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Conserved domains on  [gi|219939492|emb|CAW71156|]
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unnamed protein product [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
 70-713 0e+00

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 545.99  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  70 VLAWKSVIRCFTDQSLFSKALASFVEMRASGRCPDHNVFPSVLKSCTMMMDLRFGESVHGFIVRLGMDCDLYTGNALMNM 149
Cdd:PLN03077 152 LFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITM 231

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 150 YAKLlgmGSKISVGNVFDEMPQRT----------------------------SNSGDEDVKAETCIMP------------ 189
Cdd:PLN03077 232 YVKC---GDVVSARLVFDRMPRRDciswnamisgyfengecleglelfftmrELSVDPDLMTITSVISacellgderlgr 308

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 190 ----------FGID------------------SVRRVFEVMPRKDVVSYNTIIAGYAQSGMYEDALRMVREMGTTDLKPD 241
Cdd:PLN03077 309 emhgyvvktgFAVDvsvcnsliqmylslgswgEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPD 388

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 242 SFTLSSVLPIFSEYVDVIKGKEIHGYVIRKGIDSDVYIGSSLVDMYAKSARIEDSERVFSRLYCRDGISWNSLVAGYVQN 321
Cdd:PLN03077 389 EITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLN 468

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 322 GRYNEALRLFRQMVtAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIASALVDMYSKCGNIKAARKIF 401
Cdd:PLN03077 469 NRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF 547

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 402 DrMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQELE 481
Cdd:PLN03077 548 N-SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLK 626

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 482 HYAAVADLLGRAGKLEEAYNFISKMCVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTVDSENMGAYVLMCNMYASNGR 561
Cdd:PLN03077 627 HYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGK 706

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 562 WKEMAKLRLRMRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSMDKINEFLKAVMEQMEKEGYVADTSGVLHDvDEEHKR 641
Cdd:PLN03077 707 WDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDE-IEVSKD 785

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 219939492 642 ELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVAIKFISKITEREIIVRDNSRFHHFNRGNCSCGD 713
Cdd:PLN03077 786 DIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
 10-115 2.82e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


The actual alignment was detected with superfamily member PLN03081:

Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 41.01  E-value: 2.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  10 TLIKNPTRIKSKSQAKQLHAQFIRTQ-SLSHTSASIVISIYTNLKLLHEALLLFKTLKSPPVLAWKSVIRCFTDQSLFSK 88
Cdd:PLN03081 330 IMIRIFSRLALLEHAKQAHAGLIRTGfPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTK 409

                         90       100
                 ....*....|....*....|....*..
gi 219939492  89 ALASFVEMRASGRCPDHNVFPSVLKSC 115
Cdd:PLN03081 410 AVEMFERMIAEGVAPNHVTFLAVLSAC 436
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 70-713 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 545.99  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  70 VLAWKSVIRCFTDQSLFSKALASFVEMRASGRCPDHNVFPSVLKSCTMMMDLRFGESVHGFIVRLGMDCDLYTGNALMNM 149
Cdd:PLN03077 152 LFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITM 231

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 150 YAKLlgmGSKISVGNVFDEMPQRT----------------------------SNSGDEDVKAETCIMP------------ 189
Cdd:PLN03077 232 YVKC---GDVVSARLVFDRMPRRDciswnamisgyfengecleglelfftmrELSVDPDLMTITSVISacellgderlgr 308

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 190 ----------FGID------------------SVRRVFEVMPRKDVVSYNTIIAGYAQSGMYEDALRMVREMGTTDLKPD 241
Cdd:PLN03077 309 emhgyvvktgFAVDvsvcnsliqmylslgswgEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPD 388

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 242 SFTLSSVLPIFSEYVDVIKGKEIHGYVIRKGIDSDVYIGSSLVDMYAKSARIEDSERVFSRLYCRDGISWNSLVAGYVQN 321
Cdd:PLN03077 389 EITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLN 468

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 322 GRYNEALRLFRQMVtAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIASALVDMYSKCGNIKAARKIF 401
Cdd:PLN03077 469 NRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF 547

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 402 DrMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQELE 481
Cdd:PLN03077 548 N-SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLK 626

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 482 HYAAVADLLGRAGKLEEAYNFISKMCVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTVDSENMGAYVLMCNMYASNGR 561
Cdd:PLN03077 627 HYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGK 706

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 562 WKEMAKLRLRMRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSMDKINEFLKAVMEQMEKEGYVADTSGVLHDvDEEHKR 641
Cdd:PLN03077 707 WDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDE-IEVSKD 785

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 219939492 642 ELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVAIKFISKITEREIIVRDNSRFHHFNRGNCSCGD 713
Cdd:PLN03077 786 DIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 623-715 3.58e-48

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: 164.52  E-value: 3.58e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  623 GYVADTSGVLHDVDEEHKRELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVAIKFISKITEREIIVRDNSRFH 702
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 219939492  703 HFNRGNCSCGDYW 715
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 309-341 2.49e-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: 41.67  E-value: 2.49e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 219939492  309 ISWNSLVAGYVQNGRYNEALRLFRQMVTAKVKP 341
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 283-506 6.59e-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: 45.49  E-value: 6.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 283 LVDMYAKSARIEDSERVFSRLYCRDGIS---WNSLVAGYVQNGRYNEALRLFRQMVtaKVKPGAVafssviPACAHLATL 359
Cdd:COG2956   48 LGNLYRRRGEYDRAIRIHQKLLERDPDRaeaLLELAQDYLKAGLLDRAEELLEKLL--ELDPDDA------EALRLLAEI 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 360 HLgkQLHGYV--------LRGGFGSNIFIASALVDMYSKCGNIKAARKIFDRMNVLDEVSWTA-IIMGHALHGHGH--EA 428
Cdd:COG2956  120 YE--QEGDWEkaievlerLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARAlLLLAELYLEQGDyeEA 197

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 219939492 429 VSLFEEMKRQgvKPNQVAFVAVLTACS-HVGLVDEAwgyFNSMTKVYGLNQELEHYAAVADLLGRAGKLEEAYNFISKM 506
Cdd:COG2956  198 IAALERALEQ--DPDYLPALPRLAELYeKLGDPEEA---LELLRKALELDPSDDLLLALADLLERKEGLEAALALLERQ 271
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 10-115 2.82e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 41.01  E-value: 2.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  10 TLIKNPTRIKSKSQAKQLHAQFIRTQ-SLSHTSASIVISIYTNLKLLHEALLLFKTLKSPPVLAWKSVIRCFTDQSLFSK 88
Cdd:PLN03081 330 IMIRIFSRLALLEHAKQAHAGLIRTGfPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTK 409

                         90       100
                 ....*....|....*....|....*..
gi 219939492  89 ALASFVEMRASGRCPDHNVFPSVLKSC 115
Cdd:PLN03081 410 AVEMFERMIAEGVAPNHVTFLAVLSAC 436
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 70-713 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 545.99  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  70 VLAWKSVIRCFTDQSLFSKALASFVEMRASGRCPDHNVFPSVLKSCTMMMDLRFGESVHGFIVRLGMDCDLYTGNALMNM 149
Cdd:PLN03077 152 LFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITM 231

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 150 YAKLlgmGSKISVGNVFDEMPQRT----------------------------SNSGDEDVKAETCIMP------------ 189
Cdd:PLN03077 232 YVKC---GDVVSARLVFDRMPRRDciswnamisgyfengecleglelfftmrELSVDPDLMTITSVISacellgderlgr 308

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 190 ----------FGID------------------SVRRVFEVMPRKDVVSYNTIIAGYAQSGMYEDALRMVREMGTTDLKPD 241
Cdd:PLN03077 309 emhgyvvktgFAVDvsvcnsliqmylslgswgEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPD 388

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 242 SFTLSSVLPIFSEYVDVIKGKEIHGYVIRKGIDSDVYIGSSLVDMYAKSARIEDSERVFSRLYCRDGISWNSLVAGYVQN 321
Cdd:PLN03077 389 EITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLN 468

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 322 GRYNEALRLFRQMVtAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIASALVDMYSKCGNIKAARKIF 401
Cdd:PLN03077 469 NRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF 547

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 402 DrMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQELE 481
Cdd:PLN03077 548 N-SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLK 626

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 482 HYAAVADLLGRAGKLEEAYNFISKMCVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTVDSENMGAYVLMCNMYASNGR 561
Cdd:PLN03077 627 HYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGK 706

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 562 WKEMAKLRLRMRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSMDKINEFLKAVMEQMEKEGYVADTSGVLHDvDEEHKR 641
Cdd:PLN03077 707 WDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDE-IEVSKD 785

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 219939492 642 ELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVAIKFISKITEREIIVRDNSRFHHFNRGNCSCGD 713
Cdd:PLN03077 786 DIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 86-715 2.18e-176

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 520.58  E-value: 2.18e-176
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  86 FSKALASFVEMRAsgRCP---DHNVFPSVLKSCTMMMDLRFGESVHGFIVRLGMDCDLYTGNALMNMYAKllgmgskisv 162
Cdd:PLN03081 103 HREALELFEILEA--GCPftlPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVK---------- 170

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 163 gnvfdempqrtsnsgdedvkaetCIMpfgIDSVRRVFEVMPRKDVVSYNTIIAGYAQSGMYEDALRMVREM--GTTDLKP 240
Cdd:PLN03081 171 -----------------------CGM---LIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMweDGSDAEP 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 241 DSFT--LSSVLPIFSEYVdvikGKEIHGYVIRKGIDSDVYIGSSLVDMYAKSARIEDSERVFSRLYCRDGISWNSLVAGY 318
Cdd:PLN03081 225 RTFVvmLRASAGLGSARA----GQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGY 300

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 319 VQNGRYNEALRLFRQMVTAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIASALVDMYSKCGNIKAAR 398
Cdd:PLN03081 301 ALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDAR 380

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 399 KIFDRMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQ 478
Cdd:PLN03081 381 NVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKP 460

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 479 ELEHYAAVADLLGRAGKLEEAYNFISKMCVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTVDSENMGAYVLMCNMYAS 558
Cdd:PLN03081 461 RAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNS 540

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 559 NGRWKEMAKLRLRMRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSMDKINEFLKAVMEQMEKEGYVADTSGVLHDVDEE 638
Cdd:PLN03081 541 SGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDED 620

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 219939492 639 HKRELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVAIKFISKITEREIIVRDNSRFHHFNRGNCSCGDYW 715
Cdd:PLN03081 621 EEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 623-715 3.58e-48

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: 164.52  E-value: 3.58e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  623 GYVADTSGVLHDVDEEHKRELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVAIKFISKITEREIIVRDNSRFH 702
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 219939492  703 HFNRGNCSCGDYW 715
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PLN03077 PLN03077
Protein ECB2; Provisional
 211-545 3.54e-42

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 164.64  E-value: 3.54e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 211 NTIIAGYAQSGMYEDALRMVREMGTTDLKPDSFTLSSVLPIFSEYVDVIKGKEIHGYVIRKGIDSDVYIGSSLVDMYAKS 290
Cdd:PLN03077  55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRF 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 291 ARIEDSERVFSRLYCRDGISWNSLVAGYVQNGRYNEALRLFRQMVTAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVL 370
Cdd:PLN03077 135 GELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVV 214

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 371 RGGFGSNIFIASALVDMYSKCGNIKAARKIFDRMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAV 450
Cdd:PLN03077 215 RFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSV 294

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 451 LTAC---SHVGLVDEAWGYFNSMtkvyGLNQELEHYAAVADLLGRAGKLEEAYNFISKMCVEPTGSvWSTLLSSCSvhKN 527
Cdd:PLN03077 295 ISACellGDERLGREMHGYVVKT----GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVS-WTAMISGYE--KN 367

                        330
                 ....*....|....*...
gi 219939492 528 LeLAEKVAEKIFTVDSEN 545
Cdd:PLN03077 368 G-LPDKALETYALMEQDN 384
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 525-587 1.62e-18

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: 79.89  E-value: 1.62e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 219939492  525 HKNLELAEKVAEKIFTVDSENMGAYVLMCNMYASNGRWKEMAKLRLRMRKKGLRKKPACSWIE 587
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 311-538 5.60e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 62.97  E-value: 5.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  311 WNSLVAGYVQNGRYNEALRLFRQMVTAKVKPGAVAFSSVIPACAHLAtlHLGKQLHGY-VLRGgfgSNI----FIASALV 385
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAG--QVAKAFGAYgIMRS---KNVkpdrVVFNALI 549

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  386 dmySKCGNIKAARKIFDrmnVL------------DEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTA 453
Cdd:PLN03218  550 ---SACGQSGAVDRAFD---VLaemkaethpidpDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS 623

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  454 CSHVGLVDEAWGYFNSMTKVyGLNQELEHYAAVADLLGRAGKLEEAYNFISKMCVE--PTGSV-WSTLLSSCSVHKNLEL 530
Cdd:PLN03218  624 CSQKGDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQgiKLGTVsYSSLMGACSNAKNWKK 702


                  ....*...
gi 219939492  531 AEKVAEKI 538
Cdd:PLN03218  703 ALELYEDI 710
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 408-456 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
                  ....*....|....*....|....*....|....*....|....*....
gi 219939492  408 DEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSH 456
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 205-249 1.52e-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: 51.21  E-value: 1.52e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 219939492  205 KDVVSYNTIIAGYAQSGMYEDALRMVREMGTTDLKPDSFTLSSVL 249
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILI 45
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 137-454 2.07e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 57.96  E-value: 2.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  137 DCDLYTgnALMNMYAKllgMGSKISVGNVFDEMpqrtSNSGDE----------DVKAETCIMP--FGIDSVRRVFEVMPr 204
Cdd:PLN03218  471 DCKLYT--TLISTCAK---SGKVDAMFEVFHEM----VNAGVEanvhtfgaliDGCARAGQVAkaFGAYGIMRSKNVKP- 540

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  205 kDVVSYNTIIAGYAQSGMYEDALRMVREMG--TTDLKPDSFTLSSVLPIFSEYVDVIKGKE----IHGYVIrKGIdSDVY 278
Cdd:PLN03218  541 -DRVVFNALISACGQSGAVDRAFDVLAEMKaeTHPIDPDHITVGALMKACANAGQVDRAKEvyqmIHEYNI-KGT-PEVY 617

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  279 igSSLVDMYAKSARIEDSERVFSRLYcRDGISWNSL-------VAGYVqnGRYNEALRLFRQMVTAKVKPGAVAFSSVIP 351
Cdd:PLN03218  618 --TIAVNSCSQKGDWDFALSIYDDMK-KKGVKPDEVffsalvdVAGHA--GDLDKAFEILQDARKQGIKLGTVSYSSLMG 692

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  352 ACAHLATLHLGKQLhgyvlrggfgsnifiasalvdmYSKCGNIKaARKIFDRMNVLdevsWTAIIMGHALhghgHEAVSL 431
Cdd:PLN03218  693 ACSNAKNWKKALEL----------------------YEDIKSIK-LRPTVSTMNAL----ITALCEGNQL----PKALEV 741

                         330       340
                  ....*....|....*....|...
gi 219939492  432 FEEMKRQGVKPNQVAFVAVLTAC 454
Cdd:PLN03218  742 LSEMKRLGLCPNTITYSILLVAS 764
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 309-355 2.52e-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: 50.44  E-value: 2.52e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 219939492  309 ISWNSLVAGYVQNGRYNEALRLFRQMVTAKVKPGAVAFSSVIPACAH 355
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 435-658 1.33e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 55.27  E-value: 1.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  435 MKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMTkVYGLNQELEHYAAVADLLGRAGKLEEA---YNFISKMCVEPT 511
Cdd:PLN03218  463 VQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMV-NAGVEANVHTFGALIDGCARAGQVAKAfgaYGIMRSKNVKPD 541

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  512 GSVWSTLLSSCS----VHKNLE-LAEKVAE-KIFTVDSENMGAYVLMCNMYASNGRWKEMAKLrlrMRKKGLRKKPACSW 585
Cdd:PLN03218  542 RVVFNALISACGqsgaVDRAFDvLAEMKAEtHPIDPDHITVGALMKACANAGQVDRAKEVYQM---IHEYNIKGTPEVYT 618

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219939492  586 IEMKNKTHgfvSGDRshpsmdkinEFLKAVMEQMEKEGYVADTS--GVLHDVDeehkrellfGHSERLAVAFGII 658
Cdd:PLN03218  619 IAVNSCSQ---KGDW---------DFALSIYDDMKKKGVKPDEVffSALVDVA---------GHAGDLDKAFEIL 672
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 326-534 1.69e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.88  E-value: 1.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  326 EALRLFRQMVTAKVKpgavAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIASALVDMYSKCGNIKAARKIFDRMn 405
Cdd:PLN03218  424 EAFRFAKLIRNPTLS----TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEM- 498

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  406 VLDEV-----SWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMT-KVYGLNQE 479
Cdd:PLN03218  499 VNAGVeanvhTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKaETHPIDPD 578

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 219939492  480 LEHYAAVADLLGRAGKLE---EAYNFISKMCVEPTGSVWSTLLSSCSVHKNLELAEKV 534
Cdd:PLN03218  579 HITVGALMKACANAGQVDrakEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSI 636
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 272-521 3.90e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 53.73  E-value: 3.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  272 GIDSDVYIGSSLVDMYAKSARIEDSERVFSRLyCRDGISWN-----SLVAGYVQNGRYNEALRLFRQMVTAKVKPGAVAF 346
Cdd:PLN03218  467 GLKADCKLYTTLISTCAKSGKVDAMFEVFHEM-VNAGVEANvhtfgALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVF 545

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  347 SSVIPACAHLATL--------HLGKQLH----GYVLRGgfgsnifiasALVDMYSKCGNIKAARKIFDRMNVLD-----E 409
Cdd:PLN03218  546 NALISACGQSGAVdrafdvlaEMKAETHpidpDHITVG----------ALMKACANAGQVDRAKEVYQMIHEYNikgtpE 615

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  410 VsWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMtKVYGLNQELEHYAAVADL 489
Cdd:PLN03218  616 V-YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDA-RKQGIKLGTVSYSSLMGA 693

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 219939492  490 LGRAGKLEEA---YNFISKMCVEPTGSVWSTLLSS 521
Cdd:PLN03218  694 CSNAKNWKKAlelYEDIKSIKLRPTVSTMNALITA 728
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 206-233 8.88e-06

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: 42.72  E-value: 8.88e-06
                          10        20
                  ....*....|....*....|....*...
gi 219939492  206 DVVSYNTIIAGYAQSGMYEDALRMVREM 233
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 309-341 2.49e-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: 41.67  E-value: 2.49e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 219939492  309 ISWNSLVAGYVQNGRYNEALRLFRQMVTAKVKP 341
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 208-242 2.81e-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: 41.29  E-value: 2.81e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 219939492  208 VSYNTIIAGYAQSGMYEDALRMVREMGTTDLKPDS 242
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 410-440 3.21e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 41.30  E-value: 3.21e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 219939492  410 VSWTAIIMGHALHGHGHEAVSLFEEMKRQGV 440
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 385-522 3.44e-05

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: 45.47  E-value: 3.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  385 VDMYSKCGNIKAARKIFDRMnVLDEVSWTAIIMGHALH----------GHGHEAVS----LFEEMKRQGVKPNQVAFVAV 450
Cdd:pfam17177  18 LDKCSKHADATGALALYDAA-KAEGVRLAQYHYNVLLYlcskaadatdLKPQLAADrgfeVFEAMKAQGVSPNEATYTAV 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219939492  451 LTACSHVGLVDEAWGYFNSMTKvYGLNQELEHYAAVADLLGRAGKLEEAYNFISKMC---VEPTGSVWSTLLSSC 522
Cdd:pfam17177  97 ARLAAAKGDGDLAFDLVKEMEA-AGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLahgVELEEPELAALLKVS 170
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 410-443 4.63e-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: 40.90  E-value: 4.63e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 219939492  410 VSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPN 443
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 283-506 6.59e-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: 45.49  E-value: 6.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 283 LVDMYAKSARIEDSERVFSRLYCRDGIS---WNSLVAGYVQNGRYNEALRLFRQMVtaKVKPGAVafssviPACAHLATL 359
Cdd:COG2956   48 LGNLYRRRGEYDRAIRIHQKLLERDPDRaeaLLELAQDYLKAGLLDRAEELLEKLL--ELDPDDA------EALRLLAEI 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 360 HLgkQLHGYV--------LRGGFGSNIFIASALVDMYSKCGNIKAARKIFDRMNVLDEVSWTA-IIMGHALHGHGH--EA 428
Cdd:COG2956  120 YE--QEGDWEkaievlerLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARAlLLLAELYLEQGDyeEA 197

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 219939492 429 VSLFEEMKRQgvKPNQVAFVAVLTACS-HVGLVDEAwgyFNSMTKVYGLNQELEHYAAVADLLGRAGKLEEAYNFISKM 506
Cdd:COG2956  198 IAALERALEQ--DPDYLPALPRLAELYeKLGDPEEA---LELLRKALELDPSDDLLLALADLLERKEGLEAALALLERQ 271
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 309-335 8.49e-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: 8.49e-05
                          10        20
                  ....*....|....*....|....*..
gi 219939492  309 ISWNSLVAGYVQNGRYNEALRLFRQMV 335
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMK 27
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 208-233 9.64e-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: 39.76  E-value: 9.64e-05
                          10        20
                  ....*....|....*....|....*.
gi 219939492  208 VSYNTIIAGYAQSGMYEDALRMVREM 233
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEM 26
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 458-564 4.16e-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: 42.79  E-value: 4.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492 458 GLVDEAWGYFNSMTKVYGLNQELehYAAVADLLGRAGKLEEAYNFISKMC-VEPTGSVWSTLLSSCSV-HKNLELAEKVA 535
Cdd:COG2956   90 GLLDRAEELLEKLLELDPDDAEA--LRLLAEIYEQEGDWEKAIEVLERLLkLGPENAHAYCELAELYLeQGDYDEAIEAL 167

                         90       100
                 ....*....|....*....|....*....
gi 219939492 536 EKIFTVDSENMGAYVLMCNMYASNGRWKE 564
Cdd:COG2956  168 EKALKLDPDCARALLLLAELYLEQGDYEE 196
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 399-454 7.07e-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: 38.49  E-value: 7.07e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  399 KIFDRMNV----LDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVKPNQVAFVAVLTAC 454
Cdd:pfam13812   1 SILREMVRdgiqLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 304-335 7.74e-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: 37.33  E-value: 7.74e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 219939492  304 YCRDGISWNSLVAGYVQNGRYNEALRLFRQMV 335
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 10-115 2.82e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 41.01  E-value: 2.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219939492  10 TLIKNPTRIKSKSQAKQLHAQFIRTQ-SLSHTSASIVISIYTNLKLLHEALLLFKTLKSPPVLAWKSVIRCFTDQSLFSK 88
Cdd:PLN03081 330 IMIRIFSRLALLEHAKQAHAGLIRTGfPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTK 409

                         90       100
                 ....*....|....*....|....*..
gi 219939492  89 ALASFVEMRASGRCPDHNVFPSVLKSC 115
Cdd:PLN03081 410 AVEMFERMIAEGVAPNHVTFLAVLSAC 436
Eplus_motif pfam20430
E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins ...
 592-619 3.16e-03

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


Pssm-ID: 466579 [Multi-domain]  Cd Length: 28  Bit Score: 35.71  E-value: 3.16e-03
                          10        20
                  ....*....|....*....|....*...
gi 219939492  592 THGFVSGDRSHPSMDKINEFLKAVMEQM 619
Cdd:pfam20430   1 TYTFFAGDKSHPESKQIYEKLSDLTQRI 28
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 430-473 7.22e-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: 7.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 219939492  430 SLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMTKV 473
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKK 44
 
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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