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Conserved domains on  [gi|15219388|ref|NP_178067|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 246-598 1.88e-30

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 129.23  E-value: 1.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   246 YNQVIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIPSLAK 325
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   326 SGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMKVYMEMQGFGH--RPSATMFVSLIDSYAKAGKLDTAL 403
Cdd:PLN03218  520 AGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHpiDPDHITVGALMKACANAGQVDRAK 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   404 RLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMTNAG 483
Cdd:PLN03218  600 EVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQG 679

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   484 LRPGLSSYISLLTLLANKRLVDVAGKILLEMKAMGYSVDVCASDVLMIYIKDAS-VDLALKWLRFMGSSGIKTNNFIIRQ 562
Cdd:PLN03218  680 IKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNqLPKALEVLSEMKRLGLCPNTITYSI 759

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 15219388   563 LFESCMKNGLYDSARPLLETLVHSAGKVDLVLYTSI 598
Cdd:PLN03218  760 LLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795
SMR smart00463
Small MutS-related domain;
708-786 7.47e-11

Small MutS-related domain;


:

Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 58.85  E-value: 7.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388    708 WSLDVRNLSVGAALIAVVHTLHRFRKRMLYygvvpRRIKLVTG---------PTLKIVIAQMLSSVESPFEVSKvvlrAP 778
Cdd:smart00463   2 WSLDLHGLTVEEALTALDKFLNNARLKGLE-----QKLVIITGkgkhslggkSGVKPALKEHLRVESFRFAEEG----NS 72


                   ....*...
gi 15219388    779 GELVMEWF 786
Cdd:smart00463  73 GVLVVKLK 80
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 246-598 1.88e-30

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 129.23  E-value: 1.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   246 YNQVIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIPSLAK 325
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   326 SGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMKVYMEMQGFGH--RPSATMFVSLIDSYAKAGKLDTAL 403
Cdd:PLN03218  520 AGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHpiDPDHITVGALMKACANAGQVDRAK 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   404 RLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMTNAG 483
Cdd:PLN03218  600 EVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQG 679

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   484 LRPGLSSYISLLTLLANKRLVDVAGKILLEMKAMGYSVDVCASDVLMIYIKDAS-VDLALKWLRFMGSSGIKTNNFIIRQ 562
Cdd:PLN03218  680 IKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNqLPKALEVLSEMKRLGLCPNTITYSI 759

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 15219388   563 LFESCMKNGLYDSARPLLETLVHSAGKVDLVLYTSI 598
Cdd:PLN03218  760 LLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 314-476 5.05e-11

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: 63.18  E-value: 5.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   314 STYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMK---------VYMEMQGFGHRPSAT 384
Cdd:pfam17177  12 SELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPqlaadrgfeVFEAMKAQGVSPNEA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   385 MFVSLIDSYAKAGKLDTALRLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHA 464
Cdd:pfam17177  92 TYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSA 171

                         170
                  ....*....|..
gi 15219388   465 GSGQvdsAMKIY 476
Cdd:pfam17177 172 KAGR---ADKVY 180
SMR smart00463
Small MutS-related domain;
708-786 7.47e-11

Small MutS-related domain;


Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 58.85  E-value: 7.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388    708 WSLDVRNLSVGAALIAVVHTLHRFRKRMLYygvvpRRIKLVTG---------PTLKIVIAQMLSSVESPFEVSKvvlrAP 778
Cdd:smart00463   2 WSLDLHGLTVEEALTALDKFLNNARLKGLE-----QKLVIITGkgkhslggkSGVKPALKEHLRVESFRFAEEG----NS 72


                   ....*...
gi 15219388    779 GELVMEWF 786
Cdd:smart00463  73 GVLVVKLK 80
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 385-417 1.38e-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: 45.52  E-value: 1.38e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15219388   385 MFVSLIDSYAKAGKLDTALRLWDEMKKSGFRPN 417
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 246-514 1.58e-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: 47.42  E-value: 1.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388 246 YNQVIQYLAKaEKLEVAFCCFKKAQEsgckID---TQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIpS 322
Cdd:COG2956  12 YFKGLNYLLN-GQPDKAIDLLEEALE----LDpetVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALLELAQ-D 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388 323 LAKSGRLDAAFKLFQQMkeRKLRP-SFSVFSSLVDSMGKAGRLDTSMKVYMEMQGFGHRpSATMFVSLIDSYAKAGKLDT 401
Cdd:COG2956  86 YLKAGLLDRAEELLEKL--LELDPdDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPE-NAHAYCELAELYLEQGDYDE 162

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388 402 ALRLWDEMKKSgfRPNF-GLYTMIIESHAKSGKLEVAMTVFKDMEKAgFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMt 480
Cdd:COG2956 163 AIEALEKALKL--DPDCaRALLLLAELYLEQGDYEEAIAALERALEQ-DPDYLPALPRLAELYEKLGDPEEALELLRKA- 238

                       250       260       270
                ....*....|....*....|....*....|....
gi 15219388 481 nAGLRPGLSSYISLLTLLANKRLVDVAGKILLEM 514
Cdd:COG2956 239 -LELDPSDDLLLALADLLERKEGLEAALALLERQ 271
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 246-598 1.88e-30

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 129.23  E-value: 1.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   246 YNQVIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIPSLAK 325
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   326 SGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMKVYMEMQGFGH--RPSATMFVSLIDSYAKAGKLDTAL 403
Cdd:PLN03218  520 AGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHpiDPDHITVGALMKACANAGQVDRAK 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   404 RLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMTNAG 483
Cdd:PLN03218  600 EVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQG 679

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   484 LRPGLSSYISLLTLLANKRLVDVAGKILLEMKAMGYSVDVCASDVLMIYIKDAS-VDLALKWLRFMGSSGIKTNNFIIRQ 562
Cdd:PLN03218  680 IKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNqLPKALEVLSEMKRLGLCPNTITYSI 759

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 15219388   563 LFESCMKNGLYDSARPLLETLVHSAGKVDLVLYTSI 598
Cdd:PLN03218  760 LLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 162-581 2.78e-24

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 109.58  E-value: 2.78e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   162 QLDKLQFvpNMVHITQSLKIVKEVDAALSLFRWAKKQPwyLPSDECYVVLFDGLNQGRDFVGIQSLFEeMVQDSSSHGDL 241
Cdd:PLN03218  398 KRGLLDM--DKIYHAKFFKACKKQRAVKEAFRFAKLIR--NPTLSTFNMLMSVCASSQDIDGALRVLR-LVQEAGLKADC 472

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   242 SFnaYNQVIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIP 321
Cdd:PLN03218  473 KL--YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALIS 550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   322 SLAKSGRLDAAFKLFQQMKERK--LRPSFSVFSSLVDSMGKAGRLDTSMKVYMEMQGFGHRPSATMFVSLIDSYAKAGKL 399
Cdd:PLN03218  551 ACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDW 630

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   400 DTALRLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSM 479
Cdd:PLN03218  631 DFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   480 TNAGLRPGLSSYISLLTLLANKRLVDVAGKILLEMKAMG-------YSVDVCASDvlmiyiKDASVDLALKWLRFMGSSG 552
Cdd:PLN03218  711 KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGlcpntitYSILLVASE------RKDDADVGLDLLSQAKEDG 784

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|
gi 15219388   553 IKTNNFIIR-------QLFESCMKNGL----YDSARPLLE 581
Cdd:PLN03218  785 IKPNLVMCRcitglclRRFEKACALGEpvvsFDSGRPQIE 824
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 314-476 5.05e-11

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: 63.18  E-value: 5.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   314 STYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMK---------VYMEMQGFGHRPSAT 384
Cdd:pfam17177  12 SELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPqlaadrgfeVFEAMKAQGVSPNEA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   385 MFVSLIDSYAKAGKLDTALRLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHA 464
Cdd:pfam17177  92 TYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSA 171

                         170
                  ....*....|..
gi 15219388   465 GSGQvdsAMKIY 476
Cdd:pfam17177 172 KAGR---ADKVY 180
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 206-460 5.09e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 66.82  E-value: 5.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   206 ECYVVLFDGLNQGRDFVGIQSLFEEMVQDSSSHGDLSFNAynqVIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLM 285
Cdd:PLN03218  615 EVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSA---LVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM 691

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   286 MLFLNKGLPYKAFEIYEsmektdslldgstyeliipslaksgrldaafklfqQMKERKLRPSFSVFSSLVDSMGKAGRLD 365
Cdd:PLN03218  692 GACSNAKNWKKALELYE-----------------------------------DIKSIKLRPTVSTMNALITALCEGNQLP 736

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   366 TSMKVYMEMQGFGHRPSATMFVSLIDSYAKAGKLDTALRLWDEMKKSGFRPNFGLYTMII-------ESHA--------- 429
Cdd:PLN03218  737 KALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITglclrrfEKACalgepvvsf 816

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 15219388   430 KSGKLEV-------AMTVFKDMEKAGFLPTPSTYSCLL 460
Cdd:PLN03218  817 DSGRPQIenkwtswALMVYRETISAGTLPTMEVLSQVL 854
SMR smart00463
Small MutS-related domain;
708-786 7.47e-11

Small MutS-related domain;


Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 58.85  E-value: 7.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388    708 WSLDVRNLSVGAALIAVVHTLHRFRKRMLYygvvpRRIKLVTG---------PTLKIVIAQMLSSVESPFEVSKvvlrAP 778
Cdd:smart00463   2 WSLDLHGLTVEEALTALDKFLNNARLKGLE-----QKLVIITGkgkhslggkSGVKPALKEHLRVESFRFAEEG----NS 72


                   ....*...
gi 15219388    779 GELVMEWF 786
Cdd:smart00463  73 GVLVVKLK 80
PLN03077 PLN03077
Protein ECB2; Provisional
 239-495 8.28e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 59.48  E-value: 8.28e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  239 GDLSFnaYNQVIQYLAKAEKLEVAFCCFKKAQesgCKiDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYEL 318
Cdd:PLN03077 321 VDVSV--CNSLIQMYLSLGSWGEAEKVFSRME---TK-DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIAS 394

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  319 IIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMKVYMEMQG--------------FGHR---- 380
Cdd:PLN03077 395 VLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEkdviswtsiiaglrLNNRcfea 474

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  381 ------------PSATMFVSLIDSYAKAGKLDT-----ALRLWDEMKKSGFRPNfglytMIIESHAKSGKLEVAMTVFKD 443
Cdd:PLN03077 475 liffrqmlltlkPNSVTLIAALSACARIGALMCgkeihAHVLRTGIGFDGFLPN-----ALLDLYVRCGRMNYAWNQFNS 549

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 15219388  444 MEKagflpTPSTYSCLLEMHAGSGQVDSAMKIYNSMTNAGLRPGLSSYISLL 495
Cdd:PLN03077 550 HEK-----DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLL 596
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 239-400 4.51e-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: 54.32  E-value: 4.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   239 GDLSFNaynqvIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLMMLFLNKGLP---------YKAFEIYESMEKTDS 309
Cdd:pfam17177  12 SELRFQ-----LDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADAtdlkpqlaaDRGFEVFEAMKAQGV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   310 LLDGSTYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMKVYMEMQGFGHRPSATMFVSL 389
Cdd:pfam17177  87 SPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAAL 166

                         170
                  ....*....|.
gi 15219388   390 IDSYAKAGKLD 400
Cdd:pfam17177 167 LKVSAKAGRAD 177
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 225-521 6.07e-08

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 56.42  E-value: 6.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  225 QSLFEEMVQDSSShgdlsfnAYNQVIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESM 304
Cdd:PLN03081 279 RCVFDGMPEKTTV-------AWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGL 351

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  305 EKTDSLLDGSTYELIIPSLAKSGRLDAAFKLFQQMKERKLRPsfsvFSSLVDSMGKAGRLDTSMKVYMEMQGFGHRPSAT 384
Cdd:PLN03081 352 IRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLIS----WNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHV 427

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  385 MFVSLIDSYAKAGKLDTALRLWDEMKKS-GFRPNFGLYTMIIESHAKSGKLEVAMTVFKdmeKAGFLPTPSTYSCLL--- 460
Cdd:PLN03081 428 TFLAVLSACRYSGLSEQGWEIFQSMSENhRIKPRAMHYACMIELLGREGLLDEAYAMIR---RAPFKPTVNMWAALLtac 504

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15219388  461 EMHAGS--GQVdSAMKIYnsmtnaGLRP-GLSSYISLLTLLANKRLVDVAGKILLEMKAMGYSV 521
Cdd:PLN03081 505 RIHKNLelGRL-AAEKLY------GMGPeKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSM 561
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 388-430 8.58e-08

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 49.28  E-value: 8.58e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 15219388   388 SLIDSYAKAGKLDTALRLWDEMKKSGFRPNFGLYTMIIESHAK 430
Cdd:pfam13041   8 TLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 404-465 1.59e-07

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: 48.89  E-value: 1.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15219388   404 RLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAG 465
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 342-505 1.90e-07

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 52.40  E-value: 1.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   342 RKLRPSFSVFSSL---VDSMGKAGRLDTSMKVYMEMQGFGHRPSATMFVSLIDSYAKAG---------KLDTALRLWDEM 409
Cdd:pfam17177   2 RKKKGKQTPESELrfqLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAAdatdlkpqlAADRGFEVFEAM 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   410 KKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMTNAGLRPGLS 489
Cdd:pfam17177  82 KAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEP 161

                         170
                  ....*....|....*.
gi 15219388   490 SYISLLTLLANKRLVD 505
Cdd:pfam17177 162 ELAALLKVSAKAGRAD 177
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 421-460 1.29e-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: 45.82  E-value: 1.29e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 15219388   421 YTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLL 460
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILI 45
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 385-417 1.38e-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: 45.52  E-value: 1.38e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15219388   385 MFVSLIDSYAKAGKLDTALRLWDEMKKSGFRPN 417
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 272-509 1.89e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 51.41  E-value: 1.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  272 SGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDslldGSTYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVF 351
Cdd:PLN03081 152 SGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERN----LASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTF 227

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  352 SSLVDSMGKAGRLDTSMKVYMEMQGFGHRPSATMFVSLIDSYAKAGKLDTALRLWDEM-KKSGFRPNfglytMIIESHAK 430
Cdd:PLN03081 228 VVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMpEKTTVAWN-----SMLAGYAL 302

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15219388  431 SGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMTNAGLRpglssyislLTLLANKRLVDVAGK 509
Cdd:PLN03081 303 HGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFP---------LDIVANTALVDLYSK 372
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 280-520 2.83e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 51.02  E-value: 2.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  280 TYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMG 359
Cdd:PLN03081 191 SWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYS 270

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  360 KAGRLDTSMKVYMEMQgfghRPSATMFVSLIDSYAKAGKLDTALRLWDEMKKSGFR-PNFGLYTMI------------IE 426
Cdd:PLN03081 271 KCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSiDQFTFSIMIrifsrlallehaKQ 346

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  427 SHA----------------------KSGKLEVAMTVFKDMEKAGFLptpsTYSCLLEMHAGSGQVDSAMKIYNSMTNAGL 484
Cdd:PLN03081 347 AHAglirtgfpldivantalvdlysKWGRMEDARNVFDRMPRKNLI----SWNALIAGYGNHGRGTKAVEMFERMIAEGV 422

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 15219388  485 RPGLSSYISLLTLLANKRLVDVAGKILLEM--------KAMGYS 520
Cdd:PLN03081 423 APNHVTFLAVLSACRYSGLSEQGWEIFQSMsenhrikpRAMHYA 466
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 320-599 7.49e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 49.48  E-value: 7.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  320 IPSLAKSGRLDAAFKLFQQMKerkLRPSFSVFSSLVDSMGKAG-RLDT---SMKVYMEMQGFGHRPSATMFVSLIDSYAK 395
Cdd:PLN03081  94 IEKLVACGRHREALELFEILE---AGCPFTLPASTYDALVEACiALKSircVKAVYWHVESSGFEPDQYMMNRVLLMHVK 170

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  396 AGKLDTALRLWDEMKKSgfrpNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKI 475
Cdd:PLN03081 171 CGMLIDARRLFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQL 246

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  476 YNSMTNAGLrpGLSSYIS--LLTLLANKRLVDVAGKILlemKAMGYSVDVCASDVLMIYIKDASVDLALKWLRFMGSSGI 553
Cdd:PLN03081 247 HCCVLKTGV--VGDTFVScaLIDMYSKCGDIEDARCVF---DGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGV 321

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 15219388  554 KTNNFIIRQLFESCMKNGLYDSARPLLETLVHSAGKVDLVLYTSIL 599
Cdd:PLN03081 322 SIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALV 367
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 369-425 1.08e-05

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 43.50  E-value: 1.08e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15219388   369 KVYMEMQGFGHRPSATMFVSLIDSYAKAGKLDTALRLWDEMKKSGFRPNFGLYTMII 425
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 246-514 1.58e-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: 47.42  E-value: 1.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388 246 YNQVIQYLAKaEKLEVAFCCFKKAQEsgckID---TQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIpS 322
Cdd:COG2956  12 YFKGLNYLLN-GQPDKAIDLLEEALE----LDpetVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALLELAQ-D 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388 323 LAKSGRLDAAFKLFQQMkeRKLRP-SFSVFSSLVDSMGKAGRLDTSMKVYMEMQGFGHRpSATMFVSLIDSYAKAGKLDT 401
Cdd:COG2956  86 YLKAGLLDRAEELLEKL--LELDPdDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPE-NAHAYCELAELYLEQGDYDE 162

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388 402 ALRLWDEMKKSgfRPNF-GLYTMIIESHAKSGKLEVAMTVFKDMEKAgFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMt 480
Cdd:COG2956 163 AIEALEKALKL--DPDCaRALLLLAELYLEQGDYEEAIAALERALEQ-DPDYLPALPRLAELYEKLGDPEEALELLRKA- 238

                       250       260       270
                ....*....|....*....|....*....|....
gi 15219388 481 nAGLRPGLSSYISLLTLLANKRLVDVAGKILLEM 514
Cdd:COG2956 239 -LELDPSDDLLLALADLLERKEGLEAALALLERQ 271
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 385-414 1.94e-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: 42.07  E-value: 1.94e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 15219388   385 MFVSLIDSYAKAGKLDTALRLWDEMKKSGF 414
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 315-360 2.19e-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: 2.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15219388   315 TYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGK 360
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 237-610 3.41e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 47.54  E-value: 3.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  237 SHGDLSfnaynQVIQYLAKAEKLEVA-----------FCCFKKAQESG---CKIDTQTY--------NNLMMLFLNKGLP 294
Cdd:PLN03077  63 SHGQLE-----QALKLLESMQELRVPvdedayvalfrLCEWKRAVEEGsrvCSRALSSHpslgvrlgNAMLSMFVRFGEL 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  295 YKAFEIYESMEKTDSLldgsTYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDTSMKVYMEM 374
Cdd:PLN03077 138 VHAWYVFGKMPERDLF----SWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHV 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  375 QGFGHRPSATMFVSLIDSYAKAGKLDTALRLWDEMKksgfRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPS 454
Cdd:PLN03077 214 VRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLM 289

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  455 TYSCLLEMHAGSGQVDSAMKIYNSMTNAGLRPGLSSYISLLTLLANKRLVDVAGKILLEMK---AMGYSVdvcasdvlMI 531
Cdd:PLN03077 290 TITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMEtkdAVSWTA--------MI 361

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  532 --YIKDASVDLALKWLRFMGSSGIKTNNFIIRQLFESCMKNGLYDSARPLLEtLVHSAGKVDLVLYT-SILAHLVRCQDE 608
Cdd:PLN03077 362 sgYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHE-LAERKGLISYVVVAnALIEMYSKCKCI 440


                 ..
gi 15219388  609 DK 610
Cdd:PLN03077 441 DK 442
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 245-285 4.32e-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: 41.58  E-value: 4.32e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 15219388   245 AYNQVIQYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLM 285
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILI 45
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 377-410 4.98e-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: 40.79  E-value: 4.98e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15219388   377 FGHRPSATMFVSLIDSYAKAGKLDTALRLWDEMK 410
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 273-481 6.34e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 46.77  E-value: 6.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  273 GCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLldgsTYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFS 352
Cdd:PLN03077 217 GFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCI----SWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTIT 292

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  353 SLVDSMGKAG--RLDTSMKVYMEMQGF-----------------GHRPSATMFVS------------LIDSYAKAGKLDT 401
Cdd:PLN03077 293 SVISACELLGdeRLGREMHGYVVKTGFavdvsvcnsliqmylslGSWGEAEKVFSrmetkdavswtaMISGYEKNGLPDK 372

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  402 ALRLWDEMKKSGFRPNFGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMKIYNSMTN 481
Cdd:PLN03077 373 ALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPE 452
PLN03077 PLN03077
Protein ECB2; Provisional
 269-526 1.29e-04

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 45.61  E-value: 1.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  269 AQESGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIPSLAKSGRLDAAFKLFQQMKER-KLRPS 347
Cdd:PLN03077 545 NQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPN 624

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  348 FSVFSSLVDSMGKAGRLDTSMKVYMEMQgfgHRPSATMFVSL-----IDSYAKAGKLdTALRLWDEMKKSgfrpnFGLYT 422
Cdd:PLN03077 625 LKHYACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALlnacrIHRHVELGEL-AAQHIFELDPNS-----VGYYI 695

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388  423 MIIESHAKSGKLEVAMTVFKDMEKAGflptpstysclLEMHAGSGQVDSAMKIYNSMTNAGLRPGLssyislltllanKR 502
Cdd:PLN03077 696 LLCNLYADAGKWDEVARVRKTMRENG-----------LTVDPGCSWVEVKGKVHAFLTDDESHPQI------------KE 752

                        250       260
                 ....*....|....*....|....
gi 15219388  503 LVDVAGKILLEMKAMGYSVDVCAS 526
Cdd:PLN03077 753 INTVLEGFYEKMKASGLAGSESSS 776
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 451-500 1.39e-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: 40.04  E-value: 1.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15219388   451 PTPSTYSCLLEMHAGSGQVDSAMKIYNSMTNAGLRPGLSSYISLLTLLAN 500
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 410-590 1.50e-04

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 43.92  E-value: 1.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   410 KKSGFRPNfGLYTMIIESHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGSGQVDSAMK---------IYNSMT 480
Cdd:pfam17177   4 KKGKQTPE-SELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPqlaadrgfeVFEAMK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219388   481 NAGLRPGLSSYISLLTLLANKRLVDVAGKILLEMKAMGYSVDV-CASDVLMIYIKDASVDLALKWLRFMGSSGIKTNNFI 559
Cdd:pfam17177  83 AQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLrSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPE 162

                         170       180       190
                  ....*....|....*....|....*....|.
gi 15219388   560 IRQLFESCMKNGLYDSARPLLETLVHSAGKV 590
Cdd:pfam17177 163 LAALLKVSAKAGRADKVYAYLHRLRDAVRQV 193
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 315-347 2.29e-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: 38.98  E-value: 2.29e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15219388   315 TYELIIPSLAKSGRLDAAFKLFQQMKERKLRPS 347
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 421-452 2.96e-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: 2.96e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15219388   421 YTMIIESHAKSGKLEVAMTVFKDMEKAGFLPT 452
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 300-360 1.84e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 37.34  E-value: 1.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15219388   300 IYESMEKTDSLLDGSTYELIIPSLAKSGRLDAAFKLFQQMKERKLRPSFSVFSSLVDSMGK 360
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 421-449 5.20e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 35.13  E-value: 5.20e-03
                          10        20
                  ....*....|....*....|....*....
gi 15219388   421 YTMIIESHAKSGKLEVAMTVFKDMEKAGF 449
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 350-383 5.95e-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: 35.12  E-value: 5.95e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15219388   350 VFSSLVDSMGKAGRLDTSMKVYMEMQGFGHRPSA 383
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 277-325 6.54e-03

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: 35.42  E-value: 6.54e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15219388   277 DTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSLLDGSTYELIIPSLAK 325
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 315-340 9.23e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 34.63  E-value: 9.23e-03
                          10        20
                  ....*....|....*....|....*.
gi 15219388   315 TYELIIPSLAKSGRLDAAFKLFQQMK 340
Cdd:pfam12854   9 TYNTLINGLCRAGRVDEAFELLDEME 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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