSVcnsLIQMYLSLGSWGEAEKV 345
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 179-204 4.16e-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: 40.53  E-value: 4.16e-05
                          10        20
                  ....*....|....*....|....*.
gi 42567862   179 VAWSSMTSGYAKRGKIDEAMRLFDEM 204
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEM 26
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 229-285 6.89e-05

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 40.80  E-value: 6.89e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 42567862   229 RELFDRFTEKDVVTWNAMISGYVNCGYPKEALGIFKEMRDAGEHPDVVTILSLLSAC 285
Cdd:pfam13812   4 REMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 414-458 1.06e-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: 40.04  E-value: 1.06e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 42567862   414 PNIKHYGCMVDMLGRAGQLEEAFMFVESMK---IEPNAIVWRTLLGAC 458
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKkrgVKPNVYTYTILINGL 48
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 322-443 1.16e-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: 43.54  E-value: 1.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862   322 IDMYAKCGSIDRAIEVFRGVKDRDLS----TWNTLI-------VGLALHHAEGS---IEMFEEMQRLKVWPNEVTFIGVI 387
Cdd:pfam17177  18 LDKCSKHADATGALALYDAAKAEGVRlaqyHYNVLLylcskaaDATDLKPQLAAdrgFEVFEAMKAQGVSPNEATYTAVA 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 42567862   388 LACSHSGRVDEGrkyFSLMRDM--YNIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMK 443
Cdd:pfam17177  98 RLAAAKGDGDLA---FDLVKEMeaAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHML 152
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 393-499 1.35e-04

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: 42.10  E-value: 1.35e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42567862 393 SGRVDEGRKyfsLMRDMYNIEP-NIKHYGCMVDMLGRAGQLEEAF-MFVESMKIEPNAIVWRTLLGACKIygnvELGKYA 470
Cdd:COG4783  17 AGDYDEAEA---LLEKALELDPdNPEAFALLGEILLQLGDLDEAIvLLHEALELDPDEPEARLNLGLALL----KAGDYD 89

                        90       100       110
                ....*....|....*....|....*....|....
gi 42567862 471 N-----EKLLSMRKDESGDYVLLSNIYASTGQWD 499
Cdd:COG4783  90 EalallEKALKLDPEHPEAYLRLARAYRALGRPD 123
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 74-124 1.69e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 39.65  E-value: 1.69e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 42567862    74 KPDVSICNHVLRGSAQSMKPEKTVSLYTEMEKRGVSPDRYTFTFVLKACSK 124
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 239-267 2.10e-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: 38.48  E-value: 2.10e-04
                          10        20
                  ....*....|....*....|....*....
gi 42567862   239 DVVTWNAMISGYVNCGYPKEALGIFKEMR 267
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 179-204 4.43e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 37.71  E-value: 4.43e-04
                          10        20
                  ....*....|....*....|....*.
gi 42567862   179 VAWSSMTSGYAKRGKIDEAMRLFDEM 204
Cdd:pfam12854   8 VTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 411-443 1.50e-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: 36.17  E-value: 1.50e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 42567862   411 NIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMK 443
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 179-204 1.53e-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: 36.28  E-value: 1.53e-03
                          10        20
                  ....*....|....*....|....*.
gi 42567862   179 VAWSSMTSGYAKRGKIDEAMRLFDEM 204
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEM 26
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 344-392 2.14e-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: 36.19  E-value: 2.14e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 42567862   344 RDLSTWNTLIVGLA-LHHAEGSIEMFEEMQRLKVWPNEVTFIGVILACSH 392
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 ...
 317-357 2.32e-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: 36.19  E-value: 2.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 42567862   317 IWNALIDMYAKCGSIDRAIEVF-----RGVKdRDLSTWNTLIVGLA 357
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFnemkkRGVK-PNVYTYTILINGLC 49
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 210-240 6.30e-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: 34.36  E-value: 6.30e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 42567862   210 VAWNVMITGCLKCKEMDSARELFDRFTEKDV 240
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 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.
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