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Conserved domains on  [gi|1375022823|ref|NP_001348997|]
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small ribosomal subunit protein mS39 isoform 2 precursor [Mus musculus]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1002420)

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 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 289-343 3.39e-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: 44.28  E-value: 3.39e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1375022823 289 DVYTFNALIEAktfILNEKfeeKWNDILDLLKHMVAQKVKPNLQTFNTILKGLRK 343
Cdd:pfam13041   2 DVVTYNTLING---YCKKG---KVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 253-299 9.12e-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: 40.42  E-value: 9.12e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1375022823 253 KNARSYCTMIRGMVKHRAYAQALNVYTELLNNRLSADVYTFNALIEA 299
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
 
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 ...
 289-343 3.39e-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: 44.28  E-value: 3.39e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1375022823 289 DVYTFNALIEAktfILNEKfeeKWNDILDLLKHMVAQKVKPNLQTFNTILKGLRK 343
Cdd:pfam13041   2 DVVTYNTLING---YCKKG---KVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 253-299 9.12e-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: 40.42  E-value: 9.12e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1375022823 253 KNARSYCTMIRGMVKHRAYAQALNVYTELLNNRLSADVYTFNALIEA 299
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03077 PLN03077
Protein ECB2; Provisional
 242-293 3.69e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 3.69e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1375022823 242 NAERIFALMPEKNARSYCTMIRGMVKHRAYAQALNVYTELLNNRLSADVYTF 293
Cdd:PLN03077  139 HAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTF 190
 
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 ...
 289-343 3.39e-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: 44.28  E-value: 3.39e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1375022823 289 DVYTFNALIEAktfILNEKfeeKWNDILDLLKHMVAQKVKPNLQTFNTILKGLRK 343
Cdd:pfam13041   2 DVVTYNTLING---YCKKG---KVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 253-299 9.12e-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: 40.42  E-value: 9.12e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1375022823 253 KNARSYCTMIRGMVKHRAYAQALNVYTELLNNRLSADVYTFNALIEA 299
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 289-339 1.99e-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: 1.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1375022823 289 DVYTFNALIEAKTFILNEKfeekwnDILDLLKHMVAQKVKPNLQTFNTILK 339
Cdd:pfam13812  14 NVNTYTHLLHAYANVGNLK------LALEIFERMKKKGIKPTLDTYNAILG 58
PLN03077 PLN03077
Protein ECB2; Provisional
 242-293 3.69e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 3.69e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1375022823 242 NAERIFALMPEKNARSYCTMIRGMVKHRAYAQALNVYTELLNNRLSADVYTF 293
Cdd:PLN03077  139 HAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTF 190
 
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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