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Conserved domains on  [gi|1955831238|ref|XP_038904717|]
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pentatricopeptide repeat-containing protein At1g62914, mitochondrial-like [Benincasa hispida]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13329401)

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
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 146-484 5.08e-17

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 85.70  E-value: 5.08e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  146 ALGVLSHINLVGLKPSIETFNVVLAVFVEENRdiQEVLF-VYKEMVKAGIVPNVDTLNFLLAALFHAEQIKTAMNQFRRM 224
Cdd:PLN03218   456 ALRVLRLVQEAGLKADCKLYTTLISTCAKSGK--VDAMFeVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIM 533

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  225 SKKGCSPNSKTFEVLLNGLITKNLVDEAVLVLGIMYKIRCKLDLSFYTYA--ISLFCREDRIDVGSWLFRMMKASNIVPI 302
Cdd:PLN03218   534 RSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGalMKACANAGQVDRAKEVYQMIHEYNIKGT 613

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  303 AFIYSTLIQSLCKNLSLDEALFLLEEMVESGLMPEENVYVSIIKVFFELGKTDEAIKFVED-RCAFY---TSPHNALLEG 378
Cdd:PLN03218   614 PEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDaRKQGIklgTVSYSSLMGA 693

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  379 CSNAG--KILLANCILVKMSKMNiDDCKSWNIVIGWLCNNARIGSAFEFLSKMIVSSFVPNEDTYAALIVGNCKSRRYEA 456
Cdd:PLN03218   694 CSNAKnwKKALELYEDIKSIKLR-PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADV 772

                          330       340
                   ....*....|....*....|....*...
gi 1955831238  457 ALQLMNEVHARCWILNAGCYSELIeGLC 484
Cdd:PLN03218   773 GLDLLSQAKEDGIKPNLVMCRCIT-GLC 799
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 647-693 4.37e-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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 41.19  E-value: 4.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1955831238 647 NTATYNLLINGLWKEDRKYEACKLLDSMLEKGWVPDAMTHGLLIGSL 693
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 580-613 2.23e-03

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


:

Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.28  E-value: 2.23e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1955831238 580 TYYILIRSFSAMNRVKESILLFNRMINEGLLPDS 613
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 146-484 5.08e-17

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 85.70  E-value: 5.08e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  146 ALGVLSHINLVGLKPSIETFNVVLAVFVEENRdiQEVLF-VYKEMVKAGIVPNVDTLNFLLAALFHAEQIKTAMNQFRRM 224
Cdd:PLN03218   456 ALRVLRLVQEAGLKADCKLYTTLISTCAKSGK--VDAMFeVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIM 533

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  225 SKKGCSPNSKTFEVLLNGLITKNLVDEAVLVLGIMYKIRCKLDLSFYTYA--ISLFCREDRIDVGSWLFRMMKASNIVPI 302
Cdd:PLN03218   534 RSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGalMKACANAGQVDRAKEVYQMIHEYNIKGT 613

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  303 AFIYSTLIQSLCKNLSLDEALFLLEEMVESGLMPEENVYVSIIKVFFELGKTDEAIKFVED-RCAFY---TSPHNALLEG 378
Cdd:PLN03218   614 PEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDaRKQGIklgTVSYSSLMGA 693

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  379 CSNAG--KILLANCILVKMSKMNiDDCKSWNIVIGWLCNNARIGSAFEFLSKMIVSSFVPNEDTYAALIVGNCKSRRYEA 456
Cdd:PLN03218   694 CSNAKnwKKALELYEDIKSIKLR-PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADV 772

                          330       340
                   ....*....|....*....|....*...
gi 1955831238  457 ALQLMNEVHARCWILNAGCYSELIeGLC 484
Cdd:PLN03218   773 GLDLLSQAKEDGIKPNLVMCRCIT-GLC 799
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 196-243 7.57e-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: 7.57e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1955831238 196 PNVDTLNFLLAALFHAEQIKTAMNQFRRMSKKGCSPNSKTFEVLLNGL 243
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 647-693 4.37e-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: 41.19  E-value: 4.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1955831238 647 NTATYNLLINGLWKEDRKYEACKLLDSMLEKGWVPDAMTHGLLIGSL 693
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 650-683 3.44e-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: 3.44e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1955831238 650 TYNLLINGLWKEDRKYEACKLLDSMLEKGWVPDA 683
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 580-613 2.23e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.28  E-value: 2.23e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1955831238 580 TYYILIRSFSAMNRVKESILLFNRMINEGLLPDS 613
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 304-336 4.15e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.51  E-value: 4.15e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1955831238 304 FIYSTLIQSLCKNLSLDEALFLLEEMVESGLMP 336
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 146-484 5.08e-17

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 85.70  E-value: 5.08e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  146 ALGVLSHINLVGLKPSIETFNVVLAVFVEENRdiQEVLF-VYKEMVKAGIVPNVDTLNFLLAALFHAEQIKTAMNQFRRM 224
Cdd:PLN03218   456 ALRVLRLVQEAGLKADCKLYTTLISTCAKSGK--VDAMFeVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIM 533

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  225 SKKGCSPNSKTFEVLLNGLITKNLVDEAVLVLGIMYKIRCKLDLSFYTYA--ISLFCREDRIDVGSWLFRMMKASNIVPI 302
Cdd:PLN03218   534 RSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGalMKACANAGQVDRAKEVYQMIHEYNIKGT 613

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  303 AFIYSTLIQSLCKNLSLDEALFLLEEMVESGLMPEENVYVSIIKVFFELGKTDEAIKFVED-RCAFY---TSPHNALLEG 378
Cdd:PLN03218   614 PEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDaRKQGIklgTVSYSSLMGA 693

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  379 CSNAG--KILLANCILVKMSKMNiDDCKSWNIVIGWLCNNARIGSAFEFLSKMIVSSFVPNEDTYAALIVGNCKSRRYEA 456
Cdd:PLN03218   694 CSNAKnwKKALELYEDIKSIKLR-PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADV 772

                          330       340
                   ....*....|....*....|....*...
gi 1955831238  457 ALQLMNEVHARCWILNAGCYSELIeGLC 484
Cdd:PLN03218   773 GLDLLSQAKEDGIKPNLVMCRCIT-GLC 799
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 133-609 1.01e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 61.81  E-value: 1.01e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 133 LVNAFVRRGRTREALGVLSHINLVGLKPSIETFNVVLAVFVEENRdIQEVLFVYKEMVKAGIVpnvdTLNFLLAALFHAE 212
Cdd:PLN03081  129 LVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGM-LIDARRLFDEMPERNLA----SWGTIIGGLVDAG 203

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 213 QIKTAMNQFRRMSKKGCSPNSKTFEVLLnglitknlvdEAVLVLGIMYKIR----CKLDLSFY--TYA----ISLFCRED 282
Cdd:PLN03081  204 NYREAFALFREMWEDGSDAEPRTFVVML----------RASAGLGSARAGQqlhcCVLKTGVVgdTFVscalIDMYSKCG 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 283 RIDVGSWLFRMMKASNIVPiafiYSTLIQSLCKNLSLDEALFLLEEMVESGLMPEENVYVSIIKVFFELGKTDEAIK--- 359
Cdd:PLN03081  274 DIEDARCVFDGMPEKTTVA----WNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQaha 349

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 360 -FVEDRCAFYTSPHNALLEGCSNAGKILLANCILVKMSKMNIddcKSWNIVIGWLCNNARIGSAFEFLSKMIVSSFVPNE 438
Cdd:PLN03081  350 gLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNL---ISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNH 426

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 439 DTYAAlivgncksrryeaalqlmnevharcwILNAGCYSELIEglcqahrtlEAAEVFCYMSKNrYPLHPSVfdMLVKGM 518
Cdd:PLN03081  427 VTFLA--------------------------VLSACRYSGLSE---------QGWEIFQSMSEN-HRIKPRA--MHYACM 468

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 519 CDL----GHVDEALVLLQLACYAGTS--CKTLTYASIMHElsksnKVEFVLLVLSQMLVLGYSlNMETYYILIRSFSAMN 592
Cdd:PLN03081  469 IELlgreGLLDEAYAMIRRAPFKPTVnmWAALLTACRIHK-----NLELGRLAAEKLYGMGPE-KLNNYVVLLNLYNSSG 542

                         490
                  ....*....|....*..
gi 1955831238 593 RVKESILLFNRMINEGL 609
Cdd:PLN03081  543 RQAEAAKVVETLKRKGL 559
PLN03077 PLN03077
Protein ECB2; Provisional
 133-604 2.17e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 61.02  E-value: 2.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 133 LVNAFVRRGRTREALGVLSHINLVGLKPSIETFNVVLAVF--VEENRDIQEVlfvYKEMVKAGIVPNVDTLNFLLAALFH 210
Cdd:PLN03077  158 LVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCggIPDLARGREV---HAHVVRFGFELDVDVVNALITMYVK 234

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 211 AEQIKTAMNQFRRMSKKGC-SPN---SKTFE--VLLNGL-----ITKNLVDEAVLVL--------------------GIM 259
Cdd:PLN03077  235 CGDVVSARLVFDRMPRRDCiSWNamiSGYFEngECLEGLelfftMRELSVDPDLMTItsvisacellgderlgremhGYV 314

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 260 YKIRCKLDLSFYTYAISLFcredrIDVGSW-----LFRMMKASNIVPiafiYSTLIQSLCKNLSLDEALFLLEEMVESGL 334
Cdd:PLN03077  315 VKTGFAVDVSVCNSLIQMY-----LSLGSWgeaekVFSRMETKDAVS----WTAMISGYEKNGLPDKALETYALMEQDNV 385

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 335 MPEENVYVSIIKVFFELGKTDEAIKFVE--DRCAF--YTSPHNALLEGCSNAGKILLANCILVKMSKMNIddcKSWNIVI 410
Cdd:PLN03077  386 SPDEITIASVLSACACLGDLDVGVKLHElaERKGLisYVVVANALIEMYSKCKCIDKALEVFHNIPEKDV---ISWTSII 462

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 411 GWLCNNARIGSAFEFLSKMIVSSfVPNEDTYAALIVGNCKSrryeAALQLMNEVHARcwILNAGCYSE------LIEGLC 484
Cdd:PLN03077  463 AGLRLNNRCFEALIFFRQMLLTL-KPNSVTLIAALSACARI----GALMCGKEIHAH--VLRTGIGFDgflpnaLLDLYV 535

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 485 QAHRTLEAAEVFCYMSKNryplhPSVFDMLVKGMCDLGHVDEALVLLQLACYAGTSCKTLTYASIMHELSKSNKVEFVLL 564
Cdd:PLN03077  536 RCGRMNYAWNQFNSHEKD-----VVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLE 610

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|.
gi 1955831238 565 VLSQMLV-LGYSLNMETYYILIRSFSAMNRVKESILLFNRM 604
Cdd:PLN03077  611 YFHSMEEkYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM 651
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 177-640 7.78e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.12  E-value: 7.78e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  177 RDIQEVLFVYKEMVKAG-------IVPNVDTLNFL------LAALFHAEQIKTAMNQFRRMSKKGCSPNSKTFEVLLNGL 243
Cdd:PLN03218   368 RKSPEYIDAYNRLLRDGrikdcidLLEDMEKRGLLdmdkiyHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVC 447

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  244 ITKNLVDEAVLVLGIMYKIRCKLDLSFYTYAISLFCREDRIDVGSWLFRMMKASNIVPIAFIYSTLIQSLCKNLSLDEAL 323
Cdd:PLN03218   448 ASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAF 527

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  324 FLLEEMVESGLMPEENVYVSIIKVFFELGKTDEAIKFVEDRCAfYTSP----H---NALLEGCSNAGKILLANCILVKMS 396
Cdd:PLN03218   528 GAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKA-ETHPidpdHitvGALMKACANAGQVDRAKEVYQMIH 606

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  397 KMNIDDCKS-WNIVIGWLCNNARIGSAFEFLSKMIVSSFVPNEDTYAALIVGNCKSRRYEAALQLMNEVHARCWILNAGC 475
Cdd:PLN03218   607 EYNIKGTPEvYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVS 686

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  476 YSELIEGLCQAHRTLEAAEVfcYMSKNRYPLHPSVFDM--LVKGMCDLGHVDEALVLLQLACYAGTSCKTLTYASIMHEL 553
Cdd:PLN03218   687 YSSLMGACSNAKNWKKALEL--YEDIKSIKLRPTVSTMnaLITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVAS 764

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  554 SKSNKVEFVLLVLSQMLVLGYSLNMETYYILI----RSFSAMNRVKESILLFN-------------------RMINEGLL 610
Cdd:PLN03218   765 ERKDDADVGLDLLSQAKEDGIKPNLVMCRCITglclRRFEKACALGEPVVSFDsgrpqienkwtswalmvyrETISAGTL 844

                          490       500       510
                   ....*....|....*....|....*....|
gi 1955831238  611 PDSEGLYDLFLCIanhsQLHMISTTIDKLI 640
Cdd:PLN03218   845 PTMEVLSQVLGCL----QLPHDATLRNRLI 870
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 196-243 7.57e-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: 7.57e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1955831238 196 PNVDTLNFLLAALFHAEQIKTAMNQFRRMSKKGCSPNSKTFEVLLNGL 243
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 106-315 1.20e-06

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 52.19  E-value: 1.20e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  106 GDIEEMERTCRDLVKDGCSGVEEVIVTLVNAFVRRGRTREALGVLSHINLVGLKPSIETFNVVLAVfVEENRDIQEVLFV 185
Cdd:PLN03218   628 GDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGA-CSNAKNWKKALEL 706

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238  186 YKEMVKAGIVPNVDTLNFLLAALFHAEQIKTAMNQFRRMSKKGCSPNSKTFEVLLnglitknlvdeavlvlgimykIRCK 265
Cdd:PLN03218   707 YEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL---------------------VASE 765

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1955831238  266 ldlsfytyaislfcREDRIDVGSWLFRMMKASNIVPIAFIYSTLIqSLCK 315
Cdd:PLN03218   766 --------------RKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLCL 800
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 405-450 1.96e-06

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 45.05  E-value: 1.96e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1955831238 405 SWNIVIGWLCNNARIGSAFEFLSKMIVSSFVPNEDTYAALIVGNCK 450
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 185-241 3.70e-06

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 44.66  E-value: 3.70e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1955831238 185 VYKEMVKAGIVPNVDTLNFLLAALFHAEQIKTAMNQFRRMSKKGCSPNSKTFEVLLN 241
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 647-693 4.37e-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: 41.19  E-value: 4.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1955831238 647 NTATYNLLINGLWKEDRKYEACKLLDSMLEKGWVPDAMTHGLLIGSL 693
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 160-210 1.14e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.04  E-value: 1.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1955831238 160 PSIETFNVVLAVFVEENRdIQEVLFVYKEMVKAGIVPNVDTLNFLLAALFH 210
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGK-VEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 304-334 2.58e-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: 2.58e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1955831238 304 FIYSTLIQSLCKNLSLDEALFLLEEMVESGL 334
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 298-330 2.82e-04

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: 38.48  E-value: 2.82e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1955831238 298 NIVPIAFIYSTLIQSLCKNLSLDEALFLLEEMV 330
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 650-683 3.44e-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: 3.44e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1955831238 650 TYNLLINGLWKEDRKYEACKLLDSMLEKGWVPDA 683
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 178-347 4.23e-04

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 42.38  E-value: 4.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 178 DIQEVLFVYKEMVKAGIVPNVDTLNFLL------AALFHAEQIKTAMNQFR---RMSKKGCSPNSKTfevllnglitknl 248
Cdd:pfam17177  26 DATGALALYDAAKAEGVRLAQYHYNVLLylcskaADATDLKPQLAADRGFEvfeAMKAQGVSPNEAT------------- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 249 vdeavlvlgimykirckldlsfYTYAISLFCREDRIDVGSWLFRMMKASNIVPIAFIYSTLIQSLCKNLSLDEALFLLEE 328
Cdd:pfam17177  93 ----------------------YTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEH 150

                         170
                  ....*....|....*....
gi 1955831238 329 MVESGLMPEENVYVSIIKV 347
Cdd:pfam17177 151 MLAHGVELEEPELAALLKV 169
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 304-348 5.11e-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: 5.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1955831238 304 FIYSTLIQSLCKNLSLDEALFLLEEMVESGLMPEENVYVSIIKVF 348
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 157-207 8.14e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 38.11  E-value: 8.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1955831238 157 GLKPSIETFNVVLAVFVEeNRDIQEVLFVYKEMVKAGIVPNVDTLNFLLAA 207
Cdd:pfam13812  10 GIQLNVNTYTHLLHAYAN-VGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PLN03077 PLN03077
Protein ECB2; Provisional
 217-508 1.02e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 42.53  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 217 AMNQFRRMSKKGCSPNSKTFEVLLNGLITKNLVDEAVLVLGIMYKIRCKLDLSFYTYAISLFCREDRIDVGSWLFRMMKA 296
Cdd:PLN03077  373 ALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPE 452

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 297 SNIVPiafiYSTLIQSLCKNLSLDEALFLLEEMVESgLMPEENVYVSIIKVFFELGKTdeaikfvedRCAFYTSPHnALL 376
Cdd:PLN03077  453 KDVIS----WTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIGAL---------MCGKEIHAH-VLR 517

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 377 EGCSNAGkiLLANCIL---VKMSKMNI---------DDCKSWNIVIGWLCNNARIGSAFEFLSKMIVSSFVPNEDTYAAL 444
Cdd:PLN03077  518 TGIGFDG--FLPNALLdlyVRCGRMNYawnqfnsheKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISL 595

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1955831238 445 IVGNCKSRRYEAALQLMNEVHARCWIL-NAGCYSELIEGLCQAHRTLEAAEVFcymskNRYPLHP 508
Cdd:PLN03077  596 LCACSRSGMVTQGLEYFHSMEEKYSITpNLKHYACVVDLLGRAGKLTEAYNFI-----NKMPITP 655
PLN03077 PLN03077
Protein ECB2; Provisional
 307-411 1.39e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 42.14  E-value: 1.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831238 307 STLIQSLCKNLSLDEALFLLEEMVESGLMPEENVYVSIIKvffeLGKTDEAIKFVEDRCAFYTSPH--------NALLEG 378
Cdd:PLN03077   55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFR----LCEWKRAVEEGSRVCSRALSSHpslgvrlgNAMLSM 130

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1955831238 379 CSNAGKILLANCILVKMSKMNIddcKSWNIVIG 411
Cdd:PLN03077  131 FVRFGELVHAWYVFGKMPERDL---FSWNVLVG 160
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 580-613 2.23e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.28  E-value: 2.23e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1955831238 580 TYYILIRSFSAMNRVKESILLFNRMINEGLLPDS 613
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 304-336 4.15e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.51  E-value: 4.15e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1955831238 304 FIYSTLIQSLCKNLSLDEALFLLEEMVESGLMP 336
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
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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