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Conserved domains on  [gi|30684737|ref|NP_196912|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000585)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 383-515 2.24e-13

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 73.76  E-value: 2.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   383 KAYELLS---SKGYFSELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMF 459
Cdd:PLN03218  667 KAFEILQdarKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMK 746

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30684737   460 VEGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIeGLCKE 515
Cdd:PLN03218  747 RLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLCLR 801
PLN03077 super family cl33629
Protein ECB2; Provisional
 143-536 6.18e-07

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 52.54  E-value: 6.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  143 AFSTGQEIHPDVCNRLLAGLTSDGCYDYAQKLFVKMRHKG-VSLNTLGFG-VYIGWFCRSSETNQLLRlVDEVKKANLNI 220
Cdd:PLN03077 314 VVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDaVSWTAMISGyEKNGLPDKALETYALME-QDNVSPDEITI 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  221 NGSIIAllilhslCKCSREMDAFYILEELRNidcKPDFMAYRVIAEAFVvtgNLYERQVVLKKKrklgvaprssdyrafi 300
Cdd:PLN03077 393 ASVLSA-------CACLGDLDVGVKLHELAE---RKGLISYVVVANALI---EMYSKCKCIDKA---------------- 443

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  301 LDLIsaKRLTEAKEVAEVIVSGKFPMDNDILDALIgsvsavdpdsaveFLVYMVSTGKLPAIRTLSKLSKnlCRHdksdh 380
Cdd:PLN03077 444 LEVF--HNIPEKDVISWTSIIAGLRLNNRCFEALI-------------FFRQMLLTLKPNSVTLIAALSA--CAR----- 501

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  381 lIKAyeLLSSKgyfsELQSYSLmisflckagrvresytalqemkKEGLAPDVSLYNALIEACCKAEMIRPAkklWDEMFV 460
Cdd:PLN03077 502 -IGA--LMCGK----EIHAHVL----------------------RTGIGFDGFLPNALLDLYVRCGRMNYA---WNQFNS 549

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30684737  461 egCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIEGLCKETKIEAAMEVFRKcMERDHKTV 536
Cdd:PLN03077 550 --HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHS-MEEKYSIT 622
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 383-515 2.24e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 73.76  E-value: 2.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   383 KAYELLS---SKGYFSELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMF 459
Cdd:PLN03218  667 KAFEILQdarKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMK 746

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30684737   460 VEGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIeGLCKE 515
Cdd:PLN03218  747 RLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLCLR 801
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 430-475 1.51e-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: 59.30  E-value: 1.51e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30684737   430 PDVSLYNALIEACCKAEMIRPAKKLWDEMFVEGCKMNLTTYNVLIR 475
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PLN03077 PLN03077
Protein ECB2; Provisional
 143-536 6.18e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 52.54  E-value: 6.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  143 AFSTGQEIHPDVCNRLLAGLTSDGCYDYAQKLFVKMRHKG-VSLNTLGFG-VYIGWFCRSSETNQLLRlVDEVKKANLNI 220
Cdd:PLN03077 314 VVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDaVSWTAMISGyEKNGLPDKALETYALME-QDNVSPDEITI 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  221 NGSIIAllilhslCKCSREMDAFYILEELRNidcKPDFMAYRVIAEAFVvtgNLYERQVVLKKKrklgvaprssdyrafi 300
Cdd:PLN03077 393 ASVLSA-------CACLGDLDVGVKLHELAE---RKGLISYVVVANALI---EMYSKCKCIDKA---------------- 443

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  301 LDLIsaKRLTEAKEVAEVIVSGKFPMDNDILDALIgsvsavdpdsaveFLVYMVSTGKLPAIRTLSKLSKnlCRHdksdh 380
Cdd:PLN03077 444 LEVF--HNIPEKDVISWTSIIAGLRLNNRCFEALI-------------FFRQMLLTLKPNSVTLIAALSA--CAR----- 501

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  381 lIKAyeLLSSKgyfsELQSYSLmisflckagrvresytalqemkKEGLAPDVSLYNALIEACCKAEMIRPAkklWDEMFV 460
Cdd:PLN03077 502 -IGA--LMCGK----EIHAHVL----------------------RTGIGFDGFLPNALLDLYVRCGRMNYA---WNQFNS 549

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30684737  461 egCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIEGLCKETKIEAAMEVFRKcMERDHKTV 536
Cdd:PLN03077 550 --HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHS-MEEKYSIT 622
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 469-502 1.57e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.75  E-value: 1.57e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30684737   469 TYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDE 502
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 500-531 7.34e-03

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 35.03  E-value: 7.34e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 30684737   500 PDETIYMSLIEGLCKETKIEAAMEVFRKcMER 531
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNE-MKK 31
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 383-515 2.24e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 73.76  E-value: 2.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   383 KAYELLS---SKGYFSELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMF 459
Cdd:PLN03218  667 KAFEILQdarKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMK 746

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30684737   460 VEGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIeGLCKE 515
Cdd:PLN03218  747 RLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLCLR 801
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 229-524 1.61e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 70.68  E-value: 1.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   229 ILHSLCKCSREMD-AFYILEELRNIDCKPDFMAYRVIAEAFVVTGN---LYErqvVLKKKRKLGVAPRSSDYRAFILDLI 304
Cdd:PLN03218  442 MLMSVCASSQDIDgALRVLRLVQEAGLKADCKLYTTLISTCAKSGKvdaMFE---VFHEMVNAGVEANVHTFGALIDGCA 518

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   305 SAKRLTEAKEVAEVIVSGKFPMDNDILDALI---GSVSAVDpdSAVEFLVYMVSTGK--LPAIRTLSKLSKNLCRHDKSD 379
Cdd:PLN03218  519 RAGQVAKAFGAYGIMRSKNVKPDRVVFNALIsacGQSGAVD--RAFDVLAEMKAETHpiDPDHITVGALMKACANAGQVD 596

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   380 HLIKAYELLSSKGYFSELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMF 459
Cdd:PLN03218  597 RAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDAR 676

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30684737   460 VEGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIEGLCKETKIEAAMEV 524
Cdd:PLN03218  677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEV 741
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 430-475 1.51e-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: 59.30  E-value: 1.51e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30684737   430 PDVSLYNALIEACCKAEMIRPAKKLWDEMFVEGCKMNLTTYNVLIR 475
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 ...
 466-514 2.10e-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: 56.22  E-value: 2.10e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30684737   466 NLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIEGLCK 514
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 373-526 4.20e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.89  E-value: 4.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   373 CRHDK-SDHLIKAYELLSSKGYFSELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPA 451
Cdd:PLN03218  447 CASSQdIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKA 526

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   452 KKLWDEMFVEGCKMNLTTYNVLIRKLSEEGEAEeslRLFDKMLERG-----IEPDETIYMSLIEGLCKETKIEAAMEVFR 526
Cdd:PLN03218  527 FGAYGIMRSKNVKPDRVVFNALISACGQSGAVD---RAFDVLAEMKaethpIDPDHITVGALMKACANAGQVDRAKEVYQ 603
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 399-444 2.03e-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: 50.44  E-value: 2.03e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30684737   399 SYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCK 444
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 395-509 2.90e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 53.73  E-value: 2.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   395 SELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMFVEGCKMNLTTYNVLI 474
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 30684737   475 RKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLI 509
Cdd:PLN03218  515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALI 549
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 420-474 3.35e-07

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 47.74  E-value: 3.35e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 30684737   420 LQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMFVEGCKMNLTTYNVLI 474
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PLN03077 PLN03077
Protein ECB2; Provisional
 143-536 6.18e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 52.54  E-value: 6.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  143 AFSTGQEIHPDVCNRLLAGLTSDGCYDYAQKLFVKMRHKG-VSLNTLGFG-VYIGWFCRSSETNQLLRlVDEVKKANLNI 220
Cdd:PLN03077 314 VVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDaVSWTAMISGyEKNGLPDKALETYALME-QDNVSPDEITI 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  221 NGSIIAllilhslCKCSREMDAFYILEELRNidcKPDFMAYRVIAEAFVvtgNLYERQVVLKKKrklgvaprssdyrafi 300
Cdd:PLN03077 393 ASVLSA-------CACLGDLDVGVKLHELAE---RKGLISYVVVANALI---EMYSKCKCIDKA---------------- 443

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  301 LDLIsaKRLTEAKEVAEVIVSGKFPMDNDILDALIgsvsavdpdsaveFLVYMVSTGKLPAIRTLSKLSKnlCRHdksdh 380
Cdd:PLN03077 444 LEVF--HNIPEKDVISWTSIIAGLRLNNRCFEALI-------------FFRQMLLTLKPNSVTLIAALSA--CAR----- 501

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  381 lIKAyeLLSSKgyfsELQSYSLmisflckagrvresytalqemkKEGLAPDVSLYNALIEACCKAEMIRPAkklWDEMFV 460
Cdd:PLN03077 502 -IGA--LMCGK----EIHAHVL----------------------RTGIGFDGFLPNALLDLYVRCGRMNYA---WNQFNS 549

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30684737  461 egCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIEGLCKETKIEAAMEVFRKcMERDHKTV 536
Cdd:PLN03077 550 --HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHS-MEEKYSIT 622
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 469-502 1.57e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.75  E-value: 1.57e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30684737   469 TYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDE 502
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 426-458 4.87e-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: 43.49  E-value: 4.87e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 30684737   426 EGLAPDVSLYNALIEACCKAEMIRPAKKLWDEM 458
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 404-530 5.38e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 49.48  E-value: 5.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  404 ISFLCKAGRVRESYTALQEMKKEG-LAPDVSLYNALIEACCKAEMIRPAKKLWDEMFVEGCKMNLTTYNVLIRKLSEEGE 482
Cdd:PLN03081  94 IEKLVACGRHREALELFEILEAGCpFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGM 173

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 30684737  483 AEESLRLFDKMLERgiepDETIYMSLIEGLCKETKIEAAMEVFRKCME 530
Cdd:PLN03081 174 LIDARRLFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMWE 217
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 496-530 7.36e-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: 43.10  E-value: 7.36e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 30684737   496 RGIEPDETIYMSLIEGLCKETKIEAAMEVFRKcME 530
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDE-ME 34
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 399-538 1.48e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 48.33  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  399 SYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMfvegCKMNLTTYNVLIRKLS 478
Cdd:PLN03081 327 TFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRM----PRKNLISWNALIAGYG 402

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  479 EEGEAEESLRLFDKMLERGIEPDETIYMSLIEGLCKETKIEAAMEVFrKCMERDHKTVTR 538
Cdd:PLN03081 403 NHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIF-QSMSENHRIKPR 461
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 300-496 2.82e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 47.17  E-value: 2.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  300 ILDLISAKRLTEAKEVAEVI-VSGKFPMDNDILDALIGSVSAV-DPDSAVEFLVYMVSTGKLPAIRTLSKLsknLCRHDK 377
Cdd:PLN03081  94 IEKLVACGRHREALELFEILeAGCPFTLPASTYDALVEACIALkSIRCVKAVYWHVESSGFEPDQYMMNRV---LLMHVK 170

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  378 SDHLIKAYELLSSKGYFSELqSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDE 457
Cdd:PLN03081 171 CGMLIDARRLFDEMPERNLA-SWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCC 249

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 30684737  458 MFVEGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLER 496
Cdd:PLN03081 250 VLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEK 288
PLN03077 PLN03077
Protein ECB2; Provisional
 427-509 3.80e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 46.77  E-value: 3.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  427 GLAPDVSLYNALIEACCKAEMIRPAKKLWDEMFVEGCkmnlTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYM 506
Cdd:PLN03077 217 GFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDC----ISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTIT 292


                 ...
gi 30684737  507 SLI 509
Cdd:PLN03077 293 SVI 295
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 364-527 4.72e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 46.40  E-value: 4.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  364 TLSKLSKNLCRHDKSDHLIKAYELLSSKGYFSELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPdvslYNALIEACC 443
Cdd:PLN03081 327 TFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLIS----WNALIAGYG 402

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  444 KAEMIRPAKKLWDEMFVEGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLE-RGIEPDETIYMSLIEGLCKETKIEAAM 522
Cdd:PLN03081 403 NHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEnHRIKPRAMHYACMIELLGREGLLDEAY 482


                 ....*
gi 30684737  523 EVFRK 527
Cdd:PLN03081 483 AMIRR 487
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 407-525 4.72e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 46.79  E-value: 4.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   407 LCKAGRVRESYTALQEMKKEGLAPDVSLYNA-LIEACCKAEMIRPAKKLwdemfvegCKM----NLTTYNVLIRKLSEEG 481
Cdd:PLN03218  380 LLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAkFFKACKKQRAVKEAFRF--------AKLirnpTLSTFNMLMSVCASSQ 451

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 30684737   482 EAEESLRLFDKMLERGIEPDETIYMSLIEGLCKETKIEAAMEVF 525
Cdd:PLN03218  452 DIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVF 495
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 399-432 6.39e-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: 40.13  E-value: 6.39e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30684737   399 SYSLMISFLCKAGRVRESYTALQEMKKEGLAPDV 432
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 409-526 6.64e-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: 6.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   409 KAGRVRESYTAlqeMKKEGLAPDVSLYNALIEACCKAEMIRPAKKLWDEMFVEGCKMNLTTYNVLIRKLSEEGEAEESLR 488
Cdd:pfam17177  70 AADRGFEVFEA---MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYE 146

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 30684737   489 LFDKMLERGIEPDETIYMSLIEgLCkeTKIEAAMEVFR 526
Cdd:pfam17177 147 VEEHMLAHGVELEEPELAALLK-VS--AKAGRADKVYA 181
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 469-498 9.73e-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: 39.76  E-value: 9.73e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 30684737   469 TYNVLIRKLSEEGEAEESLRLFDKMLERGI 498
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 374-500 1.65e-04

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 44.86  E-value: 1.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  374 RHDKSDHLikaYELLSSKGYFS-ELQSYSLMISFLCKAGRVRESYTALQEMKKEGLAPDVSLYNALIEACCKAEMIRPAK 452
Cdd:PLN03081 102 RHREALEL---FEILEAGCPFTlPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDAR 178

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 30684737  453 KLWDEMfvegCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEP 500
Cdd:PLN03081 179 RLFDEM----PERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDA 222
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 435-466 6.13e-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: 37.43  E-value: 6.13e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 30684737   435 YNALIEACCKAEMIRPAKKLWDEMFVEGCKMN 466
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PLN03077 PLN03077
Protein ECB2; Provisional
 344-442 6.18e-04

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 42.91  E-value: 6.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737  344 DSAVEFLVYMVSTGKLPAIRTLSKLsknLCRHDKSDHLIKAYELLSSK----GYFSELQSYSLMISFLCKAGRVRESYTA 419
Cdd:PLN03077 571 SMAVELFNRMVESGVNPDEVTFISL---LCACSRSGMVTQGLEYFHSMeekySITPNLKHYACVVDLLGRAGKLTEAYNF 647

                         90       100
                 ....*....|....*....|...
gi 30684737  420 LQEMKkegLAPDVSLYNALIEAC 442
Cdd:PLN03077 648 INKMP---ITPDPAVWGALLNAC 667
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 435-463 1.18e-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: 36.67  E-value: 1.18e-03
                          10        20
                  ....*....|....*....|....*....
gi 30684737   435 YNALIEACCKAEMIRPAKKLWDEMFVEGC 463
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 461-493 1.19e-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: 36.55  E-value: 1.19e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 30684737   461 EGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKM 493
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 424-509 1.34e-03

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: 40.46  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684737   424 KKEGLAPDvSLYNALIEACCKAEMIRPAKKLWDEMFVEGCKMNLTTYNVLIRKLSEEGEAEESL---------RLFDKML 494
Cdd:pfam17177   4 KKGKQTPE-SELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKpqlaadrgfEVFEAMK 82

                          90
                  ....*....|....*
gi 30684737   495 ERGIEPDETIYMSLI 509
Cdd:pfam17177  83 AQGVSPNEATYTAVA 97
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 453-513 1.92e-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: 1.92e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30684737   453 KLWDEMFVEGCKMNLTTYNVLIRKLSEEGEAEESLRLFDKMLERGIEPDETIYMSLIeGLC 513
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL-GVI 60
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 399-428 2.89e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 35.52  E-value: 2.89e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 30684737   399 SYSLMISFLCKAGRVRESYTALQEMKKEGL 428
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 500-531 7.34e-03

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 35.03  E-value: 7.34e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 30684737   500 PDETIYMSLIEGLCKETKIEAAMEVFRKcMER 531
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNE-MKK 31
 
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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