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Conserved domains on  [gi|334183937|ref|NP_001185409|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13329789)

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
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 555-598 1.12e-09

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


:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 54.29  E-value: 1.12e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 334183937  555 TYNIVLHSLLEANETDMVINIFKRMKSCGCPADVATYNIMIDCC 598
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 336-664 7.39e-08

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 56.42  E-value: 7.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  336 IHACGQSKNSELAEQLMLQMQNLGLLPSSHTY----DGFIRAVAFPEGY-EYGmtllkVMQQQNLKPydstlatvaaycs 410
Cdd:PLN03218  479 ISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFgaliDGCARAGQVAKAFgAYG-----IMRSKNVKP------------- 540

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  411 kalqvdlaehllDQISecsysypFNNLLAAYDSLDQPERAVRVLARMK-ELK-LRPDMRTYELLFSL---FGNVNAPYEE 485
Cdd:PLN03218  541 ------------DRVV-------FNALISACGQSGAVDRAFDVLAEMKaETHpIDPDHITVGALMKAcanAGQVDRAKEV 601

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  486 GNMLSQ-------------VDCCKRIN------AIEMDMMRNGFQHSPISRLNVLRALGAEGMVNEMIRHLQKAENlsah 546
Cdd:PLN03218  602 YQMIHEynikgtpevytiaVNSCSQKGdwdfalSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK---- 677

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  547 SNMYLGTPTYNIVLHSLLEANETDMVINIFKRMKSCGCPADVATYNIMIDCCSLIHSYKSACALVSMMIRDGFSPKAVTF 626
Cdd:PLN03218  678 QGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY 757

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 334183937  627 TALMKILLNDANFEEALNLLDQAALEEIHLDVLSYNTI 664
Cdd:PLN03218  758 SILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795
 
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 ...
 555-598 1.12e-09

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 54.29  E-value: 1.12e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 334183937  555 TYNIVLHSLLEANETDMVINIFKRMKSCGCPADVATYNIMIDCC 598
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 336-664 7.39e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 56.42  E-value: 7.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  336 IHACGQSKNSELAEQLMLQMQNLGLLPSSHTY----DGFIRAVAFPEGY-EYGmtllkVMQQQNLKPydstlatvaaycs 410
Cdd:PLN03218  479 ISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFgaliDGCARAGQVAKAFgAYG-----IMRSKNVKP------------- 540

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  411 kalqvdlaehllDQISecsysypFNNLLAAYDSLDQPERAVRVLARMK-ELK-LRPDMRTYELLFSL---FGNVNAPYEE 485
Cdd:PLN03218  541 ------------DRVV-------FNALISACGQSGAVDRAFDVLAEMKaETHpIDPDHITVGALMKAcanAGQVDRAKEV 601

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  486 GNMLSQ-------------VDCCKRIN------AIEMDMMRNGFQHSPISRLNVLRALGAEGMVNEMIRHLQKAENlsah 546
Cdd:PLN03218  602 YQMIHEynikgtpevytiaVNSCSQKGdwdfalSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK---- 677

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  547 SNMYLGTPTYNIVLHSLLEANETDMVINIFKRMKSCGCPADVATYNIMIDCCSLIHSYKSACALVSMMIRDGFSPKAVTF 626
Cdd:PLN03218  678 QGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY 757

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 334183937  627 TALMKILLNDANFEEALNLLDQAALEEIHLDVLSYNTI 664
Cdd:PLN03218  758 SILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 587-631 2.90e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.27  E-value: 2.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 334183937  587 DVATYNIMIDCCSLIHSYKSACALVSMMIRDGFSPKAVTFTALMK 631
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 555-588 3.48e-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: 3.48e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334183937  555 TYNIVLHSLLEANETDMVINIFKRMKSCGCPADV 588
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 590-621 3.81e-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: 3.81e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 334183937  590 TYNIMIDCCSLIHSYKSACALVSMMIRDGFSP 621
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
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 ...
 555-598 1.12e-09

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 54.29  E-value: 1.12e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 334183937  555 TYNIVLHSLLEANETDMVINIFKRMKSCGCPADVATYNIMIDCC 598
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 336-664 7.39e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 56.42  E-value: 7.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  336 IHACGQSKNSELAEQLMLQMQNLGLLPSSHTY----DGFIRAVAFPEGY-EYGmtllkVMQQQNLKPydstlatvaaycs 410
Cdd:PLN03218  479 ISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFgaliDGCARAGQVAKAFgAYG-----IMRSKNVKP------------- 540

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  411 kalqvdlaehllDQISecsysypFNNLLAAYDSLDQPERAVRVLARMK-ELK-LRPDMRTYELLFSL---FGNVNAPYEE 485
Cdd:PLN03218  541 ------------DRVV-------FNALISACGQSGAVDRAFDVLAEMKaETHpIDPDHITVGALMKAcanAGQVDRAKEV 601

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  486 GNMLSQ-------------VDCCKRIN------AIEMDMMRNGFQHSPISRLNVLRALGAEGMVNEMIRHLQKAENlsah 546
Cdd:PLN03218  602 YQMIHEynikgtpevytiaVNSCSQKGdwdfalSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK---- 677

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  547 SNMYLGTPTYNIVLHSLLEANETDMVINIFKRMKSCGCPADVATYNIMIDCCSLIHSYKSACALVSMMIRDGFSPKAVTF 626
Cdd:PLN03218  678 QGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY 757

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 334183937  627 TALMKILLNDANFEEALNLLDQAALEEIHLDVLSYNTI 664
Cdd:PLN03218  758 SILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 587-631 2.90e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.27  E-value: 2.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 334183937  587 DVATYNIMIDCCSLIHSYKSACALVSMMIRDGFSPKAVTFTALMK 631
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 555-588 3.48e-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: 3.48e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334183937  555 TYNIVLHSLLEANETDMVINIFKRMKSCGCPADV 588
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 ...
 331-375 1.26e-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: 37.34  E-value: 1.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 334183937  331 SFNDVIHACGQSKNSELAEQLMLQMQNLGLLPSSHTYDGFIRAVA 375
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 555-665 1.54e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 42.17  E-value: 1.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  555 TYNIVLHSLLEANETDMVINIFKRMKSCGCPADVATYNIMIDCCSLIHSYKSACALVSMMIRDGFSPKAVTFTALMKILL 634
Cdd:PLN03218  581 TVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAG 660

                          90       100       110
                  ....*....|....*....|....*....|.
gi 334183937  635 NDANFEEALNLLDQAALEEIHLDVLSYNTIL 665
Cdd:PLN03218  661 HAGDLDKAFEILQDARKQGIKLGTVSYSSLM 691
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 590-621 3.81e-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: 3.81e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 334183937  590 TYNIMIDCCSLIHSYKSACALVSMMIRDGFSP 621
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 432-478 5.06e-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: 36.18  E-value: 5.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 334183937  432 YPFNNLLAAYDSLDQPERAVRVLARMKELKLRPDMRTYELLFSLFGN 478
Cdd:pfam13812  16 NTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 335-473 5.37e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 40.25  E-value: 5.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183937  335 VIHACGQSKNSELAEQLMLQMQNLGLLPSSHTYDGFIRAVAFPEGYEYGMTLLKVMQQQNLKPYDSTLATVAAYCS---- 410
Cdd:PLN03218  620 AVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSnakn 699

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334183937  411 --KALQV--DL-AEHLLDQISEcsysypFNNLLAAYDSLDQPERAVRVLARMKELKLRPDMRTYELLF 473
Cdd:PLN03218  700 wkKALELyeDIkSIKLRPTVST------MNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILL 761
 
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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