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Conserved domains on  [gi|334186267|ref|NP_192012|]
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pentatricopeptide (PPR) repeat-containing protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13325788)

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

CATH:  1.25.40.10
Gene Ontology:  GO:0003723
PubMed:  19004664|23635770|25882680|34065603|18031283|30809817
SCOP:  4001344

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
 24-766 1.48e-151

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 463.55  E-value: 1.48e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  24 RVVSASMGFYGRCVSLGFANKLFDEMPKRDDLAWNEIVMVNLRSGNWEKAVELFREMQFSGAKAYDSTMVKLLQVCSNKE 103
Cdd:PLN03077 122 RLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIP 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 104 GFAEGRQIHGYVLRLGLESNVSMCNSLIVMYSRNGKLELSRKVFNSMKDRnlsswnsilssytklgyvddaiglldemei 183
Cdd:PLN03077 202 DLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR------------------------------ 251

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 184 cglkpDIVTWNSLLSGYASKGLSKDAIAVLKRMQIAGLKPSTSSISSLLQAVAEPGHLKLGKAIHGYILRNQLWYDVYVE 263
Cdd:PLN03077 252 -----DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVC 326

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 264 TTLIDMYIKTGYLPYARMVFDMMDAKNIVAWNSLVSGLSYACLLKDAEALMIRMEKEGIKPDAITWNSLASGYATLGK-- 341
Cdd:PLN03077 327 NSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDld 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 342 ---------------------------------PEKALDVIGKMKEKgvapNVVSWTAIFSG-CSKNGNFRnALKVFIKM 387
Cdd:PLN03077 407 vgvklhelaerkglisyvvvanaliemyskckcIDKALEVFHNIPEK----DVISWTSIIAGlRLNNRCFE-ALIFFRQM 481

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 388 QEEgVGPNAATMSTLLKILGCLSLLHSGKEVHGFCLRKNLICDAYVATALVDMYGKSGDLQSAIEIFwGIKNKSLASWNC 467
Cdd:PLN03077 482 LLT-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNI 559

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 468 MLMGYAMFGRGEEGIAAFSVMLEAGMEPDAITFTSVLSVCKNSGLVQEGWKYFDLMRSRYGIIPTIEHCSCMVDLLGRSG 547
Cdd:PLN03077 560 LLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAG 639

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 548 YLDEAWDFIQTMSLKPDATIWGAFLSSCKIHRDLELAEIAWKRLQVLEPHNSANYMMMINLYSNLNRWEDVERIRNLMRN 627
Cdd:PLN03077 640 KLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRE 719

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 628 NRVRVQDLWSWIQIDQTVHIFYAEGKTHPDEGDIYFELYKLVSEMKKSGYVPdTSCIHQDISDSEKEKLLMGHTEKLAMT 707
Cdd:PLN03077 720 NGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAG-SESSSMDEIEVSKDDIFCGHSERLAIA 798

                        730       740       750       760       770
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 334186267 708 YGLIKKKGLAPIRVVKNTNICSDSHTVAKYMSVLRNREIVLQEGARVHHFRDGKCSCND 766
Cdd:PLN03077 799 FGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 153-201 1.08e-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: 1.08e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186267  153 RNLSSWNSILSSYTKLGYVDDAIGLLDEMEICGLKPDIVTWNSLLSGYA 201
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 24-766 1.48e-151

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 463.55  E-value: 1.48e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  24 RVVSASMGFYGRCVSLGFANKLFDEMPKRDDLAWNEIVMVNLRSGNWEKAVELFREMQFSGAKAYDSTMVKLLQVCSNKE 103
Cdd:PLN03077 122 RLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIP 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 104 GFAEGRQIHGYVLRLGLESNVSMCNSLIVMYSRNGKLELSRKVFNSMKDRnlsswnsilssytklgyvddaiglldemei 183
Cdd:PLN03077 202 DLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR------------------------------ 251

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 184 cglkpDIVTWNSLLSGYASKGLSKDAIAVLKRMQIAGLKPSTSSISSLLQAVAEPGHLKLGKAIHGYILRNQLWYDVYVE 263
Cdd:PLN03077 252 -----DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVC 326

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 264 TTLIDMYIKTGYLPYARMVFDMMDAKNIVAWNSLVSGLSYACLLKDAEALMIRMEKEGIKPDAITWNSLASGYATLGK-- 341
Cdd:PLN03077 327 NSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDld 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 342 ---------------------------------PEKALDVIGKMKEKgvapNVVSWTAIFSG-CSKNGNFRnALKVFIKM 387
Cdd:PLN03077 407 vgvklhelaerkglisyvvvanaliemyskckcIDKALEVFHNIPEK----DVISWTSIIAGlRLNNRCFE-ALIFFRQM 481

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 388 QEEgVGPNAATMSTLLKILGCLSLLHSGKEVHGFCLRKNLICDAYVATALVDMYGKSGDLQSAIEIFwGIKNKSLASWNC 467
Cdd:PLN03077 482 LLT-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNI 559

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 468 MLMGYAMFGRGEEGIAAFSVMLEAGMEPDAITFTSVLSVCKNSGLVQEGWKYFDLMRSRYGIIPTIEHCSCMVDLLGRSG 547
Cdd:PLN03077 560 LLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAG 639

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 548 YLDEAWDFIQTMSLKPDATIWGAFLSSCKIHRDLELAEIAWKRLQVLEPHNSANYMMMINLYSNLNRWEDVERIRNLMRN 627
Cdd:PLN03077 640 KLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRE 719

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 628 NRVRVQDLWSWIQIDQTVHIFYAEGKTHPDEGDIYFELYKLVSEMKKSGYVPdTSCIHQDISDSEKEKLLMGHTEKLAMT 707
Cdd:PLN03077 720 NGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAG-SESSSMDEIEVSKDDIFCGHSERLAIA 798

                        730       740       750       760       770
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 334186267 708 YGLIKKKGLAPIRVVKNTNICSDSHTVAKYMSVLRNREIVLQEGARVHHFRDGKCSCND 766
Cdd:PLN03077 799 FGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 676-768 9.94e-36

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 129.85  E-value: 9.94e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  676 GYVPDTSCIHQDISDSEKEKLLMGHTEKLAMTYGLIKKKGLAPIRVVKNTNICSDSHTVAKYMSVLRNREIVLQEGARVH 755
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 334186267  756 HFRDGKCSCNDSW 768
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 153-201 1.08e-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: 1.08e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186267  153 RNLSSWNSILSSYTKLGYVDDAIGLLDEMEICGLKPDIVTWNSLLSGYA 201
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 327-361 5.70e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.52  E-value: 5.70e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334186267  327 ITWNSLASGYATLGKPEKALDVIGKMKEKGVAPNV 361
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 157-190 1.35e-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: 39.75  E-value: 1.35e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334186267  157 SWNSILSSYTKLGYVDDAIGLLDEMEICGLKPDI 190
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
56-215 8.56e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 38.83  E-value: 8.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  56 AWNEIVMVNLRSGNWEKAVELFR---EMQFSGAKAYdstmVKLLQVCSNKEGFAEGRQIHGYVLRLGLESNVSMCNsLIV 132
Cdd:COG0457   10 AYNNLGLAYRRLGRYEEAIEDYEkalELDPDDAEAL----YNLGLAYLRLGRYEEALADYEQALELDPDDAEALNN-LGL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 133 MYSRNGKLELSRKVFN---SMKDRNLSSWNSILSSYTKLGYVDDAIGLLDemEICGLKPDIV-TWNSLLSGYASKGLSKD 208
Cdd:COG0457   85 ALQALGRYEEALEDYDkalELDPDDAEALYNLGLALLELGRYDEAIEAYE--RALELDPDDAdALYNLGIALEKLGRYEE 162


                 ....*..
gi 334186267 209 AIAVLKR 215
Cdd:COG0457  163 ALELLEK 169
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 24-766 1.48e-151

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 463.55  E-value: 1.48e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  24 RVVSASMGFYGRCVSLGFANKLFDEMPKRDDLAWNEIVMVNLRSGNWEKAVELFREMQFSGAKAYDSTMVKLLQVCSNKE 103
Cdd:PLN03077 122 RLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIP 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 104 GFAEGRQIHGYVLRLGLESNVSMCNSLIVMYSRNGKLELSRKVFNSMKDRnlsswnsilssytklgyvddaiglldemei 183
Cdd:PLN03077 202 DLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR------------------------------ 251

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 184 cglkpDIVTWNSLLSGYASKGLSKDAIAVLKRMQIAGLKPSTSSISSLLQAVAEPGHLKLGKAIHGYILRNQLWYDVYVE 263
Cdd:PLN03077 252 -----DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVC 326

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 264 TTLIDMYIKTGYLPYARMVFDMMDAKNIVAWNSLVSGLSYACLLKDAEALMIRMEKEGIKPDAITWNSLASGYATLGK-- 341
Cdd:PLN03077 327 NSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDld 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 342 ---------------------------------PEKALDVIGKMKEKgvapNVVSWTAIFSG-CSKNGNFRnALKVFIKM 387
Cdd:PLN03077 407 vgvklhelaerkglisyvvvanaliemyskckcIDKALEVFHNIPEK----DVISWTSIIAGlRLNNRCFE-ALIFFRQM 481

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 388 QEEgVGPNAATMSTLLKILGCLSLLHSGKEVHGFCLRKNLICDAYVATALVDMYGKSGDLQSAIEIFwGIKNKSLASWNC 467
Cdd:PLN03077 482 LLT-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNI 559

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 468 MLMGYAMFGRGEEGIAAFSVMLEAGMEPDAITFTSVLSVCKNSGLVQEGWKYFDLMRSRYGIIPTIEHCSCMVDLLGRSG 547
Cdd:PLN03077 560 LLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAG 639

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 548 YLDEAWDFIQTMSLKPDATIWGAFLSSCKIHRDLELAEIAWKRLQVLEPHNSANYMMMINLYSNLNRWEDVERIRNLMRN 627
Cdd:PLN03077 640 KLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRE 719

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 628 NRVRVQDLWSWIQIDQTVHIFYAEGKTHPDEGDIYFELYKLVSEMKKSGYVPdTSCIHQDISDSEKEKLLMGHTEKLAMT 707
Cdd:PLN03077 720 NGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAG-SESSSMDEIEVSKDDIFCGHSERLAIA 798

                        730       740       750       760       770
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 334186267 708 YGLIKKKGLAPIRVVKNTNICSDSHTVAKYMSVLRNREIVLQEGARVHHFRDGKCSCND 766
Cdd:PLN03077 799 FGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 68-768 1.51e-125

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 391.16  E-value: 1.51e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  68 GNWEKAVELFR--EMQFS---GAKAYDStmvkLLQVCSNKEGFAEGRQIHGYVLRLGLESNVSMCNSLIVMYSRNGKLEL 142
Cdd:PLN03081 101 GRHREALELFEilEAGCPftlPASTYDA----LVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLID 176

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 143 SRKVFNSMKDRNLSSWNSILSsytklGYVDdaiglldemeicglkpdivtwnsllsgyasKGLSKDAIAVLKRMQIAGLK 222
Cdd:PLN03081 177 ARRLFDEMPERNLASWGTIIG-----GLVD------------------------------AGNYREAFALFREMWEDGSD 221

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 223 PSTSSISSLLQAVAEPGHLKLGKAIHGYILRNQLWYDVYVETTLIDMYIKTGYLPYARMVFDMMDAKNIVAWNSLVSGls 302
Cdd:PLN03081 222 AEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAG-- 299

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 303 yacllkdaealmirmekegikpdaitwnslasgYATLGKPEKALDVIGKMKEKGVAPNvvswtaifsgcskngNFrnalk 382
Cdd:PLN03081 300 ---------------------------------YALHGYSEEALCLYYEMRDSGVSID---------------QF----- 326

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 383 vfikmqeegvgpnaaTMSTLLKILGCLSLLHSGKEVHGFCLRKNLICDAYVATALVDMYGKSGDLQSAIEIFWGIKNKSL 462
Cdd:PLN03081 327 ---------------TFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNL 391

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 463 ASWNCMLMGYAMFGRGEEGIAAFSVMLEAGMEPDAITFTSVLSVCKNSGLVQEGWKYFDLMRSRYGIIPTIEHCSCMVDL 542
Cdd:PLN03081 392 ISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIEL 471

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 543 LGRSGYLDEAWDFIQTMSLKPDATIWGAFLSSCKIHRDLELAEIAWKRLQVLEPHNSANYMMMINLYSNLNRWEDVERIR 622
Cdd:PLN03081 472 LGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVV 551

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 623 NLMRNNRVRVQDLWSWIQIDQTVHIFYAEGKTHPDEGDIYFELYKLVSEMKKSGYVPDTSCIHQDISDSEKEKLLMGHTE 702
Cdd:PLN03081 552 ETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSE 631

                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334186267 703 KLAMTYGLIKKKGLAPIRVVKNTNICSDSHTVAKYMSVLRNREIVLQEGARVHHFRDGKCSCNDSW 768
Cdd:PLN03081 632 KLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 676-768 9.94e-36

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 129.85  E-value: 9.94e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  676 GYVPDTSCIHQDISDSEKEKLLMGHTEKLAMTYGLIKKKGLAPIRVVKNTNICSDSHTVAKYMSVLRNREIVLQEGARVH 755
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 334186267  756 HFRDGKCSCNDSW 768
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 4-223 2.20e-25

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 112.27  E-value: 2.20e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267   4 FLGLTIHGGLIKRGLdNSDTRVVSASMGFYGRCVSLGFANKLFDEMPKRDDLAWNEIVMVNLRSGNWEKAVELFREMQFS 83
Cdd:PLN03081 241 RAGQQLHCCVLKTGV-VGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDS 319

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  84 GAKAYDSTMVKLLQVCSNKEGFAEGRQIHGYVLRLGLESNVSMCNSLIVMYSRNGKLELSRKVFNSMKDRNLSSWNSILS 163
Cdd:PLN03081 320 GVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIA 399

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334186267 164 SYTKLGYVDDAIGLLDEMEICGLKPDIVTWNSLLSGYASKGLSKDAIAVLKRM-QIAGLKP 223
Cdd:PLN03081 400 GYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMsENHRIKP 460
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 90-449 1.44e-21

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 100.72  E-value: 1.44e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267   90 STMVKLLQVCSNKEGFAEGRQihgyVLRL----GLESNVSMCNSLIVMYSRNGKLELSRKVFNSMK----DRNLSSWNSI 161
Cdd:PLN03218  438 STFNMLMSVCASSQDIDGALR----VLRLvqeaGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVnagvEANVHTFGAL 513

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  162 LSSYTKLGYVDDAIGLLDEMEICGLKPDIVTWNSLLSGYASKGLSKDAIAVLKRM--QIAGLKPSTSSISSLLQAVAEPG 239
Cdd:PLN03218  514 IDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMkaETHPIDPDHITVGALMKACANAG 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  240 H----LKLGKAIHGYILRNQLwyDVYveTTLIDMYIKTGYLPYARMVFDMMDAKNI----VAWNSLVSGLSYACLLKDAE 311
Cdd:PLN03218  594 QvdraKEVYQMIHEYNIKGTP--EVY--TIAVNSCSQKGDWDFALSIYDDMKKKGVkpdeVFFSALVDVAGHAGDLDKAF 669

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  312 ALMIRMEKEGIKPDAITWNSLASGYATLG-----------------KP------------------EKALDVIGKMKEKG 356
Cdd:PLN03218  670 EILQDARKQGIKLGTVSYSSLMGACSNAKnwkkalelyediksiklRPtvstmnalitalcegnqlPKALEVLSEMKRLG 749

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  357 VAPNVVSWTAIFSGCSKNGNFRNALKVFIKMQEEGVGPNaatmstlLKILGCLSllhsgkevhGFCLRKnliCDAYVATA 436
Cdd:PLN03218  750 LCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPN-------LVMCRCIT---------GLCLRR---FEKACALG 810

                         410
                  ....*....|...
gi 334186267  437 LVDMYGKSGDLQS 449
Cdd:PLN03218  811 EPVVSFDSGRPQI 823
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 137-542 3.18e-20

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 96.10  E-value: 3.18e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  137 NGKLELSRKVFNSMKDRNLSSWNSILSSYTKLGYVDDAIGLLDEMEICGL------------------------------ 186
Cdd:PLN03218  352 EEENSLAAYNGGVSGKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLldmdkiyhakffkackkqravkeafrfakl 431

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  187 --KPDIVTWNSLLSGYASKGLSKDAIAVLKRMQIAGLKPSTSSISSLLQAVAEPGHLKLGKAIHGYILRNQLWYDVYVET 264
Cdd:PLN03218  432 irNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFG 511

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  265 TLIDMYIKTGYLPYARMVFDMMDAKNI----VAWNSLVSGLSYACLLKDAEALMIRMEKEG--IKPDAITWNSLASGYAT 338
Cdd:PLN03218  512 ALIDGCARAGQVAKAFGAYGIMRSKNVkpdrVVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACAN 591

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  339 LGKPEKALDVIGKMKEKGVAPNVVSWTAIFSGCSKNGNFRNALKVFIKMQEEGVGPNAATMSTLLKILGclsllHSGKEV 418
Cdd:PLN03218  592 AGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAG-----HAGDLD 666

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  419 HGFCLRKNLICDAY-----VATALVDMYGKSGDLQSAIEIFWGIK----NKSLASWNCMLMGYAmfgRGEEGIAAFSVML 489
Cdd:PLN03218  667 KAFEILQDARKQGIklgtvSYSSLMGACSNAKNWKKALELYEDIKsiklRPTVSTMNALITALC---EGNQLPKALEVLS 743

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 334186267  490 E---AGMEPDAITFTSVLSVCKNSGLVQEGWKYFDLMRSRyGIIPTIEHCSCMVDL 542
Cdd:PLN03218  744 EmkrLGLCPNTITYSILLVASERKDDADVGLDLLSQAKED-GIKPNLVMCRCITGL 798
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 578-640 1.78e-13

E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466580 [Multi-domain]  Cd Length: 63  Bit Score: 65.64  E-value: 1.78e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334186267  578 HRDLELAEIAWKRLQVLEPHNSANYMMMINLYSNLNRWEDVERIRNLMRNNRVRVQDLWSWIQ 640
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 324-373 2.56e-11

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: 58.91  E-value: 2.56e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 334186267  324 PDAITWNSLASGYATLGKPEKALDVIGKMKEKGVAPNVVSWTAIFSGCSK 373
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 371-507 4.12e-11

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 66.80  E-value: 4.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 371 CSkNGNFRNALKVFIKMQEEGVGPNAATMSTLLKILGCLSLLHSGKEVHGFCLRKNLICDAYVATALVDMYGKSGDLQSA 450
Cdd:PLN03077  62 CS-HGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHA 140

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 334186267 451 IEIFWGIKNKSLASWNCMLMGYAMFGRGEEGIAAFSVMLEAGMEPDAITFTSVLSVC 507
Cdd:PLN03077 141 WYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTC 197
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 317-374 4.70e-10

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 55.83  E-value: 4.70e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334186267  317 MEKEGIKPDAITWNSLASGYATLGKPEKALDVIGKMKEKGVAPNVVSWTAIFSGCSKN 374
Cdd:pfam13812   6 MVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 359-404 5.90e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 55.06  E-value: 5.90e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 334186267  359 PNVVSWTAIFSGCSKNGNFRNALKVFIKMQEEGVGPNAATMSTLLK 404
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 153-201 1.08e-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: 1.08e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186267  153 RNLSSWNSILSSYTKLGYVDDAIGLLDEMEICGLKPDIVTWNSLLSGYA 201
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 328-595 1.11e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 62.20  E-value: 1.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  328 TWNSLASGYATLGKPEKALDVIGKMKEKGVAPNVVSWTAIFSGCSKNGNFRNALKVFIKMQEEGVGPNAATMSTLlkILG 407
Cdd:PLN03218  439 TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGAL--IDG 516

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  408 CLSLLHSGKE--VHGFCLRKNLICDAYVATALVDMYGKSGDLQSAIEIFWGIKNKSL------ASWNCMLMGYAMFGRGE 479
Cdd:PLN03218  517 CARAGQVAKAfgAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHpidpdhITVGALMKACANAGQVD 596

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  480 EGIAAFSVMLEAGMEPDAITFTSVLSVCKNSGLVQEGWKYFDLMRsRYGIIPTIEHCSCMVDLLGRSGYLDEAWDFIQTM 559
Cdd:PLN03218  597 RAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMK-KKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDA 675

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 334186267  560 ---SLKPDATIWGAFLSSCKIHRDLElaeiawKRLQVLE 595
Cdd:PLN03218  676 rkqGIKLGTVSYSSLMGACSNAKNWK------KALELYE 708
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 351-407 2.76e-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: 2.76e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 334186267  351 KMKEKGVAPNVVSWTAIFSGCSKNGNFRNALKVFIKMQEEGVGPNAATMSTLLKILG 407
Cdd:pfam13812   5 EMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 177-234 5.53e-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: 50.05  E-value: 5.53e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334186267  177 LLDEMEICGLKPDIVTWNSLLSGYASKGLSKDAIAVLKRMQIAGLKPSTSSISSLLQA 234
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 289-337 6.17e-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: 6.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186267  289 KNIVAWNSLVSGLSYACLLKDAEALMIRMEKEGIKPDAITWNSLASGYA 337
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 188-236 4.09e-07

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: 46.97  E-value: 4.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186267  188 PDIVTWNSLLSGYASKGLSKDAIAVLKRMQIAGLKPSTSSISSLLQAVA 236
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 185-216 3.27e-06

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: 44.26  E-value: 3.27e-06
                          10        20        30
                  ....*....|....*....|....*....|..
gi 334186267  185 GLKPDIVTWNSLLSGYASKGLSKDAIAVLKRM 216
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 464-507 2.76e-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: 41.97  E-value: 2.76e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 334186267  464 SWNCMLMGYAMFGRGEEGIAAFSVMLEAGMEPDAITFTSVLSVC 507
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 327-357 4.28e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 40.91  E-value: 4.28e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334186267  327 ITWNSLASGYATLGKPEKALDVIGKMKEKGV 357
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 362-392 5.47e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 40.53  E-value: 5.47e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334186267  362 VSWTAIFSGCSKNGNFRNALKVFIKMQEEGV 392
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 327-361 5.70e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.52  E-value: 5.70e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334186267  327 ITWNSLASGYATLGKPEKALDVIGKMKEKGVAPNV 361
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 307-405 9.00e-05

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 44.31  E-value: 9.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  307 LKDAEALMIRMEKEGIKPDAITWNSLASGYATLGKPEKALDVIGKMKEKGVAPNVVSWTAIFSGCSKNGNFRNALKVFIK 386
Cdd:pfam17177  71 ADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEH 150

                          90
                  ....*....|....*....
gi 334186267  387 MQEEGVGPNAATMSTLLKI 405
Cdd:pfam17177 151 MLAHGVELEEPELAALLKV 169
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 157-190 1.35e-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: 39.75  E-value: 1.35e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334186267  157 SWNSILSSYTKLGYVDDAIGLLDEMEICGLKPDI 190
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 117-167 1.43e-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: 40.42  E-value: 1.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 334186267  117 RLGLESNVSMCNSLIVMYSRNGKLELSRKVFNSMKDR----NLSSWNSILSSYTK 167
Cdd:pfam13812   8 RDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKgikpTLDTYNAILGVIGG 62
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 191-225 2.56e-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: 2.56e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334186267  191 VTWNSLLSGYASKGLSKDAIAVLKRMQIAGLKPST 225
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 362-396 2.88e-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: 2.88e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334186267  362 VSWTAIFSGCSKNGNFRNALKVFIKMQEEGVGPNA 396
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 191-221 5.08e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.83  E-value: 5.08e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334186267  191 VTWNSLLSGYASKGLSKDAIAVLKRMQIAGL 221
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 156-186 8.47e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.44  E-value: 8.47e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334186267  156 SSWNSILSSYTKLGYVDDAIGLLDEMEICGL 186
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 282-336 1.04e-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: 1.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 334186267  282 VFDMMDAK----NIVAWNSLVSGLSYACLLKDAEALMIRMEKEGIKPDAITWNSLASGY 336
Cdd:pfam13812   2 ILREMVRDgiqlNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 355-387 2.48e-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: 36.17  E-value: 2.48e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 334186267  355 KGVAPNVVSWTAIFSGCSKNGNFRNALKVFIKM 387
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 154-182 2.84e-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: 35.78  E-value: 2.84e-03
                          10        20
                  ....*....|....*....|....*....
gi 334186267  154 NLSSWNSILSSYTKLGYVDDAIGLLDEME 182
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 320-353 3.23e-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: 35.78  E-value: 3.23e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334186267  320 EGIKPDAITWNSLASGYATLGKPEKALDVIGKMK 353
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 68-232 3.88e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 40.63  E-value: 3.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267   68 GNWEKAVELFREMQFSGAKAYDSTMVKLLQVCSNKEGFAEGRQIHGYVLRLGLESNVSMCNSLIVMYSRNGKLELSRKVF 147
Cdd:PLN03218  698 KNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLL 777

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  148 NSMKDRNLSSwnsilssytKLGYVDDAIGLLDEM--EICGLKPDIVTWNSLLSGYASKGLSKdAIAVLKRMQIAGLKPST 225
Cdd:PLN03218  778 SQAKEDGIKP---------NLVMCRCITGLCLRRfeKACALGEPVVSFDSGRPQIENKWTSW-ALMVYRETISAGTLPTM 847


                  ....*..
gi 334186267  226 SSISSLL 232
Cdd:PLN03218  848 EVLSQVL 854
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 292-326 6.59e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 34.74  E-value: 6.59e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334186267  292 VAWNSLVSGLSYACLLKDAEALMIRMEKEGIKPDA 326
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 464-497 8.51e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 34.74  E-value: 8.51e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334186267  464 SWNCMLMGYAMFGRGEEGIAAFSVMLEAGMEPDA 497
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
56-215 8.56e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 38.83  E-value: 8.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267  56 AWNEIVMVNLRSGNWEKAVELFR---EMQFSGAKAYdstmVKLLQVCSNKEGFAEGRQIHGYVLRLGLESNVSMCNsLIV 132
Cdd:COG0457   10 AYNNLGLAYRRLGRYEEAIEDYEkalELDPDDAEAL----YNLGLAYLRLGRYEEALADYEQALELDPDDAEALNN-LGL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186267 133 MYSRNGKLELSRKVFN---SMKDRNLSSWNSILSSYTKLGYVDDAIGLLDemEICGLKPDIV-TWNSLLSGYASKGLSKD 208
Cdd:COG0457   85 ALQALGRYEEALEDYDkalELDPDDAEALYNLGLALLELGRYDEAIEAYE--RALELDPDDAdALYNLGIALEKLGRYEE 162


                 ....*..
gi 334186267 209 AIAVLKR 215
Cdd:COG0457  163 ALELLEK 169
 
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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