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Conserved domains on  [gi|1002225256|ref|XP_015621222|]
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pentatricopeptide repeat-containing protein At4g36680, mitochondrial [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 225-282 1.42e-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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 44.66  E-value: 1.42e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002225256 225 PDIVSHNGLMRAMARHGRVDEMMEVYKRLEKGSASaaaegksaPDCATYTCVVAALCK 282
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVK--------PNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 272-300 3.46e-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: 3.46e-04
                          10        20
                  ....*....|....*....|....*....
gi 1002225256 272 TYTCVVAALCKAGRWSEADDVFYEAVKRR 300
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERG 30
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 158-184 3.01e-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: 34.75  E-value: 3.01e-03
                          10        20
                  ....*....|....*....|....*..
gi 1002225256 158 FTSVIDSYYKQRKPHRAEQLWREMVED 184
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEK 29
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 225-282 1.42e-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: 44.66  E-value: 1.42e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002225256 225 PDIVSHNGLMRAMARHGRVDEMMEVYKRLEKGSASaaaegksaPDCATYTCVVAALCK 282
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVK--------PNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 189-299 3.39e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 46.02  E-value: 3.39e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002225256  189 PDAAAHNVRITYKAATGTVEEVKELIRAMR-EDAGLQPDIVSHNGLMRAMARHGRVDEMMEVYKRLEKGSAsaaaegKSA 267
Cdd:PLN03218   540 PDRVVFNALISACGQSGAVDRAFDVLAEMKaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNI------KGT 613

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1002225256  268 PDCatYTCVVAALCKAGRWSEADDVfYEAVKR 299
Cdd:PLN03218   614 PEV--YTIAVNSCSQKGDWDFALSI-YDDMKK 642
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 272-300 3.46e-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: 3.46e-04
                          10        20
                  ....*....|....*....|....*....
gi 1002225256 272 TYTCVVAALCKAGRWSEADDVFYEAVKRR 300
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERG 30
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 268-315 5.59e-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: 37.34  E-value: 5.59e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002225256 268 PDCATYTCVVAALCKAGRWSEADDVFYEAVKRRKLADLGTARVLVRGL 315
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 228-255 1.01e-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: 1.01e-03
                          10        20
                  ....*....|....*....|....*...
gi 1002225256 228 VSHNGLMRAMARHGRVDEMMEVYKRLEK 255
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKE 28
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 158-184 3.01e-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: 34.75  E-value: 3.01e-03
                          10        20
                  ....*....|....*....|....*..
gi 1002225256 158 FTSVIDSYYKQRKPHRAEQLWREMVED 184
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEK 29
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 225-282 1.42e-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: 44.66  E-value: 1.42e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002225256 225 PDIVSHNGLMRAMARHGRVDEMMEVYKRLEKGSASaaaegksaPDCATYTCVVAALCK 282
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVK--------PNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 189-299 3.39e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 46.02  E-value: 3.39e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002225256  189 PDAAAHNVRITYKAATGTVEEVKELIRAMR-EDAGLQPDIVSHNGLMRAMARHGRVDEMMEVYKRLEKGSAsaaaegKSA 267
Cdd:PLN03218   540 PDRVVFNALISACGQSGAVDRAFDVLAEMKaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNI------KGT 613

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1002225256  268 PDCatYTCVVAALCKAGRWSEADDVfYEAVKR 299
Cdd:PLN03218   614 PEV--YTIAVNSCSQKGDWDFALSI-YDDMKK 642
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 272-300 3.46e-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: 3.46e-04
                          10        20
                  ....*....|....*....|....*....
gi 1002225256 272 TYTCVVAALCKAGRWSEADDVFYEAVKRR 300
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERG 30
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 268-315 5.59e-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: 37.34  E-value: 5.59e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002225256 268 PDCATYTCVVAALCKAGRWSEADDVFYEAVKRRKLADLGTARVLVRGL 315
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03077 PLN03077
Protein ECB2; Provisional
 190-299 7.64e-04

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 41.76  E-value: 7.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002225256 190 DAAAHNVRITYKAATGTVEEVKELIRAMREdAGLQPDIVSHNGLMRAMARHGRVDEMMEVYKRLEKgsasaaaEGKSAPD 269
Cdd:PLN03077  553 DVVSWNILLTGYVAHGKGSMAVELFNRMVE-SGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEE-------KYSITPN 624

                          90       100       110
                  ....*....|....*....|....*....|
gi 1002225256 270 CATYTCVVAALCKAGRWSEAddvfYEAVKR 299
Cdd:PLN03077  625 LKHYACVVDLLGRAGKLTEA----YNFINK 650
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 268-293 9.51e-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: 36.17  E-value: 9.51e-04
                          10        20
                  ....*....|....*....|....*.
gi 1002225256 268 PDCATYTCVVAALCKAGRWSEADDVF 293
Cdd:pfam12854   5 PDVVTYNTLINGLCRAGRVDEAFELL 30
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 228-255 1.01e-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: 1.01e-03
                          10        20
                  ....*....|....*....|....*...
gi 1002225256 228 VSHNGLMRAMARHGRVDEMMEVYKRLEK 255
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKE 28
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 272-299 1.86e-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: 1.86e-03
                          10        20
                  ....*....|....*....|....*...
gi 1002225256 272 TYTCVVAALCKAGRWSEADDVFYEAVKR 299
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEK 29
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 158-184 3.01e-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: 34.75  E-value: 3.01e-03
                          10        20
                  ....*....|....*....|....*..
gi 1002225256 158 FTSVIDSYYKQRKPHRAEQLWREMVED 184
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEK 29
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 115-299 3.14e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 39.86  E-value: 3.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002225256  115 AHPSVPrDDATEGIHAKALCIATGADSAL---HLLQRESPPPSLQLFTSVIDSYYKQRKPHRAEQLWREMVEDhGIVPDA 191
Cdd:PLN03218   572 THPIDP-DHITVGALMKACANAGQVDRAKevyQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKK-GVKPDE 649

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002225256  192 AAHNVRITYKAATGTVEEVKELIRAMREDaGLQPDIVSHNGLMRAMARHGRVDEMMEVYkrlEKGSASaaaegKSAPDCA 271
Cdd:PLN03218   650 VFFSALVDVAGHAGDLDKAFEILQDARKQ-GIKLGTVSYSSLMGACSNAKNWKKALELY---EDIKSI-----KLRPTVS 720

                          170       180
                   ....*....|....*....|....*...
gi 1002225256  272 TYTCVVAALCKAGRWSEADDVFYEaVKR 299
Cdd:PLN03218   721 TMNALITALCEGNQLPKALEVLSE-MKR 747
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 222-254 6.41e-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: 33.86  E-value: 6.41e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1002225256 222 GLQPDIVSHNGLMRAMARHGRVDEMMEVYKRLE 254
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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