NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1039016141|gb|AEE80472|]
View 

Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1004806)

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
SCOP:  4001344

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
59-958 0e+00

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 572.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  59 CFDGVLTEAFQRLDVS-ENNSPVEAFAYV--LELCGKRRAVSQGRQLHSRIFKTFPSFELDfLAGKLVFMYGKCGSLDDA 135
Cdd:PLN03077   62 CSHGQLEQALKLLESMqELRVPVDEDAYValFRLCEWKRAVEEGSRVCSRALSSHPSLGVR-LGNAMLSMFVRFGELVHA 140
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 136 EKVFDEMPDRTAFAWNTMIGAYVSNGEPASALALYWNMRVEGVPLGLSSFPALLKACAKLRDIRSGSELHSLLVKLGYHS 215
Cdd:PLN03077  141 WYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFEL 220
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 216 TGFIVNALVSMYAKNDDLSAARRLFDGFQEKgDAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYTIVSALTACD 295
Cdd:PLN03077  221 DVDVVNALITMYVKCGDVVSARLVFDRMPRR-DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACE 299
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 296 GFSYAKLGKEIHASVLKSStHSSELYVCNALIAMYTRCGKMPQAERILRQMNNADVVTWNSLIKGYVQNLMYKEALEFFS 375
Cdd:PLN03077  300 LLGDERLGREMHGYVVKTG-FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYA 378
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 376 DMIAAGHKSDEVSMTSIIAASGRLSNLLAGMELHAYVIKHGWDSNLQVGNTLIDMYSKCNLTCYMGRAFLRMHDKDLISW 455
Cdd:PLN03077  379 LMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISW 458
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 456 TTVIAGYAQNDCHVEALELFRDVaKKRMEIDEMILGSILRASSVLKSMLIVKEIHCHILRKGL-LDTVIQNELVDVYGKC 534
Cdd:PLN03077  459 TSIIAGLRLNNRCFEALIFFRQM-LLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIgFDGFLPNALLDLYVRC 537
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 535 RNMGYATRVFESIKgKDVVSWTSMISSSALNGNESEAVELFRRMVETGlsadsvallcilsaaaslsalnkgreihcyll 614
Cdd:PLN03077  538 GRMNYAWNQFNSHE-KDVVSWNILLTGYVAHGKGSMAVELFNRMVESG-------------------------------- 584
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 615 rkgfclegsiavavvdmyaccgdlqsakavfdrierkgllqytsminaygmhgcgkaavelfdkmrhenVSPDHISFLAL 694
Cdd:PLN03077  585 ---------------------------------------------------------------------VNPDEVTFISL 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 695 LYACSHAGLLDEGRGFLKIMEHEYELEPWPEHYVCLVDMLGRANCVVEAFEFVKMMKTEPTAEVWCALLAACRSHSEKEI 774
Cdd:PLN03077  596 LCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVEL 675
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 775 GEIAAQRLLELEPKNPGNLVLVSNVFAEQGRWNDVEKVRAKMKASGMEKHPGCSWIEMDGKVHKFTARDKSHPESKEIYE 854
Cdd:PLN03077  676 GELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINT 755
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 855 KLSEVTRKLErEVGYvadTKFVLHNVDEGE--KVQMLHGHSERIAIAYGLLRTPDRACLRITKNLRVCRDCHTFCKLVSK 932
Cdd:PLN03077  756 VLEGFYEKMK-ASGL---AGSESSSMDEIEvsKDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISK 831
                         890       900
                  ....*....|....*....|....*.
gi 1039016141 933 LFRRDIVMRDANRFHHFESGLCSCGD 958
Cdd:PLN03077  832 IVRREISVRDTEQFHHFKDGECSCGD 857
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
656-700 7.36e-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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 46.59  E-value: 7.36e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1039016141 656 YTSMINAYGMHGCGKAAVELFDKMRHENVSPDHISFLALLYACSH 700
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
59-958 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 572.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  59 CFDGVLTEAFQRLDVS-ENNSPVEAFAYV--LELCGKRRAVSQGRQLHSRIFKTFPSFELDfLAGKLVFMYGKCGSLDDA 135
Cdd:PLN03077   62 CSHGQLEQALKLLESMqELRVPVDEDAYValFRLCEWKRAVEEGSRVCSRALSSHPSLGVR-LGNAMLSMFVRFGELVHA 140
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 136 EKVFDEMPDRTAFAWNTMIGAYVSNGEPASALALYWNMRVEGVPLGLSSFPALLKACAKLRDIRSGSELHSLLVKLGYHS 215
Cdd:PLN03077  141 WYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFEL 220
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 216 TGFIVNALVSMYAKNDDLSAARRLFDGFQEKgDAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYTIVSALTACD 295
Cdd:PLN03077  221 DVDVVNALITMYVKCGDVVSARLVFDRMPRR-DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACE 299
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 296 GFSYAKLGKEIHASVLKSStHSSELYVCNALIAMYTRCGKMPQAERILRQMNNADVVTWNSLIKGYVQNLMYKEALEFFS 375
Cdd:PLN03077  300 LLGDERLGREMHGYVVKTG-FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYA 378
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 376 DMIAAGHKSDEVSMTSIIAASGRLSNLLAGMELHAYVIKHGWDSNLQVGNTLIDMYSKCNLTCYMGRAFLRMHDKDLISW 455
Cdd:PLN03077  379 LMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISW 458
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 456 TTVIAGYAQNDCHVEALELFRDVaKKRMEIDEMILGSILRASSVLKSMLIVKEIHCHILRKGL-LDTVIQNELVDVYGKC 534
Cdd:PLN03077  459 TSIIAGLRLNNRCFEALIFFRQM-LLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIgFDGFLPNALLDLYVRC 537
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 535 RNMGYATRVFESIKgKDVVSWTSMISSSALNGNESEAVELFRRMVETGlsadsvallcilsaaaslsalnkgreihcyll 614
Cdd:PLN03077  538 GRMNYAWNQFNSHE-KDVVSWNILLTGYVAHGKGSMAVELFNRMVESG-------------------------------- 584
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 615 rkgfclegsiavavvdmyaccgdlqsakavfdrierkgllqytsminaygmhgcgkaavelfdkmrhenVSPDHISFLAL 694
Cdd:PLN03077  585 ---------------------------------------------------------------------VNPDEVTFISL 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 695 LYACSHAGLLDEGRGFLKIMEHEYELEPWPEHYVCLVDMLGRANCVVEAFEFVKMMKTEPTAEVWCALLAACRSHSEKEI 774
Cdd:PLN03077  596 LCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVEL 675
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 775 GEIAAQRLLELEPKNPGNLVLVSNVFAEQGRWNDVEKVRAKMKASGMEKHPGCSWIEMDGKVHKFTARDKSHPESKEIYE 854
Cdd:PLN03077  676 GELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINT 755
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 855 KLSEVTRKLErEVGYvadTKFVLHNVDEGE--KVQMLHGHSERIAIAYGLLRTPDRACLRITKNLRVCRDCHTFCKLVSK 932
Cdd:PLN03077  756 VLEGFYEKMK-ASGL---AGSESSSMDEIEvsKDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISK 831
                         890       900
                  ....*....|....*....|....*.
gi 1039016141 933 LFRRDIVMRDANRFHHFESGLCSCGD 958
Cdd:PLN03077  832 IVRREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
868-960 7.71e-55

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: 184.55  E-value: 7.71e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 868 GYVADTKFVLHNVDEGEKVQMLHGHSERIAIAYGLLRTPDRACLRITKNLRVCRDCHTFCKLVSKLFRRDIVMRDANRFH 947
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80
                          90
                  ....*....|...
gi 1039016141 948 HFESGLCSCGDSW 960
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 ...
656-700 7.36e-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: 46.59  E-value: 7.36e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1039016141 656 YTSMINAYGMHGCGKAAVELFDKMRHENVSPDHISFLALLYACSH 700
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
352-386 5.00e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 41.29  E-value: 5.00e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1039016141 352 VTWNSLIKGYVQNLMYKEALEFFSDMIAAGHKSDE 386
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
656-687 1.11e-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: 40.13  E-value: 1.11e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1039016141 656 YTSMINAYGMHGCGKAAVELFDKMRHENVSPD 687
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
59-958 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 572.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  59 CFDGVLTEAFQRLDVS-ENNSPVEAFAYV--LELCGKRRAVSQGRQLHSRIFKTFPSFELDfLAGKLVFMYGKCGSLDDA 135
Cdd:PLN03077   62 CSHGQLEQALKLLESMqELRVPVDEDAYValFRLCEWKRAVEEGSRVCSRALSSHPSLGVR-LGNAMLSMFVRFGELVHA 140
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 136 EKVFDEMPDRTAFAWNTMIGAYVSNGEPASALALYWNMRVEGVPLGLSSFPALLKACAKLRDIRSGSELHSLLVKLGYHS 215
Cdd:PLN03077  141 WYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFEL 220
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 216 TGFIVNALVSMYAKNDDLSAARRLFDGFQEKgDAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYTIVSALTACD 295
Cdd:PLN03077  221 DVDVVNALITMYVKCGDVVSARLVFDRMPRR-DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACE 299
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 296 GFSYAKLGKEIHASVLKSStHSSELYVCNALIAMYTRCGKMPQAERILRQMNNADVVTWNSLIKGYVQNLMYKEALEFFS 375
Cdd:PLN03077  300 LLGDERLGREMHGYVVKTG-FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYA 378
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 376 DMIAAGHKSDEVSMTSIIAASGRLSNLLAGMELHAYVIKHGWDSNLQVGNTLIDMYSKCNLTCYMGRAFLRMHDKDLISW 455
Cdd:PLN03077  379 LMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISW 458
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 456 TTVIAGYAQNDCHVEALELFRDVaKKRMEIDEMILGSILRASSVLKSMLIVKEIHCHILRKGL-LDTVIQNELVDVYGKC 534
Cdd:PLN03077  459 TSIIAGLRLNNRCFEALIFFRQM-LLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIgFDGFLPNALLDLYVRC 537
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 535 RNMGYATRVFESIKgKDVVSWTSMISSSALNGNESEAVELFRRMVETGlsadsvallcilsaaaslsalnkgreihcyll 614
Cdd:PLN03077  538 GRMNYAWNQFNSHE-KDVVSWNILLTGYVAHGKGSMAVELFNRMVESG-------------------------------- 584
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 615 rkgfclegsiavavvdmyaccgdlqsakavfdrierkgllqytsminaygmhgcgkaavelfdkmrhenVSPDHISFLAL 694
Cdd:PLN03077  585 ---------------------------------------------------------------------VNPDEVTFISL 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 695 LYACSHAGLLDEGRGFLKIMEHEYELEPWPEHYVCLVDMLGRANCVVEAFEFVKMMKTEPTAEVWCALLAACRSHSEKEI 774
Cdd:PLN03077  596 LCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVEL 675
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 775 GEIAAQRLLELEPKNPGNLVLVSNVFAEQGRWNDVEKVRAKMKASGMEKHPGCSWIEMDGKVHKFTARDKSHPESKEIYE 854
Cdd:PLN03077  676 GELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINT 755
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 855 KLSEVTRKLErEVGYvadTKFVLHNVDEGE--KVQMLHGHSERIAIAYGLLRTPDRACLRITKNLRVCRDCHTFCKLVSK 932
Cdd:PLN03077  756 VLEGFYEKMK-ASGL---AGSESSSMDEIEvsKDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISK 831
                         890       900
                  ....*....|....*....|....*.
gi 1039016141 933 LFRRDIVMRDANRFHHFESGLCSCGD 958
Cdd:PLN03077  832 IVRREISVRDTEQFHHFKDGECSCGD 857
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
367-960 1.42e-143

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 443.93  E-value: 1.42e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 367 YKEALEFFSDM-IAAGHKSDEVSMTSIIAASGRLSNLLAGMELHAYVIKHGWDSNLQVGNTLIDMYSKCNLTCYMGRAFL 445
Cdd:PLN03081  103 HREALELFEILeAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFD 182
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 446 RMHDKDLISWTTVIAGYAQNDCHVEALELFRDVAKKRMEIDEMILGSILRASSVLKSMLIVKEIHCHILRKGLL-DTVIQ 524
Cdd:PLN03081  183 EMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVgDTFVS 262
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 525 NELVDVYGKCRNMGYATRVFESIKGKDVVSWTSMISSSALNGNESEAVELFRRMVETGLSADSVALLCILSAAASLSALN 604
Cdd:PLN03081  263 CALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLE 342
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 605 KGREIHCYLLRKGFCLEGSIAVAVVDMYACCGDLQSAKAVFDRIERKGLLQYTSMINAYGMHGCGKAAVELFDKMRHENV 684
Cdd:PLN03081  343 HAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGV 422
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 685 SPDHISFLALLYACSHAGLLDEGRGFLKIMEHEYELEPWPEHYVCLVDMLGRANCVVEAFEFVKMMKTEPTAEVWCALLA 764
Cdd:PLN03081  423 APNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLT 502
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 765 ACRSHSEKEIGEIAAQRLLELEPKNPGNLVLVSNVFAEQGRWNDVEKVRAKMKASGMEKHPGCSWIEMDGKVHKFTARDK 844
Cdd:PLN03081  503 ACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDR 582
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 845 SHPESKEIYEKLSEVTRKLeREVGYVADTKFVLHNVDEGEKVQMLHGHSERIAIAYGLLRTPDRACLRITKNLRVCRDCH 924
Cdd:PLN03081  583 LHPQSREIYQKLDELMKEI-SEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCH 661
                         570       580       590
                  ....*....|....*....|....*....|....*.
gi 1039016141 925 TFCKLVSKLFRRDIVMRDANRFHHFESGLCSCGDSW 960
Cdd:PLN03081  662 KVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
868-960 7.71e-55

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: 184.55  E-value: 7.71e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 868 GYVADTKFVLHNVDEGEKVQMLHGHSERIAIAYGLLRTPDRACLRITKNLRVCRDCHTFCKLVSKLFRRDIVMRDANRFH 947
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80
                          90
                  ....*....|...
gi 1039016141 948 HFESGLCSCGDSW 960
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
4-395 4.68e-51

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 192.01  E-value: 4.68e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141   4 AVTNMRLLSN---MMYSASAISFPRVRLHCSiPTEPSCRRNP-FRQSNQPVQVPSPKLACFD------------------ 61
Cdd:PLN03081   19 SLSNPRLLHSprkFSLRGRRTKTPFSSISCS-SVEQGLKPRPrLKPEPIRIEVSESKDARLDdtqirksgvslcsqiekl 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  62 ---GVLTEAFQRLDVSENNSP----VEAFAYVLELCGKRRAVSQGRQLHSRIFKTfpSFELD-FLAGKLVFMYGKCGSLD 133
Cdd:PLN03081   98 vacGRHREALELFEILEAGCPftlpASTYDALVEACIALKSIRCVKAVYWHVESS--GFEPDqYMMNRVLLMHVKCGMLI 175
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 134 DAEKVFDEMPDRTAFAWNTMIGAYVSNGEPASALALYWNMRVEGVPLGLSSFPALLKACAKLRDIRSGSELHSLLVKLGY 213
Cdd:PLN03081  176 DARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGV 255
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 214 HSTGFIVNALVSMYAKNDDLSAARRLFDGFQEKgDAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYTIVSALTA 293
Cdd:PLN03081  256 VGDTFVSCALIDMYSKCGDIEDARCVFDGMPEK-TTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRI 334
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 294 CDGFSYAKLGKEIHASVLKSSThSSELYVCNALIAMYTRCGKMPQAERILRQMNNADVVTWNSLIKGYVQNLMYKEALEF 373
Cdd:PLN03081  335 FSRLALLEHAKQAHAGLIRTGF-PLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEM 413
                         410       420
                  ....*....|....*....|..
gi 1039016141 374 FSDMIAAGHKSDEVSMTSIIAA 395
Cdd:PLN03081  414 FERMIAEGVAPNHVTFLAVLSA 435
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
79-345 1.99e-33

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 138.08  E-value: 1.99e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  79 PVEAFAYVLEL------CGKR------RAVS------QGRQLHSRIFKTfPSFELDFLAGKLVFMYGKCGSLDDAEKVFD 140
Cdd:PLN03081  205 YREAFALFREMwedgsdAEPRtfvvmlRASAglgsarAGQQLHCCVLKT-GVVGDTFVSCALIDMYSKCGDIEDARCVFD 283
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 141 EMPDRTAFAWNTMIGAYVSNGEPASALALYWNMRVEGVPLGLSSFPALLKACAKLRDIRSGSELHSLLVKLGYHSTGFIV 220
Cdd:PLN03081  284 GMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVAN 363
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141 221 NALVSMYAKNDDLSAARRLFDGFQEKgDAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYTIVSALTACDGFSYA 300
Cdd:PLN03081  364 TALVDLYSKWGRMEDARNVFDRMPRK-NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLS 442
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1039016141 301 KLGKEIHASVlkSSTHSSE----LYVCnaLIAMYTRCGKMPQAERILRQ 345
Cdd:PLN03081  443 EQGWEIFQSM--SENHRIKpramHYAC--MIELLGREGLLDEAYAMIRR 487
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
769-831 1.80e-32

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: 119.96  E-value: 1.80e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039016141 769 HSEKEIGEIAAQRLLELEPKNPGNLVLVSNVFAEQGRWNDVEKVRAKMKASGMEKHPGCSWIE 831
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
Eplus_motif pfam20430
E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins ...
836-863 3.30e-10

E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins which contain a C-terminal 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 th RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466579 [Multi-domain]  Cd Length: 28  Bit Score: 55.74  E-value: 3.30e-10
                          10        20
                  ....*....|....*....|....*...
gi 1039016141 836 VHKFTARDKSHPESKEIYEKLSEVTRKL 863
Cdd:pfam20430   1 TYTFFAGDKSHPESKQIYEKLSDLTQRI 28
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
350-393 9.87e-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: 51.98  E-value: 9.87e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1039016141 350 DVVTWNSLIKGYVQNLMYKEALEFFSDMIAAGHKSDEVSMTSII 393
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILI 45
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
656-700 7.36e-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: 46.59  E-value: 7.36e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1039016141 656 YTSMINAYGMHGCGKAAVELFDKMRHENVSPDHISFLALLYACSH 700
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
631-765 2.63e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 51.42  E-value: 2.63e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  631 MYACC--GDLQSAKAVFDRIER---KGLLQ-YTSMINAYGMHGCGKAAVELFDKMRHENVSPDHISFLALLYACSHAGLL 704
Cdd:PLN03218   586 MKACAnaGQVDRAKEVYQMIHEyniKGTPEvYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDL 665
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039016141  705 DEGRGFLKIMEHEyELEPWPEHYVCLVDM---LGRANCVVEAFEFVKMMKTEPTAEVWCALLAA 765
Cdd:PLN03218   666 DKAFEILQDARKQ-GIKLGTVSYSSLMGAcsnAKNWKKALELYEDIKSIKLRPTVSTMNALITA 728
PLN03218 PLN03218
maturation of RBCL 1; Provisional
143-430 4.38e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 50.65  E-value: 4.38e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  143 PDRTAFawNTMIGAYVSNGEPASALALYWNMRVEGVPLGLS--SFPALLKACAKLRDIRSGSELHSLLVKLGYHSTGFIV 220
Cdd:PLN03218   540 PDRVVF--NALISACGQSGAVDRAFDVLAEMKAETHPIDPDhiTVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVY 617
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  221 NALVSMYAKNDDLSAARRLFDGFQEKG---DAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYTIVSALTACdgf 297
Cdd:PLN03218   618 TIAVNSCSQKGDWDFALSIYDDMKKKGvkpDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGAC--- 694
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  298 syaklgkeihaSVLKSSTHSSELYvcnaliamytrcgkmpqaERILRQMNNADVVTWNSLIKGYVQNLMYKEALEFFSDM 377
Cdd:PLN03218   695 -----------SNAKNWKKALELY------------------EDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEM 745
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039016141  378 IAAGHKSDEVSMTSIIAASGRLSNLLAGMELHAYVIKHGWDSNLQVGNTLIDM 430
Cdd:PLN03218   746 KRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGL 798
PLN03218 PLN03218
maturation of RBCL 1; Provisional
221-377 9.24e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 49.88  E-value: 9.24e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  221 NALVSMYAKNDDLSAARRLFDGFQEKG---DAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYTIVSALTACdgf 297
Cdd:PLN03218   441 NMLMSVCASSQDIDGALRVLRLVQEAGlkaDCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGC--- 517
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  298 syAKLGKEIHA----SVLKSSTHSSELYVCNALIAMYTRCGKMPQAERILRQMN------NADVVTWNSLIKGYVQNLMY 367
Cdd:PLN03218   518 --ARAGQVAKAfgayGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKaethpiDPDHITVGALMKACANAGQV 595
                          170
                   ....*....|
gi 1039016141  368 KEALEFFSDM 377
Cdd:PLN03218   596 DRAKEVYQMI 605
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
352-382 1.42e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 42.45  E-value: 1.42e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1039016141 352 VTWNSLIKGYVQNLMYKEALEFFSDMIAAGH 382
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
352-386 5.00e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 41.29  E-value: 5.00e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1039016141 352 VTWNSLIKGYVQNLMYKEALEFFSDMIAAGHKSDE 386
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03218 PLN03218
maturation of RBCL 1; Provisional
656-766 5.13e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 47.18  E-value: 5.13e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039016141  656 YTSMINaygmhGCGKA-----AVELFDKMRHENVSPDHISFLALLYACSHAGLLDegRGFLKIMEHEYELEPW-PEH--Y 727
Cdd:PLN03218   510 FGALID-----GCARAgqvakAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVD--RAFDVLAEMKAETHPIdPDHitV 582
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1039016141  728 VCLVDMLGRANCVVEAFEFVKMMK---TEPTAEVWCALLAAC 766
Cdd:PLN03218   583 GALMKACANAGQVDRAKEVYQMIHeynIKGTPEVYTIAVNSC 624
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
656-687 1.11e-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: 40.13  E-value: 1.11e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1039016141 656 YTSMINAYGMHGCGKAAVELFDKMRHENVSPD 687
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
145-194 2.01e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.65  E-value: 2.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1039016141 145 RTAFAWNTMIGAYVSNGEPASALALYWNMRVEGVPLGLSSFPALLKACAK 194
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
248-286 2.75e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.27  E-value: 2.75e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1039016141 248 DAVLWNSILSSYSTSGKSLETLELFREMHMTGPAPNSYT 286
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
656-684 3.45e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 38.60  E-value: 3.45e-04
                          10        20
                  ....*....|....*....|....*....
gi 1039016141 656 YTSMINAYGMHGCGKAAVELFDKMRHENV 684
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
323-361 5.06e-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: 38.50  E-value: 5.06e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1039016141 323 CNALIAMYTRCGKMPQAERILRQMNNA----DVVTWNSLIKGY 361
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGL 48
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
553-583 1.17e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.06  E-value: 1.17e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1039016141 553 VSWTSMISSSALNGNESEAVELFRRMVETGL 583
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
350-377 1.52e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 36.94  E-value: 1.52e-03
                          10        20
                  ....*....|....*....|....*...
gi 1039016141 350 DVVTWNSLIKGYVQNLMYKEALEFFSDM 377
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
644-698 3.02e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 36.95  E-value: 3.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039016141 644 VFDRIERKGL----LQYTSMINAYGMHGCGKAAVELFDKMRHENVSPDHISFLALLYAC 698
Cdd:pfam13812   2 ILREMVRDGIqlnvNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
553-587 8.90e-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: 8.90e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1039016141 553 VSWTSMISSSALNGNESEAVELFRRMVETGLSADS 587
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH