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Conserved domains on  [gi|1063697154|ref|NP_001322987|]
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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
 101-439 9.23e-28

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 117.29  E-value: 9.23e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  101 YHMMIESTAKIRQYKLMWDLINAMRKKKM-LNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 179
Cdd:PLN03218   475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVeANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  180 SKNVRKAQEVFENMRDRFT---PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEAL 256
Cdd:PLN03218   555 SGAVDRAFDVLAEMKAETHpidPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  257 GIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKG 336
Cdd:PLN03218   635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  337 VTPNSKSCNIILRHLIERGEKDEAFDVFRKM--IKVCePDADTYTMVIKMfCEKKEM-ETADKVWKYMRKKGVFPSMHTF 413
Cdd:PLN03218   715 LRPTVSTMNALITALCEGNQLPKALEVLSEMkrLGLC-PNTITYSILLVA-SERKDDaDVGLDLLSQAKEDGIKPNLVMC 792

                          330       340
                   ....*....|....*....|....*.
gi 1063697154  414 SVLInGLCEERtTQKACVLLEEMIEM 439
Cdd:PLN03218   793 RCIT-GLCLRR-FEKACALGEPVVSF 816
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 101-439 9.23e-28

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 117.29  E-value: 9.23e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  101 YHMMIESTAKIRQYKLMWDLINAMRKKKM-LNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 179
Cdd:PLN03218   475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVeANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  180 SKNVRKAQEVFENMRDRFT---PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEAL 256
Cdd:PLN03218   555 SGAVDRAFDVLAEMKAETHpidPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  257 GIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKG 336
Cdd:PLN03218   635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  337 VTPNSKSCNIILRHLIERGEKDEAFDVFRKM--IKVCePDADTYTMVIKMfCEKKEM-ETADKVWKYMRKKGVFPSMHTF 413
Cdd:PLN03218   715 LRPTVSTMNALITALCEGNQLPKALEVLSEMkrLGLC-PNTITYSILLVA-SERKDDaDVGLDLLSQAKEDGIKPNLVMC 792

                          330       340
                   ....*....|....*....|....*.
gi 1063697154  414 SVLInGLCEERtTQKACVLLEEMIEM 439
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 ...
 373-421 6.84e-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: 6.84e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063697154 373 PDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFSVLINGLC 421
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 142-332 8.67e-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: 8.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 142 YARAQKVDEAIYAFNVMEKYDlPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDRFTPDSKTYSILLEGWGKEPNLPKAR 221
Cdd:COG2956    86 YLKAGLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAI 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 222 EVFREMIDAgcHPDIVTYSIM-VDILCKAGRVDEALGIVRSM---DPSickpTTFIYSVLVHTYGTENRLEEAVDTFLEM 297
Cdd:COG2956   165 EALEKALKL--DPDCARALLLlAELYLEQGDYEEAIAALERAleqDPD----YLPALPRLAELYEKLGDPEEALELLRKA 238

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1063697154 298 ERSgmKADVAVFNSLIGAFCKANRMKNVYRVLKEM 332
Cdd:COG2956   239 LEL--DPSDDLLLALADLLERKEGLEAALALLERQ 271
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 308-341 5.26e-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: 5.26e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063697154 308 VFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNS 341
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 101-439 9.23e-28

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 117.29  E-value: 9.23e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  101 YHMMIESTAKIRQYKLMWDLINAMRKKKM-LNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 179
Cdd:PLN03218   475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVeANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  180 SKNVRKAQEVFENMRDRFT---PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEAL 256
Cdd:PLN03218   555 SGAVDRAFDVLAEMKAETHpidPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  257 GIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKG 336
Cdd:PLN03218   635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  337 VTPNSKSCNIILRHLIERGEKDEAFDVFRKM--IKVCePDADTYTMVIKMfCEKKEM-ETADKVWKYMRKKGVFPSMHTF 413
Cdd:PLN03218   715 LRPTVSTMNALITALCEGNQLPKALEVLSEMkrLGLC-PNTITYSILLVA-SERKDDaDVGLDLLSQAKEDGIKPNLVMC 792

                          330       340
                   ....*....|....*....|....*.
gi 1063697154  414 SVLInGLCEERtTQKACVLLEEMIEM 439
Cdd:PLN03218   793 RCIT-GLCLRR-FEKACALGEPVVSF 816
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 141-462 2.17e-27

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 116.13  E-value: 2.17e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  141 KYARAQKVDEAIYAFNvmeKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPDSKTYSILLEGWGKEPNLPK 219
Cdd:PLN03218   414 KACKKQRAVKEAFRFA---KLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAgLKADCKLYTTLISTCAKSGKVDA 490

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  220 AREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEALG---IVRSMDpsiCKPTTFIYSVLVHTYGTENRLEEAVDTFLE 296
Cdd:PLN03218   491 MFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGaygIMRSKN---VKPDRVVFNALISACGQSGAVDRAFDVLAE 567

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  297 M--ERSGMKADVAVFNSLIGAFCKA---NRMKNVYRVLKE--------------------------------MKSKGVTP 339
Cdd:PLN03218   568 MkaETHPIDPDHITVGALMKACANAgqvDRAKEVYQMIHEynikgtpevytiavnscsqkgdwdfalsiyddMKKKGVKP 647

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  340 NSkscnIILRHLIE----RGEKDEAFDVFRKM-IKVCEPDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFS 414
Cdd:PLN03218   648 DE----VFFSALVDvaghAGDLDKAFEILQDArKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMN 723

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 1063697154  415 VLINGLCEERTTQKACVLLEEMIEMGIRPSGVTFGrlrQLLIKEERED 462
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 ...
 373-421 6.84e-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: 6.84e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063697154 373 PDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFSVLINGLC 421
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 134-448 1.34e-12

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 69.90  E-value: 1.34e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 134 TFCIVMRKYARAQKVDEAIYAFNVME---KYDLPPNlvAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPDSKTYSILLE 209
Cdd:PLN03081   89 SLCSQIEKLVACGRHREALELFEILEagcPFTLPAS--TYDALVEACIALKSIRCVKAVYWHVESSgFEPDQYMMNRVLL 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 210 GWGKEPNLPKAREVFREMIDAgchpDIVTYSIMVDILCKAGRVDEALGIVRSM--DPSICKPTTFIYSV----------- 276
Cdd:PLN03081  167 MHVKCGMLIDARRLFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMweDGSDAEPRTFVVMLrasaglgsara 242

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 277 ----------------------LVHTYGTENRLEEAVDTFLEMERsgmKADVAvFNSLIGAFCKANRMKNVYRVLKEMKS 334
Cdd:PLN03081  243 gqqlhccvlktgvvgdtfvscaLIDMYSKCGDIEDARCVFDGMPE---KTTVA-WNSMLAGYALHGYSEEALCLYYEMRD 318

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 335 KGVTPNSKSCNIILRHLIERGEKDEAFDVFRKMIKVCEP-DADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFpsmhTF 413
Cdd:PLN03081  319 SGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPlDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLI----SW 394

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 1063697154 414 SVLINGLCEERTTQKACVLLEEMIEMGIRPSGVTF 448
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 ...
 305-351 2.11e-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: 2.11e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063697154 305 DVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNSKSCNIILRHL 351
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 ...
 199-248 2.32e-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: 2.32e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063697154 199 PDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCK 248
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 ...
 165-210 2.83e-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: 2.83e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063697154 165 PNLVAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPDSKTYSILLEG 210
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgVKPNVYTYTILING 47
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 95-363 3.88e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 62.20  E-value: 3.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  95 EHSVRAYHMMIESTAKIRQYklmwdlinamrkkkmlnveTFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLL 174
Cdd:PLN03081  307 EEALCLYYEMRDSGVSIDQF-------------------TFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALV 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 175 SALCKSKNVRKAQEVFENMRDRftpDSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDE 254
Cdd:PLN03081  368 DLYSKWGRMEDARNVFDRMPRK---NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQ 444

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 255 ALGIVRSMDPSI-CKPTTFIYSVLVHTYGTENRLEEAvdtFLEMERSGMKADVAVFNSLIGAfCKANRMKNVYRVLKEmK 333
Cdd:PLN03081  445 GWEIFQSMSENHrIKPRAMHYACMIELLGREGLLDEA---YAMIRRAPFKPTVNMWAALLTA-CRIHKNLELGRLAAE-K 519

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1063697154 334 SKGVTPNSKSCNIILRHL-IERGEKDEAFDV 363
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 ...
 339-386 9.06e-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: 53.91  E-value: 9.06e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063697154 339 PNSKSCNIILRHLIERGEKDEAFDVFRKMIKV-CEPDADTYTMVIKMFC 386
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgVKPNVYTYTILINGLC 49
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 231-262 2.03e-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: 2.03e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1063697154 231 GCHPDIVTYSIMVDILCKAGRVDEALGIVRSM 262
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 136-366 2.56e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 59.50  E-value: 2.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 136 CIVMRKYARAQKVDEAIYAFNVMEKydlpPNLVAFNGLLSALCKSKNVRKAQEVFENMRD-RFTPDSKTYSILLEGWGKE 214
Cdd:PLN03081  263 CALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDsGVSIDQFTFSIMIRIFSRL 338

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 215 PNLPKAREVFREMIDAGCHPDIVTYSIMVDILCKAGRVDEALGIVRSMdpsickPTTFIYS--VLVHTYGTENRLEEAVD 292
Cdd:PLN03081  339 ALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRM------PRKNLISwnALIAGYGNHGRGTKAVE 412

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1063697154 293 TFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEM-KSKGVTPNSKSCNIILRHLIERGEKDEAFDVFRK 366
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 ...
 269-318 4.33e-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: 4.33e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063697154 269 PTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCK 318
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 142-338 1.38e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 54.09  E-value: 1.38e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 142 YARAQKVDEAIYAFNVMEKydlppNLVAFNGLLSALCKSKNVRKAQEVFENM-RDRFTPDSKTYSILLEGWGKEPNLPKA 220
Cdd:PLN03077  534 YVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHGKGSMAVELFNRMvESGVNPDEVTFISLLCACSRSGMVTQG 608

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 221 REVFREM-IDAGCHPDIVTYSIMVDILCKAGRVDEALGIVRSMDpsiCKPTTFIYSVLVHTYGTENRL---EEAVDTFLE 296
Cdd:PLN03077  609 LEYFHSMeEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACRIHRHVelgELAAQHIFE 685

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1063697154 297 MErsgmKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVT 338
Cdd:PLN03077  686 LD----PNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLT 723
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 290-408 4.35e-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: 50.47  E-value: 4.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 290 AVDTFLEMERSGMKADVAVFNSLI---------GAFCKANRMKNVYRVLKEMKSKGVTPNSKSCNIILRHLIERGEKDEA 360
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1063697154 361 FDVFRKMIKV-CEPDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFP 408
Cdd:pfam17177 110 FDLVKEMEAAgVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PLN03077 PLN03077
Protein ECB2; Provisional
 150-369 4.53e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 49.46  E-value: 4.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 150 EAIYAFNVMeKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENM------RDRFTP------------------------ 199
Cdd:PLN03077  473 EALIFFRQM-LLTLKPNSVTLIAALSACARIGALMCGKEIHAHVlrtgigFDGFLPnalldlyvrcgrmnyawnqfnshe 551

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 200 -DSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTYsimVDILC---KAGRVDEALGIVRSMDPSI-CKPTTFIY 274
Cdd:PLN03077  552 kDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTF---ISLLCacsRSGMVTQGLEYFHSMEEKYsITPNLKHY 628

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 275 SVLVHTYGTENRLEEAVDTFLEMErsgMKADVAVFNSLIGAfCKANRmkNVyrVLKEMKSKGV---TPNSKSCNIILRHL 351
Cdd:PLN03077  629 ACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNA-CRIHR--HV--ELGELAAQHIfelDPNSVGYYILLCNL 700

                         250
                  ....*....|....*....
gi 1063697154 352 -IERGEKDEAFDVfRKMIK 369
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 ...
 131-179 6.69e-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: 6.69e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063697154 131 NVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCK 179
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 142-332 8.67e-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: 8.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 142 YARAQKVDEAIYAFNVMEKYDlPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDRFTPDSKTYSILLEGWGKEPNLPKAR 221
Cdd:COG2956    86 YLKAGLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAI 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 222 EVFREMIDAgcHPDIVTYSIM-VDILCKAGRVDEALGIVRSM---DPSickpTTFIYSVLVHTYGTENRLEEAVDTFLEM 297
Cdd:COG2956   165 EALEKALKL--DPDCARALLLlAELYLEQGDYEEAIAALERAleqDPD----YLPALPRLAELYEKLGDPEEALELLRKA 238

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1063697154 298 ERSgmKADVAVFNSLIGAFCKANRMKNVYRVLKEM 332
Cdd:COG2956   239 LEL--DPSDDLLLALADLLERKEGLEAALALLERQ 271
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 301-333 1.19e-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: 1.19e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063697154 301 GMKADVAVFNSLIGAFCKANRMKNVYRVLKEMK 333
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 150-448 1.77e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 47.54  E-value: 1.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 150 EAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFE-NMRDRFTPDSKTYSILLEGWGKEPNLPKAREVFREMi 228
Cdd:PLN03077  271 EGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGyVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRM- 349

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 229 daGCHpDIVTYSIMVDILCKAGRVDEALGIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAV 308
Cdd:PLN03077  350 --ETK-DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVV 426

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 309 FNSLIGAFCKANRMKNVYRVLKEMKSKGVTpnskSCNIILRHLIERGEKDEAFDVFRKMIKVCEPDADTYTMVIKMFCEK 388
Cdd:PLN03077  427 ANALIEMYSKCKCIDKALEVFHNIPEKDVI----SWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARI 502

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 389 KEMETADKVWKYMRKKGV--------------------------FPS----MHTFSVLINGLCEERTTQKACVLLEEMIE 438
Cdd:PLN03077  503 GALMCGKEIHAHVLRTGIgfdgflpnalldlyvrcgrmnyawnqFNShekdVVSWNILLTGYVAHGKGSMAVELFNRMVE 582

                         330
                  ....*....|
gi 1063697154 439 MGIRPSGVTF 448
Cdd:PLN03077  583 SGVNPDEVTF 592
PLN03077 PLN03077
Protein ECB2; Provisional
 117-448 2.61e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 46.77  E-value: 2.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 117 MWDLINAMRKKKMLNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFEN-MRD 195
Cdd:PLN03077  137 LVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHvVRF 216

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 196 RFTPDSKTYSILLEGWGKEPNLPKAREVFREMidagCHPDIVTYSIMVDILCKAGRVDEALGIVRSM-----DPSICKPT 270
Cdd:PLN03077  217 GFELDVDVVNALITMYVKCGDVVSARLVFDRM----PRRDCISWNAMISGYFENGECLEGLELFFTMrelsvDPDLMTIT 292

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 271 TFIysVLVHTYGTEnRLEEAVDTFleMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVTpnskSCNIILRH 350
Cdd:PLN03077  293 SVI--SACELLGDE-RLGREMHGY--VVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAV----SWTAMISG 363

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 351 LIERGEKDEAFDVFRKM-IKVCEPDADT-------------------------------YTMV----IKMFCEKKEMETA 394
Cdd:PLN03077  364 YEKNGLPDKALETYALMeQDNVSPDEITiasvlsacaclgdldvgvklhelaerkglisYVVVanalIEMYSKCKCIDKA 443

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1063697154 395 DKVWKYMRKKGVFpsmhTFSVLINGLCEERTTQKACVLLEEMIeMGIRPSGVTF 448
Cdd:PLN03077  444 LEVFHNIPEKDVI----SWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTL 492
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 296-348 3.44e-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: 3.44e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063697154 296 EMERSGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNSKSCNIIL 348
Cdd:pfam13812   5 EMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 179-329 3.92e-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: 44.69  E-value: 3.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 179 KSKNVRKAQEVFENMRDRFTPDSK-TYSILL-------EGWGKEPNLPKAR--EVFREMIDAGCHPDIVTYSIMVDILCK 248
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVRLAQyHYNVLLylcskaaDATDLKPQLAADRgfEVFEAMKAQGVSPNEATYTAVARLAAA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 249 AGRVDEALGIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADVAVFNSLIGAFCKANRMKNVYRV 328
Cdd:pfam17177 103 KGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAY 182


                  .
gi 1063697154 329 L 329
Cdd:pfam17177 183 L 183
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 327-385 5.04e-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: 41.19  E-value: 5.04e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 327 RVLKEMKSKGVTPNSKSCNIILRHLIERGEKDEAFDVFRKMIKV-CEPDADTYTMVIKMF 385
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 ...
 408-448 5.11e-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: 5.11e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063697154 408 PSMHTFSVLINGLCEERTTQKACVLLEEMIEMGIRPSGVTF 448
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTY 41
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 308-341 5.26e-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: 5.26e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063697154 308 VFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNS 341
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 123-209 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 1063697154 123 AMRKKKML-NVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENMRDR-FTPD 200
Cdd:pfam17177  80 AMKAQGVSpNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHgVELE 159


                  ....*....
gi 1063697154 201 SKTYSILLE 209
Cdd:pfam17177 160 EPELAALLK 168
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 404-436 2.34e-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: 2.34e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063697154 404 KGVFPSMHTFSVLINGLCEERTTQKACVLLEEM 436
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 ...
 308-337 3.14e-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: 3.14e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1063697154 308 VFNSLIGAFCKANRMKNVYRVLKEMKSKGV 337
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 377-409 4.06e-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: 37.82  E-value: 4.06e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063697154 377 TYTMVIKMFCEKKEMETADKVWKYMRKKGVFPS 409
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 237-262 8.40e-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: 8.40e-04
                          10        20
                  ....*....|....*....|....*.
gi 1063697154 237 VTYSIMVDILCKAGRVDEALGIVRSM 262
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEM 26
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 113-302 1.19e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 41.39  E-value: 1.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 113 QYKLMWDLINAMRKKKMLNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFEN 192
Cdd:PLN03081  372 KWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQS 451

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 193 MRD--RFTPDSKTYSILLEGWGKEPNLPKAREVFREMidagchPDIVTYSiMVDILCKAGRVDEALGIVR-------SMD 263
Cdd:PLN03081  452 MSEnhRIKPRAMHYACMIELLGREGLLDEAYAMIRRA------PFKPTVN-MWAALLTACRIHKNLELGRlaaeklyGMG 524

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1063697154 264 PSICKPttfiYSVLVHTYGTENRLEEAVDTFLEMERSGM 302
Cdd:PLN03081  525 PEKLNN----YVVLLNLYNSSGRQAEAAKVVETLKRKGL 559
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 363-418 1.29e-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: 36.95  E-value: 1.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063697154 363 VFRKM-IKVCEPDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFSVLIN 418
Cdd:pfam13812   2 ILREMvRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 95-262 1.47e-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: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154  95 EHSVRAYHMMIESTAKIRQYKLMWDLINAMRKKKMLNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDlPPNLVAFNGLL 174
Cdd:COG2956   107 PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKLD-PDCARALLLLA 185

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 175 SALCKSKNVRKAQEVFENMRDRFTPDSKTYSILLEGWGKEPNLPKAREVFREMIDAgcHPDIVTYSIMVDILCKAGRVDE 254
Cdd:COG2956   186 ELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALEL--DPSDDLLLALADLLERKEGLEA 263


                  ....*...
gi 1063697154 255 ALGIVRSM 262
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 ...
 237-262 1.68e-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: 1.68e-03
                          10        20
                  ....*....|....*....|....*.
gi 1063697154 237 VTYSIMVDILCKAGRVDEALGIVRSM 262
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEM 26
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 216-399 2.38e-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: 2.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 216 NLPKAREVFREMIDAgcHPDIV-TYSIMVDILCKAGRVDEALGIVRSM---DPSickpTTFIYSVLVHTYGTENRLEEAV 291
Cdd:COG2956    23 QPDKAIDLLEEALEL--DPETVeAHLALGNLYRRRGEYDRAIRIHQKLlerDPD----RAEALLELAQDYLKAGLLDRAE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063697154 292 DTFLEMERSGMKaDVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGvtPNSKSCNIIL-RHLIERGEKDEAFDVFRKMIKV 370
Cdd:COG2956    97 ELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELaELYLEQGDYDEAIEALEKALKL 173

                         170       180
                  ....*....|....*....|....*....
gi 1063697154 371 CEPDADTYTMVIKMFCEKKEMETADKVWK 399
Cdd:COG2956   174 DPDCARALLLLAELYLEQGDYEEAIAALE 202
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 371-402 4.51e-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: 4.51e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1063697154 371 CEPDADTYTMVIKMFCEKKEMETADKVWKYMR 402
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 411-444 5.14e-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: 34.74  E-value: 5.14e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063697154 411 HTFSVLINGLCEERTTQKACVLLEEMIEMGIRPS 444
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 272-306 5.67e-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: 5.67e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063697154 272 FIYSVLVHTYGTENRLEEAVDTFLEMERSGMKADV 306
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 158-214 5.78e-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: 5.78e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063697154 158 MEKYDLPPNLVAFNGLLSALCKSKNVRKAQEVFENMR-DRFTPDSKTYSILLEGWGKE 214
Cdd:pfam13812   6 MVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKkKGIKPTLDTYNAILGVIGGR 63
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 223-284 6.70e-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: 35.03  E-value: 6.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063697154 223 VFREMIDAGCHPDIVTYSIMVDILCKAGRVDEALGIVRSMDPSICKPTTFIYSVLVHTYGTE 284
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 203-236 7.47e-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: 7.47e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063697154 203 TYSILLEGWGKEPNLPKAREVFREMIDAGCHPDI 236
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 168-196 9.24e-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: 33.98  E-value: 9.24e-03
                          10        20
                  ....*....|....*....|....*....
gi 1063697154 168 VAFNGLLSALCKSKNVRKAQEVFENMRDR 196
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEK 29
 
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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