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Conserved domains on  [gi|6321589|ref|NP_011666|]
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Ccm1p [Saccharomyces cerevisiae S288C]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13595511)

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

Gene Ontology:  GO:0003723

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 ...
 355-398 1.48e-07

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


:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 48.51  E-value: 1.48e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 6321589    355 PDICTYNTMLRICEKERNFPKALDLFQEIQDHNIKPTTNTY-IMM 398
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYtILI 45
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 324-365 7.09e-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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 38.11  E-value: 7.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 6321589    324 TTVIQFYSRKEMTKQAWNTFDTMKFLSTKhfPDICTYNTMLR 365
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKKRGVK--PNVYTYTILIN 46
 
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 ...
 355-398 1.48e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 48.51  E-value: 1.48e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 6321589    355 PDICTYNTMLRICEKERNFPKALDLFQEIQDHNIKPTTNTY-IMM 398
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYtILI 45
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 324-365 7.09e-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: 38.11  E-value: 7.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 6321589    324 TTVIQFYSRKEMTKQAWNTFDTMKFLSTKhfPDICTYNTMLR 365
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKKRGVK--PNVYTYTILIN 46
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 358-392 7.12e-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: 37.82  E-value: 7.12e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 6321589    358 CTYNTMLRICEKERNFPKALDLFQEIQDHNIKPTT 392
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 297-395 9.09e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 42.94  E-value: 9.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321589    297 CSSFHDMDYFITKFRD--DYGITPNKQNLTTVIQFYSRKEMTKQAWNTFDTMKFLSTKhfPDICTYNTMLRICEKERNFP 374
Cdd:PLN03218  624 CSQKGDWDFALSIYDDmkKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK--LGTVSYSSLMGACSNAKNWK 701

                          90       100
                  ....*....|....*....|.
gi 6321589    375 KALDLFQEIQDHNIKPTTNTY 395
Cdd:PLN03218  702 KALELYEDIKSIKLRPTVSTM 722
 
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 ...
 355-398 1.48e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 48.51  E-value: 1.48e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 6321589    355 PDICTYNTMLRICEKERNFPKALDLFQEIQDHNIKPTTNTY-IMM 398
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYtILI 45
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 324-365 7.09e-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: 38.11  E-value: 7.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 6321589    324 TTVIQFYSRKEMTKQAWNTFDTMKFLSTKhfPDICTYNTMLR 365
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKKRGVK--PNVYTYTILIN 46
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 358-392 7.12e-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: 37.82  E-value: 7.12e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 6321589    358 CTYNTMLRICEKERNFPKALDLFQEIQDHNIKPTT 392
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 297-395 9.09e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 42.94  E-value: 9.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321589    297 CSSFHDMDYFITKFRD--DYGITPNKQNLTTVIQFYSRKEMTKQAWNTFDTMKFLSTKhfPDICTYNTMLRICEKERNFP 374
Cdd:PLN03218  624 CSQKGDWDFALSIYDDmkKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK--LGTVSYSSLMGACSNAKNWK 701

                          90       100
                  ....*....|....*....|.
gi 6321589    375 KALDLFQEIQDHNIKPTTNTY 395
Cdd:PLN03218  702 KALELYEDIKSIKLRPTVSTM 722
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 359-388 6.10e-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: 35.13  E-value: 6.10e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 6321589    359 TYNTMLRICEKERNFPKALDLFQEIQDHNI 388
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 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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