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Conserved domains on  [gi|1002244416|ref|XP_015626415|]
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large ribosomal subunit protein mL102 (rPPR5) [Oryza sativa Japonica Group]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000225)

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

Gene Ontology:  GO:0003723|GO:0009451
PubMed:  24471833|19004664

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
 198-630 2.55e-21

pentatricopeptide (PPR) repeat-containing protein; Provisional


The actual alignment was detected with superfamily member PLN03081:

Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 99.17  E-value: 2.55e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 198 MPDLGIARTALSYNAVLKAILCRGREAMARRIYN-AMIADAVTPDLSTYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPD 276
Cdd:PLN03081   78 LDDTQIRKSGVSLCSQIEKLVACGRHREALELFEiLEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPD 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 277 VTTYNTLLNAWVRAGDLESARKVFDEMPgagfAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAalmpg 356
Cdd:PLN03081  158 QYMMNRVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFV----- 228

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 357 lcddegrvvearkamddmaerrltpkdksVFLRLVTTL--CRAGDldgalDVH---QKSGQFKHV-----LVDprqygvl 426
Cdd:PLN03081  229 -----------------------------VMLRASAGLgsARAGQ-----QLHccvLKTGVVGDTfvscaLID------- 267

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 427 MESLCagGKCDGAVEVMDELLEKGTLlspkspvlegpAYNPVIEYLCSNGNTSKAETFFRQLMKKGVD-DKAAFNSLIRG 505
Cdd:PLN03081  268 MYSKC--GDIEDARCVFDGMPEKTTV-----------AWNSMLAGYALHGYSEEALCLYYEMRDSGVSiDQFTFSIMIRI 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 506 HAKEGVPEAAQEILAIMTRRGVRTDPESHALLVDSFLKKNEPADAKTALDsMMEQGHVPSpslFMSVMVALFNSGRVQTA 585
Cdd:PLN03081  335 FSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFD-RMPRKNLIS---WNALIAGYGNHGRGTKA 410

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 1002244416 586 SRVMKSMIEKGVTENMDMAHKILEALFMRGHVEEAIGRVNLMVEN 630
Cdd:PLN03081  411 VEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEN 455
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 198-630 2.55e-21

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 99.17  E-value: 2.55e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 198 MPDLGIARTALSYNAVLKAILCRGREAMARRIYN-AMIADAVTPDLSTYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPD 276
Cdd:PLN03081   78 LDDTQIRKSGVSLCSQIEKLVACGRHREALELFEiLEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPD 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 277 VTTYNTLLNAWVRAGDLESARKVFDEMPgagfAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAalmpg 356
Cdd:PLN03081  158 QYMMNRVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFV----- 228

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 357 lcddegrvvearkamddmaerrltpkdksVFLRLVTTL--CRAGDldgalDVH---QKSGQFKHV-----LVDprqygvl 426
Cdd:PLN03081  229 -----------------------------VMLRASAGLgsARAGQ-----QLHccvLKTGVVGDTfvscaLID------- 267

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 427 MESLCagGKCDGAVEVMDELLEKGTLlspkspvlegpAYNPVIEYLCSNGNTSKAETFFRQLMKKGVD-DKAAFNSLIRG 505
Cdd:PLN03081  268 MYSKC--GDIEDARCVFDGMPEKTTV-----------AWNSMLAGYALHGYSEEALCLYYEMRDSGVSiDQFTFSIMIRI 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 506 HAKEGVPEAAQEILAIMTRRGVRTDPESHALLVDSFLKKNEPADAKTALDsMMEQGHVPSpslFMSVMVALFNSGRVQTA 585
Cdd:PLN03081  335 FSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFD-RMPRKNLIS---WNALIAGYGNHGRGTKA 410

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 1002244416 586 SRVMKSMIEKGVTENMDMAHKILEALFMRGHVEEAIGRVNLMVEN 630
Cdd:PLN03081  411 VEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEN 455
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 240-286 1.03e-13

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: 1.03e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1002244416 240 PDLSTYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPDVTTYNTLLNA 286
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 288-560 3.48e-08

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: 55.51  E-value: 3.48e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 288 VRAGDLESARKVFDEMPgAGFAQNSVSYNVMIKGYVEAGKVEEAVGLFsemgEKGLRLSEKTFAALMpGLCDD---EGRV 364
Cdd:COG2956    19 LLNGQPDKAIDLLEEAL-ELDPETVEAHLALGNLYRRRGEYDRAIRIH----QKLLERDPDRAEALL-ELAQDylkAGLL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 365 VEARKAMDDMAERRltPKDKSVFLRLVTTLCRAGDLDGALDVHQK----SGQFKHVLVdprQYGVLMESLcagGKCDGAV 440
Cdd:COG2956    93 DRAEELLEKLLELD--PDDAEALRLLAEIYEQEGDWEKAIEVLERllklGPENAHAYC---ELAELYLEQ---GDYDEAI 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 441 EVMDELLEkgtlLSPKSPvlegPAYNPVIEYLCSNGNTSKAETFFRQLMKKGVDDKAAFNSLIRGHAKEGVPEAAQEILa 520
Cdd:COG2956   165 EALEKALK----LDPDCA----RALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELL- 235

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1002244416 521 imtRRGVRTDPESHAL--LVDSFLKKNEPADAKTALDSMMEQ 560
Cdd:COG2956   236 ---RKALELDPSDDLLlaLADLLERKEGLEAALALLERQLRR 274
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 313-347 2.16e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.75  E-value: 2.16e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002244416 313 VSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSE 347
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 198-630 2.55e-21

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 99.17  E-value: 2.55e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 198 MPDLGIARTALSYNAVLKAILCRGREAMARRIYN-AMIADAVTPDLSTYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPD 276
Cdd:PLN03081   78 LDDTQIRKSGVSLCSQIEKLVACGRHREALELFEiLEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPD 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 277 VTTYNTLLNAWVRAGDLESARKVFDEMPgagfAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAalmpg 356
Cdd:PLN03081  158 QYMMNRVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFV----- 228

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 357 lcddegrvvearkamddmaerrltpkdksVFLRLVTTL--CRAGDldgalDVH---QKSGQFKHV-----LVDprqygvl 426
Cdd:PLN03081  229 -----------------------------VMLRASAGLgsARAGQ-----QLHccvLKTGVVGDTfvscaLID------- 267

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 427 MESLCagGKCDGAVEVMDELLEKGTLlspkspvlegpAYNPVIEYLCSNGNTSKAETFFRQLMKKGVD-DKAAFNSLIRG 505
Cdd:PLN03081  268 MYSKC--GDIEDARCVFDGMPEKTTV-----------AWNSMLAGYALHGYSEEALCLYYEMRDSGVSiDQFTFSIMIRI 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 506 HAKEGVPEAAQEILAIMTRRGVRTDPESHALLVDSFLKKNEPADAKTALDsMMEQGHVPSpslFMSVMVALFNSGRVQTA 585
Cdd:PLN03081  335 FSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFD-RMPRKNLIS---WNALIAGYGNHGRGTKA 410

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 1002244416 586 SRVMKSMIEKGVTENMDMAHKILEALFMRGHVEEAIGRVNLMVEN 630
Cdd:PLN03081  411 VEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEN 455
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 252-601 2.57e-19

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 93.40  E-value: 2.57e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  252 FGLCKKMEA---ALRVFGDMKdhgvTPDVTTYNTLLNAWVRAGDLESARKVFDEMPGAGFAQNSVSYNVMIKGYVEAGKV 328
Cdd:PLN03218   413 FKACKKQRAvkeAFRFAKLIR----NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKV 488

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  329 EEAVGLFSEMGEKGLRLSEKTFAALMPGlCDDEGRVVEARKAMDDMAERRLTPkDKSVFLRLVTTLCRAGDLDGALDVHQ 408
Cdd:PLN03218   489 DAMFEVFHEMVNAGVEANVHTFGALIDG-CARAGQVAKAFGAYGIMRSKNVKP-DRVVFNALISACGQSGAVDRAFDVLA 566

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  409 KSGQFKH-VLVDPRQYGVLMESLCAGGKCDGAVEV---MDELLEKGTllspkspvlegPAYNPVIEYLCS-NGNTSKAET 483
Cdd:PLN03218   567 EMKAETHpIDPDHITVGALMKACANAGQVDRAKEVyqmIHEYNIKGT-----------PEVYTIAVNSCSqKGDWDFALS 635

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  484 FFRQLMKKGVD-DKAAFNSLI--RGHAkeGVPEAAQEILAIMTRRGVR--TDPESHALLVDSFLKknepaDAKTALD--- 555
Cdd:PLN03218   636 IYDDMKKKGVKpDEVFFSALVdvAGHA--GDLDKAFEILQDARKQGIKlgTVSYSSLMGACSNAK-----NWKKALElye 708

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1002244416  556 SMMEQGHVPSPSLFMSVMVALFNSGRVQTASRVMKSMIEKGVTENM 601
Cdd:PLN03218   709 DIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNT 754
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 126-446 1.67e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 77.61  E-value: 1.67e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  126 AYRRAGFSPEP--ATFSLLIPILASHRMLNHARCILLdTMPSFSIAPEEATVAALIAAYGKANIPQESVKLFRLMPDLGI 203
Cdd:PLN03218   425 AFRFAKLIRNPtlSTFNMLMSVCASSQDIDGALRVLR-LVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGV 503

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  204 ARTALSYNAVLKAILCRGREAMARRIYNAMIADAVTPDLSTYNTLIWGFGLCKKMEAALRVFGDMK--DHGVTPDVTTYN 281
Cdd:PLN03218   504 EANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKaeTHPIDPDHITVG 583

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  282 TLLNAWVRAGDLESARKVFDEMPGAGFAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAALMpGLCDDE 361
Cdd:PLN03218   584 ALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALV-DVAGHA 662

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  362 GRVVEARKAMDDMAERRLTPkDKSVFLRLVTTLCRAGDLDGALDVHQKsgqFKHVLVDP--RQYGVLMESLCAGGKCDGA 439
Cdd:PLN03218   663 GDLDKAFEILQDARKQGIKL-GTVSYSSLMGACSNAKNWKKALELYED---IKSIKLRPtvSTMNALITALCEGNQLPKA 738


                   ....*..
gi 1002244416  440 VEVMDEL 446
Cdd:PLN03218   739 LEVLSEM 745
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 240-286 1.03e-13

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: 1.03e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1002244416 240 PDLSTYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPDVTTYNTLLNA 286
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 120-450 1.79e-13

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 74.14  E-value: 1.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 120 LQFFRFAYRRAGFSPEPATFSLLIPILAShrmLNHARCI--LLDTMPSFSIAPEEATVAALIAAYGKANIPQESVKLFRL 197
Cdd:PLN03081  107 LELFEILEAGCPFTLPASTYDALVEACIA---LKSIRCVkaVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDE 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 198 MPDlgiaRTALSYNAVLKAILCRGREAMARRIYNAMIADAVTPDLSTYNTLIwgfglckKMEAAL-RVFGDMKDH----- 271
Cdd:PLN03081  184 MPE----RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVML-------RASAGLgSARAGQQLHccvlk 252

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 272 -GVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPgagfAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTF 350
Cdd:PLN03081  253 tGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTF 328

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 351 aALMPGLCDDEGRVVEARKAMDDMAERRLtPKDKSVFLRLVTTLCRAGDLDGALDVHQKSgqfkhvlvdPRQYGVLMESL 430
Cdd:PLN03081  329 -SIMIRIFSRLALLEHAKQAHAGLIRTGF-PLDIVANTALVDLYSKWGRMEDARNVFDRM---------PRKNLISWNAL 397

                         330       340
                  ....*....|....*....|....
gi 1002244416 431 CAG----GKCDGAVEVMDELLEKG 450
Cdd:PLN03081  398 IAGygnhGRGTKAVEMFERMIAEG 421
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 168-375 2.43e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 73.76  E-value: 2.43e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  168 IAPEEATVAALIAAYGKANIPQESVKLFRLMPDLGIARTALSYNAVLKAILCRGREAMARRIYNAMIADAVTPDLSTYNT 247
Cdd:PLN03218   575 IDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSA 654

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  248 LIWGFGLCKKMEAALRVFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPGAGFAQNSVSYNVMIKGYVEAGK 327
Cdd:PLN03218   655 LVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQ 734

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1002244416  328 VEEAVGLFSEMGEKGLRLSEKTFAALMpglcddegrVVEARKAMDDMA 375
Cdd:PLN03218   735 LPKALEVLSEMKRLGLCPNTITYSILL---------VASERKDDADVG 773
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 177-382 2.71e-13

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 73.37  E-value: 2.71e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 177 ALIAAYGKANIPQESVKLFRLMPDlgiaRTALSYNAVLKAILCRGREAMARRIYNAMIADAVTPDLSTYNTLIWGFGLCK 256
Cdd:PLN03081  264 ALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLA 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 257 KMEAALRVFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPgagfAQNSVSYNVMIKGYVEAGKVEEAVGLFS 336
Cdd:PLN03081  340 LLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKNLISWNALIAGYGNHGRGTKAVEMFE 415

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1002244416 337 EMGEKGLRLSEKTFAALMPGlCDDEGRVVEARKAMDDMAE-RRLTPK 382
Cdd:PLN03081  416 RMIAEGVAPNHVTFLAVLSA-CRYSGLSEQGWEIFQSMSEnHRIKPR 461
PLN03077 PLN03077
Protein ECB2; Provisional
 178-627 4.81e-13

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 72.96  E-value: 4.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 178 LIAAYGKANIPQESVKLFRLMPDLGIARTALSYNAVLKAI-----LCRGREAMAR----------RIYNAMI------AD 236
Cdd:PLN03077  158 LVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCggipdLARGREVHAHvvrfgfeldvDVVNALItmyvkcGD 237

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 237 AV----------TPDLSTYNTLIWGF---GLCkkmEAALRVFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEM 303
Cdd:PLN03077  238 VVsarlvfdrmpRRDCISWNAMISGYfenGEC---LEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYV 314

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 304 PGAGFAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLrlseKTFAALMPGlCDDEGRVVEARKAMDDMAERRLTPKD 383
Cdd:PLN03077  315 VKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDA----VSWTAMISG-YEKNGLPDKALETYALMEQDNVSPDE 389

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 384 KSVFLRLVTTLCrAGDLDGALDVH---QKSGQFKHVLVDPRQygVLMESLCaggKC-DGAVEVMDELLEKGTLlspkspv 459
Cdd:PLN03077  390 ITIASVLSACAC-LGDLDVGVKLHelaERKGLISYVVVANAL--IEMYSKC---KCiDKALEVFHNIPEKDVI------- 456

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 460 legpAYNPVIEYLCSNGNTSKAETFFRQLMKKGVDDKAAFNSLIRGHAKEGVPEAAQEILAIMTRRGV------------ 527
Cdd:PLN03077  457 ----SWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIgfdgflpnalld 532

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 528 ------------------RTDPESHALLVDSFLKKNEPADAKTALDSMMEQGHVPSPSLFMSVMVALFNSGRVQTASRVM 589
Cdd:PLN03077  533 lyvrcgrmnyawnqfnshEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYF 612

                         490       500       510
                  ....*....|....*....|....*....|....*....
gi 1002244416 590 KSMIEK-GVTENMDMAHKILEALFMRGHVEEAIGRVNLM 627
Cdd:PLN03077  613 HSMEEKySITPNLKHYACVVDLLGRAGKLTEAYNFINKM 651
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 275-322 7.97e-13

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: 63.15  E-value: 7.97e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002244416 275 PDVTTYNTLLNAWVRAGDLESARKVFDEMPGAGFAQNSVSYNVMIKGY 322
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 311-359 1.85e-12

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 62.38  E-value: 1.85e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1002244416 311 NSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAALMPGLCD 359
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 211-530 7.05e-12

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 69.11  E-value: 7.05e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 211 NAVLKAILCRGREAMARRIYNAMIADAVTPDLSTYNTLiwgFGLC---KKMEAALRVFGDMKDHGVTPDVTTYNTLLNAW 287
Cdd:PLN03077   55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVAL---FRLCewkRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMF 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 288 VRAGDLESARKVFDEMPgagfAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAALM---PGLCD-DEGR 363
Cdd:PLN03077  132 VRFGELVHAWYVFGKMP----ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLrtcGGIPDlARGR 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 364 VVEARKAMDDMAErrltpkDKSVFLRLVTTLCRAGDLDGALDVHQKSgqfkhvlvdPRQYGVLMESLCAG----GKCDGA 439
Cdd:PLN03077  208 EVHAHVVRFGFEL------DVDVVNALITMYVKCGDVVSARLVFDRM---------PRRDCISWNAMISGyfenGECLEG 272

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 440 VEV---MDELLEKGTLLSPKSPV-------------------------LEGPAYNPVIEYLCSNGNTSKAETFFRQLMKK 491
Cdd:PLN03077  273 LELfftMRELSVDPDLMTITSVIsacellgderlgremhgyvvktgfaVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK 352

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 1002244416 492 gvdDKAAFNSLIRGHAKEGVPEAAQEILAIMTRRGVRTD 530
Cdd:PLN03077  353 ---DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPD 388
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 229-611 8.81e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 68.75  E-value: 8.81e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  229 IYNAMIADAVTPDLSTYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPGAG- 307
Cdd:PLN03218   494 VFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETh 573

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  308 -FAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAALMPGlCDDEGRVVEARKAMDDMAERRLTPkDKSV 386
Cdd:PLN03218   574 pIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS-CSQKGDWDFALSIYDDMKKKGVKP-DEVF 651

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  387 FLRLVTTLCRAGDLDGALDVHQ---KSGQFKHVLVdprqYGVLMESLCAGGKCDGAVEVMDELleKGTLLSPKSPVlegp 463
Cdd:PLN03218   652 FSALVDVAGHAGDLDKAFEILQdarKQGIKLGTVS----YSSLMGACSNAKNWKKALELYEDI--KSIKLRPTVST---- 721

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  464 aYNPVIEYLCSNGNTSKAETFFRQLMKKGV-DDKAAFNSLIRGHAKEGVPEAAQEILAIMTRRGVRTDPeshaLLVDSFl 542
Cdd:PLN03218   722 -MNALITALCEGNQLPKALEVLSEMKRLGLcPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNL----VMCRCI- 795

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002244416  543 kknepadakTALDSMMEQGHVPSPSLFMSvmvalFNSGRVQT-------ASRVMKSMIEKGVTENMDMAHKILEAL 611
Cdd:PLN03218   796 ---------TGLCLRRFEKACALGEPVVS-----FDSGRPQIenkwtswALMVYRETISAGTLPTMEVLSQVLGCL 857
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 263-323 1.74e-10

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: 56.98  E-value: 1.74e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002244416 263 RVFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPGAGFAQNSVSYNVMIKGYV 323
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PLN03077 PLN03077
Protein ECB2; Provisional
 177-427 2.78e-10

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 63.72  E-value: 2.78e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 177 ALIAAYGKANIPQESVKLFRLMPDlgiaRTALSYNAVLKAILCRGREAMARRIYNAMIADaVTPDLSTyntLIWGFGLCK 256
Cdd:PLN03077  429 ALIEMYSKCKCIDKALEVFHNIPE----KDVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVT---LIAALSACA 500

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 257 KMeAALRVFGDMKDH----GVTPDVTTYNTLLNAWVRAGDLESARKVFDEMpgagfAQNSVSYNVMIKGYVEAGKVEEAV 332
Cdd:PLN03077  501 RI-GALMCGKEIHAHvlrtGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-----EKDVVSWNILLTGYVAHGKGSMAV 574

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 333 GLFSEMGEKGLRLSEKTFAALMPGlCDDEGRVVEARKAMDDMAER-RLTPKDKSvFLRLVTTLCRAGDLDGALDVHQKsg 411
Cdd:PLN03077  575 ELFNRMVESGVNPDEVTFISLLCA-CSRSGMVTQGLEYFHSMEEKySITPNLKH-YACVVDLLGRAGKLTEAYNFINK-- 650

                         250
                  ....*....|....*.
gi 1002244416 412 qfKHVLVDPRQYGVLM 427
Cdd:PLN03077  651 --MPITPDPAVWGALL 664
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 228-288 1.26e-09

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: 54.67  E-value: 1.26e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002244416 228 RIYNAMIADAVTPDLSTYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPDVTTYNTLLNAWV 288
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 157-319 4.76e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.89  E-value: 4.76e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  157 CILLDTMPSFSIAPEEATVAALIAAYGKANIPQESVKLFRLMPDLGIARTALSYNAVLKAILCRGREAMARRIYNAMIAD 236
Cdd:PLN03218   634 LSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI 713

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  237 AVTPDLSTYNTLIwgFGLC--KKMEAALRVFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPGAGFAQNSVS 314
Cdd:PLN03218   714 KLRPTVSTMNALI--TALCegNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVM 791


                   ....*
gi 1002244416  315 YNVMI 319
Cdd:PLN03218   792 CRCIT 796
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 271-303 1.72e-08

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: 50.42  E-value: 1.72e-08
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1002244416 271 HGVTPDVTTYNTLLNAWVRAGDLESARKVFDEM 303
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 177-345 2.46e-08

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 57.57  E-value: 2.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 177 ALIAAYGKANIPQESVKLFRLMPDLGIARTALSYNAVLKAILCRGREAMARRIYNAMIAD-AVTPDLSTYNTLIWGFGLC 255
Cdd:PLN03081  396 ALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENhRIKPRAMHYACMIELLGRE 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 256 KKMEAAlrvFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPGAGfAQNSVSYNVMIKGYVEAGKVEEAVGLF 335
Cdd:PLN03081  476 GLLDEA---YAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMG-PEKLNNYVVLLNLYNSSGRQAEAAKVV 551

                         170
                  ....*....|
gi 1002244416 336 SEMGEKGLRL 345
Cdd:PLN03081  552 ETLKRKGLSM 561
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 288-560 3.48e-08

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: 55.51  E-value: 3.48e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 288 VRAGDLESARKVFDEMPgAGFAQNSVSYNVMIKGYVEAGKVEEAVGLFsemgEKGLRLSEKTFAALMpGLCDD---EGRV 364
Cdd:COG2956    19 LLNGQPDKAIDLLEEAL-ELDPETVEAHLALGNLYRRRGEYDRAIRIH----QKLLERDPDRAEALL-ELAQDylkAGLL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 365 VEARKAMDDMAERRltPKDKSVFLRLVTTLCRAGDLDGALDVHQK----SGQFKHVLVdprQYGVLMESLcagGKCDGAV 440
Cdd:COG2956    93 DRAEELLEKLLELD--PDDAEALRLLAEIYEQEGDWEKAIEVLERllklGPENAHAYC---ELAELYLEQ---GDYDEAI 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 441 EVMDELLEkgtlLSPKSPvlegPAYNPVIEYLCSNGNTSKAETFFRQLMKKGVDDKAAFNSLIRGHAKEGVPEAAQEILa 520
Cdd:COG2956   165 EALEKALK----LDPDCA----RALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELL- 235

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1002244416 521 imtRRGVRTDPESHAL--LVDSFLKKNEPADAKTALDSMMEQ 560
Cdd:COG2956   236 ---RKALELDPSDDLLlaLADLLERKEGLEAALALLERQLRR 274
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 226-363 4.93e-08

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: 53.94  E-value: 4.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 226 ARRIYNAMIADAVTPDLSTYNTLIWgfgLCKKMEAA------------LRVFGDMKDHGVTPDVTTYNTLLNAWVRAGDL 293
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLY---LCSKAADAtdlkpqlaadrgFEVFEAMKAQGVSPNEATYTAVARLAAAKGDG 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 294 ESARKVFDEMPGAGFAQNSVSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSEKTFAALMPgLCDDEGR 363
Cdd:pfam17177 107 DLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLK-VSAKAGR 175
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 313-343 8.76e-08

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: 48.62  E-value: 8.76e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1002244416 313 VSYNVMIKGYVEAGKVEEAVGLFSEMGEKGL 343
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03077 PLN03077
Protein ECB2; Provisional
 129-353 1.29e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 55.24  E-value: 1.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 129 RAGFSPEPATFSLLIPILASHRMLNHARcILLDTMPSFSIApeeaTVAALIAAYGKANIPQESVKLFRLMPDLGIARTAL 208
Cdd:PLN03077  215 RFGFELDVDVVNALITMYVKCGDVVSAR-LVFDRMPRRDCI----SWNAMISGYFENGECLEGLELFFTMRELSVDPDLM 289

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 209 SYNAVLKAILCRGREAMARRIYNAMIADAVTPDLSTYNTLI--------WGFG--LCKKMEA------------------ 260
Cdd:PLN03077  290 TITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIqmylslgsWGEAekVFSRMETkdavswtamisgyekngl 369

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 261 ---ALRVFGDMKDHGVTPDVTTYNTLLNAWVRAGDLESARKVFDEMPGAGFAQNSVSYNVMIKGYVEAGKVEEAVGLFSE 337
Cdd:PLN03077  370 pdkALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHN 449

                         250       260
                  ....*....|....*....|....*.
gi 1002244416 338 MGEK----------GLRLSEKTFAAL 353
Cdd:PLN03077  450 IPEKdviswtsiiaGLRLNNRCFEAL 475
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 315-598 3.19e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 54.11  E-value: 3.19e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  315 YNVMIKgyveAGKVEEAVGLFSEMGEKGLRLSEKTFAALMPGLCDDEGRVVEARKamddMAERRLTPKdKSVFLRLVTTL 394
Cdd:PLN03218   377 YNRLLR----DGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFR----FAKLIRNPT-LSTFNMLMSVC 447

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  395 CRAGDLDGALDVHQ--KSGQFKhvlVDPRQYGVLMESLCAGGKCDGAVEVMDELLEKGTllspkSPVLEgpAYNPVIEYL 472
Cdd:PLN03218   448 ASSQDIDGALRVLRlvQEAGLK---ADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGV-----EANVH--TFGALIDGC 517

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416  473 CSNGNTSKAETFFRQLMKKGVD-DKAAFNSLIRGHAKEGVPEAAQEILAIMTRRGVRTDPE--SHALLVDSFLKKNEPAD 549
Cdd:PLN03218   518 ARAGQVAKAFGAYGIMRSKNVKpDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDhiTVGALMKACANAGQVDR 597

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 1002244416  550 AKTALDSMMEQGHVPSPSLFMSVMVALFNSGRVQTASRVMKSMIEKGVT 598
Cdd:PLN03218   598 AKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVK 646
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 313-347 2.16e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.75  E-value: 2.16e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002244416 313 VSYNVMIKGYVEAGKVEEAVGLFSEMGEKGLRLSE 347
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 244-277 5.92e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 43.60  E-value: 5.92e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1002244416 244 TYNTLIWGFGLCKKMEAALRVFGDMKDHGVTPDV 277
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 311-338 1.46e-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: 42.33  E-value: 1.46e-05
                          10        20
                  ....*....|....*....|....*...
gi 1002244416 311 NSVSYNVMIKGYVEAGKVEEAVGLFSEM 338
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 464-508 2.08e-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: 42.35  E-value: 2.08e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1002244416 464 AYNPVIEYLCSNGNTSKAETFFRQLMKKGVD-DKAAFNSLIRGHAK 508
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKpNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 279-308 5.44e-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: 40.52  E-value: 5.44e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1002244416 279 TYNTLLNAWVRAGDLESARKVFDEMPGAGF 308
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 279-308 7.57e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 40.14  E-value: 7.57e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1002244416 279 TYNTLLNAWVRAGDLESARKVFDEMPGAGF 308
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 260-359 9.55e-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: 44.31  E-value: 9.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 260 AALRVFGDMKDHGVTPDVTTYNTLLNAWVRAGD---------LESARKVFDEMPGAGFAQNSVSYNVMIKGYVEAGKVEE 330
Cdd:pfam17177  29 GALALYDAAKAEGVRLAQYHYNVLLYLCSKAADatdlkpqlaADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDL 108

                          90       100
                  ....*....|....*....|....*....
gi 1002244416 331 AVGLFSEMGEKGLRLSEKTFAALMPGLCD 359
Cdd:pfam17177 109 AFDLVKEMEAAGVSPRLRSYSPALHAYCE 137
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 238-269 1.29e-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: 39.64  E-value: 1.29e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1002244416 238 VTPDLSTYNTLIwgFGLCK--KMEAALRVFGDMK 269
Cdd:pfam12854   3 LKPDVVTYNTLI--NGLCRagRVDEAFELLDEME 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 209-256 2.03e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.65  E-value: 2.03e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1002244416 209 SYNAVLKAiLCR-GREAMARRIYNAMIADAVTPDLSTYNTLIwgFGLCK 256
Cdd:pfam13041   5 TYNTLING-YCKkGKVEEAFKLFNEMKKRGVKPNVYTYTILI--NGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 243-273 2.17e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 38.99  E-value: 2.17e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1002244416 243 STYNTLIWGFGLCKKMEAALRVFGDMKDHGV 273
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
Actin pfam00022
Actin;
513-581 6.36e-03

Actin;


Pssm-ID: 394979 [Multi-domain]  Cd Length: 407  Bit Score: 39.60  E-value: 6.36e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244416 513 EAAQEILAIMTRRGVRTDPESHALLV-DSFLkkNEPADAKTALDSMMEQGHVPSPSLFMSVMVALFNSGR 581
Cdd:pfam00022  73 DAMEEIWEHVLKEELQVDPEEHPLLLtEPPW--NPPANREKAAEIMFEKFGVPALYLAKNPVLSAFASGR 140
 
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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