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Conserved domains on  [gi|1002302656|ref|XP_015614707|]
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pentatricopeptide repeat-containing protein MRL1, chloroplastic isoform X1 [Oryza sativa Japonica Group]

Protein Classification

PLN03218 family protein( domain architecture ID 11477578)

PLN03218 family protein

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 103-1089 0e+00

maturation of RBCL 1; Provisional


:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 1614.56  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  103 RWRGGDSPEEEEVSHEHdkRIVNNKALGTSTDLLDDS------------SYSSRRTHENVFSEPSVSGRMTVDRTDCQ-- 168
Cdd:PLN03218    52 RLRGGKSKSIRSRIRSP--RLVVNASLGSGLVLVVVAvtafsaisfaylQHTRRRKSSPLVATPSGGGISTLNREDVQsl 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  169 -TDVFSGVDT------------VNNTTQVGSVISTYRSLDTFEGVYGPANTSSIEKVqdilpqsRSVSDGQHQSRHFANR 235
Cdd:PLN03218   130 dGDVHKGTSTeinvgfrdlveeVEHTEEEKTHQAQERALMEEESVVVEGSESSRESV-------RVVADEHTLSDESASS 202

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  236 RAQLGGLPHQFLSLSKQNEQTKNGQGPPDNKTDSEGANLLGCHQSDQGDYVDFTSLSSFKRINEHPLNFIPEAHASN--- 312
Cdd:PLN03218   203 RVVHGSVALLSLSFGVENPELQNGNSPDQTKLELDLSQLVVGRHSIAESLFTQTVLDSLDYDSYEYNGLLQEAAISSgkg 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  313 LFEPRKASEFTNSYAGG-SYLRAGRLVPVACLRDGPVSKQ-----KKAMNDHDDAKLIGWSISNLLSKENPENSTSANRA 386
Cdd:PLN03218   283 IFAESKREELYTFYEEKqSRAKSSRLPNVKGLRKGVSSATnslslDKKNNGVKDAELPGQSSGQAASDVEEENSLAAYNG 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  387 GLRGTKDVPDYLRRYNSLLIDGRLKDSVDLLESMEQKGLLDMNKIHHASFLNACKKQRAVPEAVRFCKLINNPKMSTFNM 466
Cdd:PLN03218   363 GVSGKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNM 442

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  467 LLSVCANSQDFDGALQVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNVNTYSALIDGCAKAGQ 546
Cdd:PLN03218   443 LMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQ 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  547 VAKAFGAYGIMSSKKVKPDRVVFNALISACGESGAVARAFDVLSEMTAEAseskgsKPILPDHVTVGALMKTCIQAGQAD 626
Cdd:PLN03218   523 VAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET------HPIDPDHITVGALMKACANAGQVD 596

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  627 RAREVYKMLQEYNIKGTPEVYTIALRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDVAGHARRADAAFEIMKDAR 706
Cdd:PLN03218   597 RAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDAR 676

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  707 AKGYQVGTIAYSSLMGACCNAKDWKKALQLFEEIKSIKLMPTVSMMNALITALCDGDQVLKSFEVLSEMKRLGVCPNMIT 786
Cdd:PLN03218   677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTIT 756

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  787 YSVLFVACERNAEAQLGLDLFEQLKIDSIDLNPTIVGCLTGLCLQMFDNDLSLGNIVVTFNLGKPQIENKWTSSAIKVYR 866
Cdd:PLN03218   757 YSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYR 836

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  867 EAISTGLLPSSDVLSQVLGCLRFPHDNTLTNTFIENMGISCDIPHHPNVNSLLEGFGEYDIRAFSILEEAASLGAVESIS 946
Cdd:PLN03218   837 ETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEYDPRAFSLLEEAASLGVVPSVS 916

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  947 MKDTRILVDARKSKIYTAEVSVLTTLRSLKHRLAAGARLPNVTILLPTEKKQVGLDEREKTLKLAGRVGQAVGSLLRRLG 1026
Cdd:PLN03218   917 FKKSPIVIDAEELPVFAAEVYLLTILKGLKHRLAAGAKLPNVTILLPTEKKEIYTPKGEKTINLAGRVGQAVAALLRRLG 996

                          970       980       990      1000      1010      1020
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002302656 1027 IKYHGEESHGKMRINGLTLRRWFNPKLTSTSStGTPADLLPLPSRLAKGIADQQRNIR--NLSLE 1089
Cdd:PLN03218   997 LPYQGSESHGKLRINGLSLRRWFQPKLKSPFS-GKPEDLSSSQSRLGKGIADQQRAIRlgNLSLE 1060
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 103-1089 0e+00

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 1614.56  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  103 RWRGGDSPEEEEVSHEHdkRIVNNKALGTSTDLLDDS------------SYSSRRTHENVFSEPSVSGRMTVDRTDCQ-- 168
Cdd:PLN03218    52 RLRGGKSKSIRSRIRSP--RLVVNASLGSGLVLVVVAvtafsaisfaylQHTRRRKSSPLVATPSGGGISTLNREDVQsl 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  169 -TDVFSGVDT------------VNNTTQVGSVISTYRSLDTFEGVYGPANTSSIEKVqdilpqsRSVSDGQHQSRHFANR 235
Cdd:PLN03218   130 dGDVHKGTSTeinvgfrdlveeVEHTEEEKTHQAQERALMEEESVVVEGSESSRESV-------RVVADEHTLSDESASS 202

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  236 RAQLGGLPHQFLSLSKQNEQTKNGQGPPDNKTDSEGANLLGCHQSDQGDYVDFTSLSSFKRINEHPLNFIPEAHASN--- 312
Cdd:PLN03218   203 RVVHGSVALLSLSFGVENPELQNGNSPDQTKLELDLSQLVVGRHSIAESLFTQTVLDSLDYDSYEYNGLLQEAAISSgkg 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  313 LFEPRKASEFTNSYAGG-SYLRAGRLVPVACLRDGPVSKQ-----KKAMNDHDDAKLIGWSISNLLSKENPENSTSANRA 386
Cdd:PLN03218   283 IFAESKREELYTFYEEKqSRAKSSRLPNVKGLRKGVSSATnslslDKKNNGVKDAELPGQSSGQAASDVEEENSLAAYNG 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  387 GLRGTKDVPDYLRRYNSLLIDGRLKDSVDLLESMEQKGLLDMNKIHHASFLNACKKQRAVPEAVRFCKLINNPKMSTFNM 466
Cdd:PLN03218   363 GVSGKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNM 442

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  467 LLSVCANSQDFDGALQVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNVNTYSALIDGCAKAGQ 546
Cdd:PLN03218   443 LMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQ 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  547 VAKAFGAYGIMSSKKVKPDRVVFNALISACGESGAVARAFDVLSEMTAEAseskgsKPILPDHVTVGALMKTCIQAGQAD 626
Cdd:PLN03218   523 VAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET------HPIDPDHITVGALMKACANAGQVD 596

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  627 RAREVYKMLQEYNIKGTPEVYTIALRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDVAGHARRADAAFEIMKDAR 706
Cdd:PLN03218   597 RAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDAR 676

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  707 AKGYQVGTIAYSSLMGACCNAKDWKKALQLFEEIKSIKLMPTVSMMNALITALCDGDQVLKSFEVLSEMKRLGVCPNMIT 786
Cdd:PLN03218   677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTIT 756

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  787 YSVLFVACERNAEAQLGLDLFEQLKIDSIDLNPTIVGCLTGLCLQMFDNDLSLGNIVVTFNLGKPQIENKWTSSAIKVYR 866
Cdd:PLN03218   757 YSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYR 836

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  867 EAISTGLLPSSDVLSQVLGCLRFPHDNTLTNTFIENMGISCDIPHHPNVNSLLEGFGEYDIRAFSILEEAASLGAVESIS 946
Cdd:PLN03218   837 ETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEYDPRAFSLLEEAASLGVVPSVS 916

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  947 MKDTRILVDARKSKIYTAEVSVLTTLRSLKHRLAAGARLPNVTILLPTEKKQVGLDEREKTLKLAGRVGQAVGSLLRRLG 1026
Cdd:PLN03218   917 FKKSPIVIDAEELPVFAAEVYLLTILKGLKHRLAAGAKLPNVTILLPTEKKEIYTPKGEKTINLAGRVGQAVAALLRRLG 996

                          970       980       990      1000      1010      1020
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002302656 1027 IKYHGEESHGKMRINGLTLRRWFNPKLTSTSStGTPADLLPLPSRLAKGIADQQRNIR--NLSLE 1089
Cdd:PLN03218   997 LPYQGSESHGKLRINGLSLRRWFQPKLKSPFS-GKPEDLSSSQSRLGKGIADQQRAIRlgNLSLE 1060
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 538-702 1.12e-14

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: 74.36  E-value: 1.12e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  538 IDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISACGESG---------AVARAFDVLSEMTAEASEskgskpilPD 608
Cdd:pfam17177   18 LDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAAdatdlkpqlAADRGFEVFEAMKAQGVS--------PN 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  609 HVTVGALMKTCIQAGQADRAREVYKMLQEYNIKGTPEVYTIALRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDV 688
Cdd:pfam17177   90 EATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKV 169

                          170
                   ....*....|....
gi 1002302656  689 AGHARRADAAFEIM 702
Cdd:pfam17177  170 SAKAGRADKVYAYL 183
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 499-531 9.11e-08

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: 48.99  E-value: 9.11e-08
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1002302656  499 YTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNV 531
Cdd:TIGR00756    3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 620-813 7.76e-05

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 45.88  E-value: 7.76e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  620 IQAGQADRAREVYKMLQEYNIKgTPEVYTIALRSCSLTGDLGFALKIYEDMNKIGvQPDEMFLSALVDVAGHARRADAAF 699
Cdd:COG2956     87 LKAGLLDRAEELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLKLG-PENAHAYCELAELYLEQGDYDEAI 164

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  700 EIMKDARAKgYQVGTIAYSSLMGACCNAKDWKKALQLFEEIksIKLMP-TVSMMNALITALCDGDQVLKSFEVLSEMKRL 778
Cdd:COG2956    165 EALEKALKL-DPDCARALLLLAELYLEQGDYEEAIAALERA--LEQDPdYLPALPRLAELYEKLGDPEEALELLRKALEL 241

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1002302656  779 GVC-PNMITYSVLFVACERNAEAQlgLDLFEQLKID 813
Cdd:COG2956    242 DPSdDLLLALADLLERKEGLEAAL--ALLERQLRRH 275
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 103-1089 0e+00

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 1614.56  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  103 RWRGGDSPEEEEVSHEHdkRIVNNKALGTSTDLLDDS------------SYSSRRTHENVFSEPSVSGRMTVDRTDCQ-- 168
Cdd:PLN03218    52 RLRGGKSKSIRSRIRSP--RLVVNASLGSGLVLVVVAvtafsaisfaylQHTRRRKSSPLVATPSGGGISTLNREDVQsl 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  169 -TDVFSGVDT------------VNNTTQVGSVISTYRSLDTFEGVYGPANTSSIEKVqdilpqsRSVSDGQHQSRHFANR 235
Cdd:PLN03218   130 dGDVHKGTSTeinvgfrdlveeVEHTEEEKTHQAQERALMEEESVVVEGSESSRESV-------RVVADEHTLSDESASS 202

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  236 RAQLGGLPHQFLSLSKQNEQTKNGQGPPDNKTDSEGANLLGCHQSDQGDYVDFTSLSSFKRINEHPLNFIPEAHASN--- 312
Cdd:PLN03218   203 RVVHGSVALLSLSFGVENPELQNGNSPDQTKLELDLSQLVVGRHSIAESLFTQTVLDSLDYDSYEYNGLLQEAAISSgkg 282

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  313 LFEPRKASEFTNSYAGG-SYLRAGRLVPVACLRDGPVSKQ-----KKAMNDHDDAKLIGWSISNLLSKENPENSTSANRA 386
Cdd:PLN03218   283 IFAESKREELYTFYEEKqSRAKSSRLPNVKGLRKGVSSATnslslDKKNNGVKDAELPGQSSGQAASDVEEENSLAAYNG 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  387 GLRGTKDVPDYLRRYNSLLIDGRLKDSVDLLESMEQKGLLDMNKIHHASFLNACKKQRAVPEAVRFCKLINNPKMSTFNM 466
Cdd:PLN03218   363 GVSGKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNM 442

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  467 LLSVCANSQDFDGALQVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNVNTYSALIDGCAKAGQ 546
Cdd:PLN03218   443 LMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQ 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  547 VAKAFGAYGIMSSKKVKPDRVVFNALISACGESGAVARAFDVLSEMTAEAseskgsKPILPDHVTVGALMKTCIQAGQAD 626
Cdd:PLN03218   523 VAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET------HPIDPDHITVGALMKACANAGQVD 596

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  627 RAREVYKMLQEYNIKGTPEVYTIALRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDVAGHARRADAAFEIMKDAR 706
Cdd:PLN03218   597 RAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDAR 676

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  707 AKGYQVGTIAYSSLMGACCNAKDWKKALQLFEEIKSIKLMPTVSMMNALITALCDGDQVLKSFEVLSEMKRLGVCPNMIT 786
Cdd:PLN03218   677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTIT 756

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  787 YSVLFVACERNAEAQLGLDLFEQLKIDSIDLNPTIVGCLTGLCLQMFDNDLSLGNIVVTFNLGKPQIENKWTSSAIKVYR 866
Cdd:PLN03218   757 YSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYR 836

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  867 EAISTGLLPSSDVLSQVLGCLRFPHDNTLTNTFIENMGISCDIPHHPNVNSLLEGFGEYDIRAFSILEEAASLGAVESIS 946
Cdd:PLN03218   837 ETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEYDPRAFSLLEEAASLGVVPSVS 916

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  947 MKDTRILVDARKSKIYTAEVSVLTTLRSLKHRLAAGARLPNVTILLPTEKKQVGLDEREKTLKLAGRVGQAVGSLLRRLG 1026
Cdd:PLN03218   917 FKKSPIVIDAEELPVFAAEVYLLTILKGLKHRLAAGAKLPNVTILLPTEKKEIYTPKGEKTINLAGRVGQAVAALLRRLG 996

                          970       980       990      1000      1010      1020
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002302656 1027 IKYHGEESHGKMRINGLTLRRWFNPKLTSTSStGTPADLLPLPSRLAKGIADQQRNIR--NLSLE 1089
Cdd:PLN03218   997 LPYQGSESHGKLRINGLSLRRWFQPKLKSPFS-GKPEDLSSSQSRLGKGIADQQRAIRlgNLSLE 1060
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 538-702 1.12e-14

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: 74.36  E-value: 1.12e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  538 IDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISACGESG---------AVARAFDVLSEMTAEASEskgskpilPD 608
Cdd:pfam17177   18 LDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAAdatdlkpqlAADRGFEVFEAMKAQGVS--------PN 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  609 HVTVGALMKTCIQAGQADRAREVYKMLQEYNIKGTPEVYTIALRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDV 688
Cdd:pfam17177   90 EATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKV 169

                          170
                   ....*....|....
gi 1002302656  689 AGHARRADAAFEIM 702
Cdd:pfam17177  170 SAKAGRADKVYAYL 183
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 462-638 2.94e-14

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: 72.81  E-value: 2.94e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  462 STFNMLLSVCANSQDFDGALQVMVLLKEAGLKPDCKLYTTLISTCAKCG---------KVDAMFEVFHEMVSAGIEPNVN 532
Cdd:pfam17177   12 SELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAAdatdlkpqlAADRGFEVFEAMKAQGVSPNEA 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  533 TYSALIDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISACGESGAVARAFDVLSEMTAEASEskgskpilPDHVTV 612
Cdd:pfam17177   92 TYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVE--------LEEPEL 163

                          170       180
                   ....*....|....*....|....*.
gi 1002302656  613 GALMKTCIQAGQADRareVYKMLQEY 638
Cdd:pfam17177  164 AALLKVSAKAGRADK---VYAYLHRL 186
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 499-543 5.70e-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: 67.00  E-value: 5.70e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1002302656  499 YTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNVNTYSALIDGCAK 543
Cdd:pfam13041    6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 518-577 6.65e-12

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: 61.61  E-value: 6.65e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  518 VFHEMVSAGIEPNVNTYSALIDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISACG 577
Cdd:pfam13812    2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PLN03077 PLN03077
Protein ECB2; Provisional
 400-813 5.96e-11

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 66.80  E-value: 5.96e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  400 RYNSLLIDGRLKDSVDLLESMeQKGLLDMNKIHHASFLNACKKQRAVPEAVRFCKLINNpKMSTF-----NMLLSVCANS 474
Cdd:PLN03077    57 QLRALCSHGQLEQALKLLESM-QELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALS-SHPSLgvrlgNAMLSMFVRF 134

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  475 QDFDGALQVMVLLKEAglkpDCKLYTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNVNTY-------------------- 534
Cdd:PLN03077   135 GELVHAWYVFGKMPER----DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFpcvlrtcggipdlargrevh 210

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  535 ---------------SALIDGCAKAGQVAKAFGAYGIMSSK-------------------------------KVKPDRVV 568
Cdd:PLN03077   211 ahvvrfgfeldvdvvNALITMYVKCGDVVSARLVFDRMPRRdciswnamisgyfengecleglelfftmrelSVDPDLMT 290

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  569 FNALISACGESG-----------AVARAFDV-------LSEMTAEA-----SESKGSKPILPDHVTVGALMKTCIQAGQA 625
Cdd:PLN03077   291 ITSVISACELLGderlgremhgyVVKTGFAVdvsvcnsLIQMYLSLgswgeAEKVFSRMETKDAVSWTAMISGYEKNGLP 370

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  626 DRAREVYKMLQEYNIKgtPEVYTIA--LRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDVAGHARRADAAFEIMK 703
Cdd:PLN03077   371 DKALETYALMEQDNVS--PDEITIAsvLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFH 448

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  704 DARAKgyqvGTIAYSSLM-GACCNAKDWkKALQLFEEIKsIKLMP-TVSMMNAL-----ITALCDGDQ----VLKS---- 768
Cdd:PLN03077   449 NIPEK----DVISWTSIIaGLRLNNRCF-EALIFFRQML-LTLKPnSVTLIAALsacarIGALMCGKEihahVLRTgigf 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  769 ---------------------------------------------------FEVLSEMKRLGVCPNMITYSVLFVACERN 797
Cdd:PLN03077   523 dgflpnalldlyvrcgrmnyawnqfnshekdvvswnilltgyvahgkgsmaVELFNRMVESGVNPDEVTFISLLCACSRS 602

                          570
                   ....*....|....*.
gi 1002302656  798 AEAQLGLDLFEQLKID 813
Cdd:PLN03077   603 GMVTQGLEYFHSMEEK 618
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 618-790 1.76e-10

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: 62.03  E-value: 1.76e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  618 TCIQAGQADRAREVYKMLQEYNIKGTPEVYTIALRSCSLTGD---------LGFALKIYEDMNKIGVQPDEMFLSALVDV 688
Cdd:pfam17177   20 KCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADatdlkpqlaADRGFEVFEAMKAQGVSPNEATYTAVARL 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  689 AGHARRADAAFEIMKDARAKGYQVGTIAYSSLMGACCNAKDWKKALQLFEEIKSIKLMPTVSMMNALITALCDGDQVLKS 768
Cdd:pfam17177  100 AAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKV 179

                          170       180
                   ....*....|....*....|..
gi 1002302656  769 FEVLSEMKRLGVCPNMITYSVL 790
Cdd:pfam17177  180 YAYLHRLRDAVRQVSESTAGVL 201
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 437-810 2.02e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 64.89  E-value: 2.02e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  437 LNACKKQRAVPEAVRFCKLINNPKM--STFNMLLSVCANSQDFDGALQVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDA 514
Cdd:PLN03081    97 LVACGRHREALELFEILEAGCPFTLpaSTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLID 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  515 MFEVFHEMVsagiEPNVNTYSALIDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISACGESGAvARAFDVLSEMTA 594
Cdd:PLN03081   177 ARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGS-ARAGQQLHCCVL 251

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  595 EASeskgskpILPDHVTVGALMKTCIQAGQADRAREVYkmlqeyniKGTPEVYTIA----LRSCSLTGDLGFALKIYEDM 670
Cdd:PLN03081   252 KTG-------VVGDTFVSCALIDMYSKCGDIEDARCVF--------DGMPEKTTVAwnsmLAGYALHGYSEEALCLYYEM 316

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  671 NKIGVQPDEMFLSALVDVAGHArradAAFEIMKDARA----KGYQVGTIAYSSLMGACCNAKDWKKALQLFEEiksiklM 746
Cdd:PLN03081   317 RDSGVSIDQFTFSIMIRIFSRL----ALLEHAKQAHAglirTGFPLDIVANTALVDLYSKWGRMEDARNVFDR------M 386

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002302656  747 PTVSMM--NALITALCDGDQVLKSFEVLSEMKRLGVCPNMITYSVLFVACERNAEAQLGLDLFEQL 810
Cdd:PLN03081   387 PRKNLIswNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSM 452
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 445-589 3.86e-10

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: 60.87  E-value: 3.86e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  445 AVPEAVRFCKLInnpkmstFNMLLSVCANSQD---------FDGALQVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDAM 515
Cdd:pfam17177   37 AKAEGVRLAQYH-------YNVLLYLCSKAADatdlkpqlaADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002302656  516 FEVFHEMVSAGIEPNVNTYSALIDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISACGESGAVARAFDVL 589
Cdd:pfam17177  110 FDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAYL 183
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 747-794 1.96e-09

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 54.29  E-value: 1.96e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1002302656  747 PTVSMMNALITALCDGDQVLKSFEVLSEMKRLGVCPNMITYSVLFVAC 794
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 ...
 529-576 3.78e-09

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 53.14  E-value: 3.78e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1002302656  529 PNVNTYSALIDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISAC 576
Cdd:pfam13041    1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 405-741 1.10e-08

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 59.11  E-value: 1.10e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  405 LID-----GRLKDSVDLLESMEQKGLLDMNKIHHASFLNACKKqravpEAVRFCKLINNPKMS----TFNMLLSVCANSQ 475
Cdd:PLN03081   265 LIDmyskcGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSE-----EALCLYYEMRDSGVSidqfTFSIMIRIFSRLA 339

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  476 DFDGALQVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMVsagiEPNVNTYSALIDGCAKAGQVAKAFGAYG 555
Cdd:PLN03081   340 LLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKNLISWNALIAGYGNHGRGTKAVEMFE 415

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  556 IMSSKKVKPDRVVFNALISACGESGAVARAFDVLSEMTaeasESKGSKPilpdhvtvGALMKTCIQA--GQADRAREVYK 633
Cdd:PLN03081   416 RMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMS----ENHRIKP--------RAMHYACMIEllGREGLLDEAYA 483

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  634 MLQEYNIKGTPEVYTIALRSCSLTGDLGFALKIYEDMnkIGVQPDEM-FLSALVDVAGHARRADAAFEIMKDARAKGY-- 710
Cdd:PLN03081   484 MIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKL--YGMGPEKLnNYVVLLNLYNSSGRQAEAAKVVETLKRKGLsm 561

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|.
gi 1002302656  711 -------QVGTIAYSSLMGACC---NAKDWKKALQLFEEIK 741
Cdd:PLN03081   562 hpactwiEVKKQDHSFFSGDRLhpqSREIYQKLDELMKEIS 602
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 643-801 1.10e-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: 56.64  E-value: 1.10e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  643 TPEV-YTIALRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDVAGHA---------RRADAAFEIMKDARAKGYQV 712
Cdd:pfam17177    9 TPESeLRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAadatdlkpqLAADRGFEVFEAMKAQGVSP 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  713 GTIAYSSLMGACCNAKDWKKALQLFEEIKSIKLMPTVSMMNALITALCDGDQVLKSFEVLSEMKRLGVCPNMITYSVLFV 792
Cdd:pfam17177   89 NEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLK 168


                   ....*....
gi 1002302656  793 ACERNAEAQ 801
Cdd:pfam17177  169 VSAKAGRAD 177
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 491-543 3.71e-08

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: 50.82  E-value: 3.71e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1002302656  491 GLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNVNTYSALIDGCAK 543
Cdd:pfam13812   10 GIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PLN03077 PLN03077
Protein ECB2; Provisional
 451-654 5.22e-08

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 57.17  E-value: 5.22e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  451 RFCKLINNPKMSTFNMLLSVCANSqdfdGAL----QVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMvsag 526
Cdd:PLN03077   479 RQMLLTLKPNSVTLIAALSACARI----GALmcgkEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH---- 550

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  527 iEPNVNTYSALIDGCAKAGQVAKAFGAYGIMSSKKVKPDRVVFNALISACGESGAVARAFDVLSEMTAEASESkgskPIL 606
Cdd:PLN03077   551 -EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSIT----PNL 625

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1002302656  607 PDHVTVGALMktciqaGQADRAREVYKMLQEYNIKGTPEVYTIALRSC 654
Cdd:PLN03077   626 KHYACVVDLL------GRAGKLTEAYNFINKMPITPDPAVWGALLNAC 667
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 499-531 9.11e-08

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: 48.99  E-value: 9.11e-08
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1002302656  499 YTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNV 531
Cdd:TIGR00756    3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 480-800 9.66e-07

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 52.95  E-value: 9.66e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  480 ALQVMVLLKEAGLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMVSAGIEPNVNTYSALIDGCAKAGQVAKAFGAYGIMSS 559
Cdd:PLN03081   309 ALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR 388

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  560 KKVkpdrVVFNALISACGESGAVARAFDVLSEMTAEAseskgskpILPDHVTVGALMKTCIQAGQADRAREVYKMLQEYN 639
Cdd:PLN03081   389 KNL----ISWNALIAGYGNHGRGTKAVEMFERMIAEG--------VAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENH 456

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  640 ikgtpevytialrscsltgdlgfalkiyedmnkiGVQPDEMFLSALVDVAGHARRADAAFEIMKDArakgyqvgtiayss 719
Cdd:PLN03081   457 ----------------------------------RIKPRAMHYACMIELLGREGLLDEAYAMIRRA-------------- 488

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  720 lmgaccnakdwkkalqlfeeiksiKLMPTVSMMNALITAlcdgDQVLKSFEV--LSEMKRLGVCPNMI-TYSVL---FVA 793
Cdd:PLN03081   489 ------------------------PFKPTVNMWAALLTA----CRIHKNLELgrLAAEKLYGMGPEKLnNYVVLlnlYNS 540


                   ....*..
gi 1002302656  794 CERNAEA 800
Cdd:PLN03081   541 SGRQAEA 547
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 713-761 1.27e-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: 46.20  E-value: 1.27e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1002302656  713 GTIAYSSLMGACCNAKDWKKALQLFEEIKSIKLMPTVSMMNALITALCD 761
Cdd:pfam13041    2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 701-758 2.97e-06

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: 45.43  E-value: 2.97e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002302656  701 IMKDARAKGYQVGTIAYSSLMGACCNAKDWKKALQLFEEIKSIKLMPTVSMMNALITA 758
Cdd:pfam13812    2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 485-741 7.16e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 50.25  E-value: 7.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  485 VLLKEAGLKPDCKLYTTlISTCAKCGKVDAMFEVFhEMVSAG--IEPNVNTYSALIDGCAKAGQVAKAFGAYGIMSSKKV 562
Cdd:PLN03081    77 RLDDTQIRKSGVSLCSQ-IEKLVACGRHREALELF-EILEAGcpFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGF 154

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  563 KPDRVVFNALISACGESGAVARAFDVLSEMTAEaseskgskpilpDHVTVGALMKTCIQAGQADRAREVYKMLQEYNIKG 642
Cdd:PLN03081   155 EPDQYMMNRVLLMHVKCGMLIDARRLFDEMPER------------NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDA 222

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  643 TPEVYTIALRSCSLTGDLGFALKIYEDMNKIGVQPDEMFLSALVDV---AGHARRADAAFEIMKDArakgyqvGTIAYSS 719
Cdd:PLN03081   223 EPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMyskCGDIEDARCVFDGMPEK-------TTVAWNS 295

                          250       260
                   ....*....|....*....|..
gi 1002302656  720 LMGACCNAKDWKKALQLFEEIK 741
Cdd:PLN03081   296 MLAGYALHGYSEEALCLYYEMR 317
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 491-523 1.84e-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: 1.84e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1002302656  491 GLKPDCKLYTTLISTCAKCGKVDAMFEVFHEMV 523
Cdd:pfam12854    2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 526-551 3.16e-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: 3.16e-05
                           10        20
                   ....*....|....*....|....*.
gi 1002302656  526 GIEPNVNTYSALIDGCAKAGQVAKAF 551
Cdd:pfam12854    2 GLKPDVVTYNTLINGLCRAGRVDEAF 27
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 499-527 4.42e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 41.30  E-value: 4.42e-05
                           10        20
                   ....*....|....*....|....*....
gi 1002302656  499 YTTLISTCAKCGKVDAMFEVFHEMVSAGI 527
Cdd:pfam01535    3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 533-565 4.89e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 41.29  E-value: 4.89e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1002302656  533 TYSALIDGCAKAGQVAKAFGAYGIMSSKKVKPD 565
Cdd:TIGR00756    2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 620-813 7.76e-05

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 45.88  E-value: 7.76e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  620 IQAGQADRAREVYKMLQEYNIKgTPEVYTIALRSCSLTGDLGFALKIYEDMNKIGvQPDEMFLSALVDVAGHARRADAAF 699
Cdd:COG2956     87 LKAGLLDRAEELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLKLG-PENAHAYCELAELYLEQGDYDEAI 164

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302656  700 EIMKDARAKgYQVGTIAYSSLMGACCNAKDWKKALQLFEEIksIKLMP-TVSMMNALITALCDGDQVLKSFEVLSEMKRL 778
Cdd:COG2956    165 EALEKALKL-DPDCARALLLLAELYLEQGDYEEAIAALERA--LEQDPdYLPALPRLAELYEKLGDPEEALELLRKALEL 241

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1002302656  779 GVC-PNMITYSVLFVACERNAEAQlgLDLFEQLKID 813
Cdd:COG2956    242 DPSdDLLLALADLLERKEGLEAAL--ALLERQLRRH 275
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 564-619 1.08e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.81  E-value: 1.08e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002302656  564 PDRVVFNALISACGESGAVARAFDVLSEMtaeasESKGskpILPDHVTVGALMKTC 619
Cdd:pfam13041    1 PDVVTYNTLINGYCKKGKVEEAFKLFNEM-----KKRG---VKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 459-508 1.21e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.42  E-value: 1.21e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1002302656  459 PKMSTFNMLLSVCANSQDFDGALQVMVLLKEAGLKPDCKLYTTLISTCAK 508
Cdd:pfam13041    1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 715-742 5.07e-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: 38.59  E-value: 5.07e-04
                           10        20
                   ....*....|....*....|....*...
gi 1002302656  715 IAYSSLMGACCNAKDWKKALQLFEEIKS 742
Cdd:TIGR00756    1 VTYNTLIDGLCKAGRVEEALELFKEMKE 28
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 736-797 9.66e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 38.49  E-value: 9.66e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002302656  736 LFEEIKSIKLMPTVSMMNALITALCD-GDQVLkSFEVLSEMKRLGVCPNMITYSVLFVACERN 797
Cdd:pfam13812    2 ILREMVRDGIQLNVNTYTHLLHAYANvGNLKL-ALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 715-742 1.01e-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: 37.44  E-value: 1.01e-03
                           10        20
                   ....*....|....*....|....*...
gi 1002302656  715 IAYSSLMGACCNAKDWKKALQLFEEIKS 742
Cdd:pfam01535    1 VTYNSLISGYCKNGKLEEALELFKEMKE 28
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 459-508 1.52e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 38.11  E-value: 1.52e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1002302656  459 PKMSTFNMLLSVCANSQDFDGALQVMVLLKEAGLKPDCKLYTTLISTCAK 508
Cdd:pfam13812   13 LNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 562-593 1.89e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 36.94  E-value: 1.89e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1002302656  562 VKPDRVVFNALISACGESGAVARAFDVLSEMT 593
Cdd:pfam12854    3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 463-496 1.89e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.66  E-value: 1.89e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1002302656  463 TFNMLLSVCANSQDFDGALQVMVLLKEAGLKPDC 496
Cdd:TIGR00756    2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 665-726 3.08e-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: 3.08e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002302656  665 KIYEDMNKIGVQPDEMFLSALVDVAGHARRADAAFEIMKDARAKGYQVGTIAYSSLMGACCN 726
Cdd:pfam13812    1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 753-783 4.59e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.89  E-value: 4.59e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1002302656  753 NALITALCDGDQVLKSFEVLSEMKRLGVCPN 783
Cdd:TIGR00756    4 NTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
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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