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Conserved domains on  [gi|334183972|ref|NP_177860|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000098)

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
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 137-475 1.03e-27

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 118.06  E-value: 1.03e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  137 YHMMIESTAKIRQYKLMWDLINAMRKKKM-LNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 215
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVeANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  216 SKNVRKAQEVFENMRDRFT---PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEAL 292
Cdd:PLN03218  555 SGAVDRAFDVLAEMKAETHpidPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  293 GIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKG 372
Cdd:PLN03218  635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  373 VTPNSKSCNIILRHLIERGEKDEAFDVFRKM--IKVCePDADTYTMVIKMfCEKKEM-ETADKVWKYMRKKGVFPSMHTF 449
Cdd:PLN03218  715 LRPTVSTMNALITALCEGNQLPKALEVLSEMkrLGLC-PNTITYSILLVA-SERKDDaDVGLDLLSQAKEDGIKPNLVMC 792

                         330       340
                  ....*....|....*....|....*.
gi 334183972  450 SVLInGLCEERtTQKACVLLEEMIEM 475
Cdd:PLN03218  793 RCIT-GLCLRR-FEKACALGEPVVSF 816
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 137-475 1.03e-27

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 118.06  E-value: 1.03e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  137 YHMMIESTAKIRQYKLMWDLINAMRKKKM-LNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 215
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVeANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  216 SKNVRKAQEVFENMRDRFT---PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEAL 292
Cdd:PLN03218  555 SGAVDRAFDVLAEMKAETHpidPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  293 GIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKG 372
Cdd:PLN03218  635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  373 VTPNSKSCNIILRHLIERGEKDEAFDVFRKM--IKVCePDADTYTMVIKMfCEKKEM-ETADKVWKYMRKKGVFPSMHTF 449
Cdd:PLN03218  715 LRPTVSTMNALITALCEGNQLPKALEVLSEMkrLGLC-PNTITYSILLVA-SERKDDaDVGLDLLSQAKEDGIKPNLVMC 792

                         330       340
                  ....*....|....*....|....*.
gi 334183972  450 SVLInGLCEERtTQKACVLLEEMIEM 475
Cdd:PLN03218  793 RCIT-GLCLRR-FEKACALGEPVVSF 816
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 409-457 7.02e-14

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: 65.85  E-value: 7.02e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334183972  409 PDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFSVLINGLC 457
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 178-368 9.60e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.42  E-value: 9.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 178 YARAQKVDEAIYAFNVMEKYDlPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDRFTPDSKTYSILLEGWGKEPNLPKAR 257
Cdd:COG2956   86 YLKAGLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAI 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 258 EVFREMIDAgcHPDIVTYSIM-VDILCKAGRVDEALGIVRSM---DPSickpTTFIYSVLVHTYGTENRLEEAVDTFLEM 333
Cdd:COG2956  165 EALEKALKL--DPDCARALLLlAELYLEQGDYEEAIAALERAleqDPD----YLPALPRLAELYEKLGDPEEALELLRKA 238

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 334183972 334 ERSgmKADVAVFNSLIGAFCKANRMKNVYRVLKEM 368
Cdd:COG2956  239 LEL--DPSDDLLLALADLLERKEGLEAALALLERQ 271
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 344-377 6.17e-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: 40.13  E-value: 6.17e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334183972  344 VFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNS 377
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 137-475 1.03e-27

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 118.06  E-value: 1.03e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  137 YHMMIESTAKIRQYKLMWDLINAMRKKKM-LNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 215
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVeANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  216 SKNVRKAQEVFENMRDRFT---PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEAL 292
Cdd:PLN03218  555 SGAVDRAFDVLAEMKAETHpidPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  293 GIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKG 372
Cdd:PLN03218  635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  373 VTPNSKSCNIILRHLIERGEKDEAFDVFRKM--IKVCePDADTYTMVIKMfCEKKEM-ETADKVWKYMRKKGVFPSMHTF 449
Cdd:PLN03218  715 LRPTVSTMNALITALCEGNQLPKALEVLSEMkrLGLC-PNTITYSILLVA-SERKDDaDVGLDLLSQAKEDGIKPNLVMC 792

                         330       340
                  ....*....|....*....|....*.
gi 334183972  450 SVLInGLCEERtTQKACVLLEEMIEM 475
Cdd:PLN03218  793 RCIT-GLCLRR-FEKACALGEPVVSF 816
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 177-498 2.33e-27

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 116.90  E-value: 2.33e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  177 KYARAQKVDEAIYAFNvmeKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPDSKTYSILLEGWGKEPNLPK 255
Cdd:PLN03218  414 KACKKQRAVKEAFRFA---KLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAgLKADCKLYTTLISTCAKSGKVDA 490

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  256 AREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEALG---IVRSMDpsiCKPTTFIYSVLVHTYGTENRLEEAVDTFLE 332
Cdd:PLN03218  491 MFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGaygIMRSKN---VKPDRVVFNALISACGQSGAVDRAFDVLAE 567

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  333 M--ERSGMKADVAVFNSLIGAFCKA---NRMKNVYRVLKE--------------------------------MKSKGVTP 375
Cdd:PLN03218  568 MkaETHPIDPDHITVGALMKACANAgqvDRAKEVYQMIHEynikgtpevytiavnscsqkgdwdfalsiyddMKKKGVKP 647

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  376 NSkscnIILRHLIE----RGEKDEAFDVFRKM-IKVCEPDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFS 450
Cdd:PLN03218  648 DE----VFFSALVDvaghAGDLDKAFEILQDArKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMN 723

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 334183972  451 VLINGLCEERTTQKACVLLEEMIEMGIRPSGVTFGrlrQLLIKEERED 498
Cdd:PLN03218  724 ALITALCEGNQLPKALEVLSEMKRLGLCPNTITYS---ILLVASERKD 768
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 409-457 7.02e-14

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: 65.85  E-value: 7.02e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334183972  409 PDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFSVLINGLC 457
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 170-484 1.75e-12

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 69.90  E-value: 1.75e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 170 TFCIVMRKYARAQKVDEAIYAFNVME---KYDLPPNlvAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPDSKTYSILLE 245
Cdd:PLN03081  89 SLCSQIEKLVACGRHREALELFEILEagcPFTLPAS--TYDALVEACIALKSIRCVKAVYWHVESSgFEPDQYMMNRVLL 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 246 GWGKEPNLPKAREVFREMIDAgchpDIVTYSIMVDILCKAGRVDEALGIVRSM--DPSICKPTTFIYSV----------- 312
Cdd:PLN03081 167 MHVKCGMLIDARRLFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMweDGSDAEPRTFVVMLrasaglgsara 242

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 313 ----------------------LVHTYGTENRLEEAVDTFLEMERsgmKADVAvFNSLIGAFCKANRMKNVYRVLKEMKS 370
Cdd:PLN03081 243 gqqlhccvlktgvvgdtfvscaLIDMYSKCGDIEDARCVFDGMPE---KTTVA-WNSMLAGYALHGYSEEALCLYYEMRD 318

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 371 KGVTPNSKSCNIILRHLIERGEKDEAFDVFRKMIKVCEP-DADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFpsmhTF 449
Cdd:PLN03081 319 SGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPlDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLI----SW 394

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 334183972 450 SVLINGLCEERTTQKACVLLEEMIEMGIRPSGVTF 484
Cdd:PLN03081 395 NALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTF 429
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 341-387 2.16e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 55.83  E-value: 2.16e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 334183972  341 DVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNSKSCNIILRHL 387
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 235-284 2.43e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 55.83  E-value: 2.43e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334183972  235 PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCK 284
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 ...
 201-246 2.98e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 55.45  E-value: 2.98e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 334183972  201 PNLVAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPDSKTYSILLEG 246
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgVKPNVYTYTILING 47
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 131-399 4.71e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 62.20  E-value: 4.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 131 EHSVRAYHMMIESTAKIRQYklmwdlinamrkkkmlnveTFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLL 210
Cdd:PLN03081 307 EEALCLYYEMRDSGVSIDQF-------------------TFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALV 367

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 211 SALCKSKNVRKAQEVFENMRDRftpDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDE 290
Cdd:PLN03081 368 DLYSKWGRMEDARNVFDRMPRK---NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQ 444

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 291 ALGIVRSMDPSI-CKPTTFIYSVLVHTYGTENRLEEAvdtFLEMERSGMKADVAVFNSLIGAfCKANRMKNVYRVLKEmK 369
Cdd:PLN03081 445 GWEIFQSMSENHrIKPRAMHYACMIELLGREGLLDEA---YAMIRRAPFKPTVNMWAALLTA-CRIHKNLELGRLAAE-K 519

                        250       260       270
                 ....*....|....*....|....*....|.
gi 334183972 370 SKGVTPNSKSCNIILRHL-IERGEKDEAFDV 399
Cdd:PLN03081 520 LYGMGPEKLNNYVVLLNLyNSSGRQAEAAKV 550
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 375-422 9.46e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 54.29  E-value: 9.46e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334183972  375 PNSKSCNIILRHLIERGEKDEAFDVFRKMIKV-CEPDADTYTMVIKMFC 422
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgVKPNVYTYTILINGLC 49
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 267-298 2.10e-09

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: 52.73  E-value: 2.10e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 334183972  267 GCHPDIVTYSIMVDILCKAGRVDEALGIVRSM 298
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 172-402 3.26e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 59.50  E-value: 3.26e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 172 CIVMRKYARAQKVDEAIYAFNVMEKydlpPNLVAFNGLLSALCKSKNVRKAQEVFENMRD-RFTPDSKTYSILLEGWGKE 250
Cdd:PLN03081 263 CALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDsGVSIDQFTFSIMIRIFSRL 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 251 PNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEALGIVRSMdpsickPTTFIYS--VLVHTYGTENRLEEAVD 328
Cdd:PLN03081 339 ALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRM------PRKNLISwnALIAGYGNHGRGTKAVE 412

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334183972 329 TFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEM-KSKGVTPNSKSCNIILRHLIERGEKDEAFDVFRK 402
Cdd:PLN03081 413 MFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMsENHRIKPRAMHYACMIELLGREGLLDEAYAMIRR 487
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 305-354 4.35e-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: 49.28  E-value: 4.35e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334183972  305 PTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCK 354
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 178-374 1.85e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 54.09  E-value: 1.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 178 YARAQKVDEAIYAFNVMEKydlppNLVAFNGLLSALCKSKNVRKAQEVFENM-RDRFTPDSKTYSILLEGWGKEPNLPKA 256
Cdd:PLN03077 534 YVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHGKGSMAVELFNRMvESGVNPDEVTFISLLCACSRSGMVTQG 608

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 257 REVFREM-IDAGCHPDIVTYSIMVDILCKAGRVDEALGIVRSMDpsiCKPTTFIYSVLVHTYGTENRL---EEAVDTFLE 332
Cdd:PLN03077 609 LEYFHSMeEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACRIHRHVelgELAAQHIFE 685

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 334183972 333 MErsgmKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVT 374
Cdd:PLN03077 686 LD----PNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLT 723
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 326-444 4.20e-07

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: 50.86  E-value: 4.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  326 AVDTFLEMERSGMKADVAVFNSLI---------GAFCKANRMKNVYRVLKEMKSKGVTPNSKSCNIILRHLIERGEKDEA 396
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 334183972  397 FDVFRKMIKV-CEPDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFP 444
Cdd:pfam17177 110 FDLVKEMEAAgVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PLN03077 PLN03077
Protein ECB2; Provisional
 186-405 6.32e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 49.08  E-value: 6.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 186 EAIYAFNVMeKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENM------RDRFTP------------------------ 235
Cdd:PLN03077 473 EALIFFRQM-LLTLKPNSVTLIAALSACARIGALMCGKEIHAHVlrtgigFDGFLPnalldlyvrcgrmnyawnqfnshe 551

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 236 -DSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYsimVDILC---KAGRVDEALGIVRSMDPSI-CKPTTFIY 310
Cdd:PLN03077 552 kDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTF---ISLLCacsRSGMVTQGLEYFHSMEEKYsITPNLKHY 628

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 311 SVLVHTYGTENRLEEAVDTFLEMErsgMKADVAVFNSLIGAfCKANRmkNVyrVLKEMKSKGV---TPNSKSCNIILRHL 387
Cdd:PLN03077 629 ACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNA-CRIHR--HV--ELGELAAQHIfelDPNSVGYYILLCNL 700

                        250
                 ....*....|....*....
gi 334183972 388 -IERGEKDEAFDVfRKMIK 405
Cdd:PLN03077 701 yADAGKWDEVARV-RKTMR 718
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 167-215 6.99e-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: 43.12  E-value: 6.99e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334183972  167 NVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 215
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 178-368 9.60e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.42  E-value: 9.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 178 YARAQKVDEAIYAFNVMEKYDlPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDRFTPDSKTYSILLEGWGKEPNLPKAR 257
Cdd:COG2956   86 YLKAGLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAI 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 258 EVFREMIDAgcHPDIVTYSIM-VDILCKAGRVDEALGIVRSM---DPSickpTTFIYSVLVHTYGTENRLEEAVDTFLEM 333
Cdd:COG2956  165 EALEKALKL--DPDCARALLLlAELYLEQGDYEEAIAALERAleqDPD----YLPALPRLAELYEKLGDPEEALELLRKA 238

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 334183972 334 ERSgmKADVAVFNSLIGAFCKANRMKNVYRVLKEM 368
Cdd:COG2956  239 LEL--DPSDDLLLALADLLERKEGLEAALALLERQ 271
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 337-369 1.23e-05

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: 41.95  E-value: 1.23e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334183972  337 GMKADVAVFNSLIGAFCKANRMKNVYRVLKEMK 369
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 186-484 2.09e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 47.15  E-value: 2.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 186 EAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFE-NMRDRFTPDSKTYSILLEGWGKEPNLPKAREVFREMi 264
Cdd:PLN03077 271 EGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGyVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRM- 349

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 265 daGCHpDIVTYSIMVDILCKAGRVDEALGIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAV 344
Cdd:PLN03077 350 --ETK-DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVV 426

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 345 FNSLIGAFCKANRMKNVYRVLKEMKSKGVTpnskSCNIILRHLIERGEKDEAFDVFRKMIKVCEPDADTYTMVIKMFCEK 424
Cdd:PLN03077 427 ANALIEMYSKCKCIDKALEVFHNIPEKDVI----SWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARI 502

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 425 KEMETADKVWKYMRKKGV--------------------------FPS----MHTFSVLINGLCEERTTQKACVLLEEMIE 474
Cdd:PLN03077 503 GALMCGKEIHAHVLRTGIgfdgflpnalldlyvrcgrmnyawnqFNShekdVVSWNILLTGYVAHGKGSMAVELFNRMVE 582

                        330
                 ....*....|
gi 334183972 475 MGIRPSGVTF 484
Cdd:PLN03077 583 SGVNPDEVTF 592
PLN03077 PLN03077
Protein ECB2; Provisional
 153-484 3.05e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 46.77  E-value: 3.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 153 MWDLINAMRKKKMLNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFEN-MRD 231
Cdd:PLN03077 137 LVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHvVRF 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 232 RFTPDSKTYSILLEGWGKEPNLPKAREVFREMidagCHPDIVTYSIMVDILCKAGRVDEALGIVRSM-----DPSICKPT 306
Cdd:PLN03077 217 GFELDVDVVNALITMYVKCGDVVSARLVFDRM----PRRDCISWNAMISGYFENGECLEGLELFFTMrelsvDPDLMTIT 292

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 307 TFIysVLVHTYGTEnRLEEAVDTFleMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVTpnskSCNIILRH 386
Cdd:PLN03077 293 SVI--SACELLGDE-RLGREMHGY--VVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAV----SWTAMISG 363

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 387 LIERGEKDEAFDVFRKM-IKVCEPDADT-------------------------------YTMV----IKMFCEKKEMETA 430
Cdd:PLN03077 364 YEKNGLPDKALETYALMeQDNVSPDEITiasvlsacaclgdldvgvklhelaerkglisYVVVanalIEMYSKCKCIDKA 443

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 334183972 431 DKVWKYMRKKGVFpsmhTFSVLINGLCEERTTQKACVLLEEMIeMGIRPSGVTF 484
Cdd:PLN03077 444 LEVFHNIPEKDVI----SWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTL 492
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 332-384 3.11e-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: 41.96  E-value: 3.11e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 334183972  332 EMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNSKSCNIIL 384
Cdd:pfam13812   5 EMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 215-365 3.72e-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: 45.08  E-value: 3.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  215 KSKNVRKAQEVFENMRDRFTPDSK-TYSILL-------EGWGKEPNLPKAR--EVFREMIDAGCHPDIVTYSIMVDILCK 284
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVRLAQyHYNVLLylcskaaDATDLKPQLAADRgfEVFEAMKAQGVSPNEATYTAVARLAAA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  285 AGRVDEALGIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRV 364
Cdd:pfam17177 103 KGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAY 182


                  .
gi 334183972  365 L 365
Cdd:pfam17177 183 L 183
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 363-421 4.13e-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: 41.57  E-value: 4.13e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  363 RVLKEMKSKGVTPNSKSCNIILRHLIERGEKDEAFDVFRKMIKV-CEPDADTYTMVIKMF 421
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKgIKPTLDTYNAILGVI 60
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 444-484 5.34e-05

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.81  E-value: 5.34e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 334183972  444 PSMHTFSVLINGLCEERTTQKACVLLEEMIEMGIRPSGVTF 484
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 344-377 6.17e-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: 40.13  E-value: 6.17e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334183972  344 VFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNS 377
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 159-245 1.35e-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: 43.15  E-value: 1.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972  159 AMRKKKML-NVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPD 236
Cdd:pfam17177  80 AMKAQGVSpNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHgVELE 159


                  ....*....
gi 334183972  237 SKTYSILLE 245
Cdd:pfam17177 160 EPELAALLK 168
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 440-472 2.41e-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: 2.41e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334183972  440 KGVFPSMHTFSVLINGLCEERTTQKACVLLEEM 472
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 344-373 3.50e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.83  E-value: 3.50e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 334183972  344 VFNSLIGAFCKANRMKNVYRVLKEMKSKGV 373
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 413-445 4.67e-04

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 37.43  E-value: 4.67e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334183972  413 TYTMVIKMFCEKKEMETADKVWKYMRKKGVFPS 445
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 273-298 9.67e-04

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.66  E-value: 9.67e-04
                          10        20
                  ....*....|....*....|....*.
gi 334183972  273 VTYSIMVDILCKAGRVDEALGIVRSM 298
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEM 26
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 399-454 1.12e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 37.34  E-value: 1.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 334183972  399 VFRKM-IKVCEPDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFSVLIN 454
Cdd:pfam13812   2 ILREMvRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 149-338 1.37e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 41.39  E-value: 1.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 149 QYKLMWDLINAMRKKKMLNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFEN 228
Cdd:PLN03081 372 KWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQS 451

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 229 MRD--RFTPDSKTYSILLEGWGKEPNLPKAREVFREMidagchPDIVTYSiMVDILCKAGRVDEALGIVR-------SMD 299
Cdd:PLN03081 452 MSEnhRIKPRAMHYACMIELLGREGLLDEAYAMIRRA------PFKPTVN-MWAALLTACRIHKNLELGRlaaeklyGMG 524

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 334183972 300 PSICKPttfiYSVLVHTYGTENRLEEAVDTFLEMERSGM 338
Cdd:PLN03081 525 PEKLNN----YVVLLNLYNSSGRQAEAAKVVETLKRKGL 559
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 131-298 1.62e-03

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: 40.48  E-value: 1.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 131 EHSVRAYHMMIESTAKIRQYKLMWDLINAMRKKKMLNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDlPPNLVAFNGLL 210
Cdd:COG2956  107 PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKLD-PDCARALLLLA 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 211 SALCKSKNVRKAQEVFENMRDRFTPDSKTYSILLEGWGKEPNLPKAREVFREMIDAgcHPDIVTYSIMVDILCKAGRVDE 290
Cdd:COG2956  186 ELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALEL--DPSDDLLLALADLLERKEGLEA 263


                 ....*...
gi 334183972 291 ALGIVRSM 298
Cdd:COG2956  264 ALALLERQ 271
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 273-298 1.86e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 35.90  E-value: 1.86e-03
                          10        20
                  ....*....|....*....|....*.
gi 334183972  273 VTYSIMVDILCKAGRVDEALGIVRSM 298
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEM 26
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 252-435 2.62e-03

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: 39.71  E-value: 2.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 252 NLPKAREVFREMIDAgcHPDIV-TYSIMVDILCKAGRVDEALGIVRSM---DPSickpTTFIYSVLVHTYGTENRLEEAV 327
Cdd:COG2956   23 QPDKAIDLLEEALEL--DPETVeAHLALGNLYRRRGEYDRAIRIHQKLlerDPD----RAEALLELAQDYLKAGLLDRAE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183972 328 DTFLEMERSGMKaDVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGvtPNSKSCNIIL-RHLIERGEKDEAFDVFRKMIKV 406
Cdd:COG2956   97 ELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELaELYLEQGDYDEAIEALEKALKL 173

                        170       180
                 ....*....|....*....|....*....
gi 334183972 407 CEPDADTYTMVIKMFCEKKEMETADKVWK 435
Cdd:COG2956  174 DPDCARALLLLAELYLEQGDYEEAIAALE 202
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 407-438 4.80e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 34.63  E-value: 4.80e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 334183972  407 CEPDADTYTMVIKMFCEKKEMETADKVWKYMR 438
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 194-250 5.27e-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: 5.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334183972  194 MEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENMR-DRFTPDSKTYSILLEGWGKE 250
Cdd:pfam13812   6 MVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKkKGIKPTLDTYNAILGVIGGR 63
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 447-480 5.92e-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: 34.35  E-value: 5.92e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334183972  447 HTFSVLINGLCEERTTQKACVLLEEMIEMGIRPS 480
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 259-320 6.30e-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: 6.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334183972  259 VFREMIDAGCHPDIVTYSIMVDILCKAGRVDEALGIVRSMDPSICKPTTFIYSVLVHTYGTE 320
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 308-342 6.59e-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: 34.35  E-value: 6.59e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334183972  308 FIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADV 342
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 239-272 8.35e-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: 33.97  E-value: 8.35e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334183972  239 TYSILLEGWGKEPNLPKAREVFREMIDAGCHPDI 272
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 225-276 9.52e-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: 34.64  E-value: 9.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 334183972  225 VFENM-RDRFTPDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYS 276
Cdd:pfam13812   2 ILREMvRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYN 54
 
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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