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Conserved domains on  [gi|1958770926|ref|XP_038964072|]
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small ribosomal subunit protein mS39 isoform X2 [Rattus norvegicus]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1007099)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner; similar to small ribosomal subunit protein mS39, a mitochondrial RNA-binding protein that has a role in mitochondrial translation

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_3 super family cl37870
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 217-280 2.77e-05

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.


The actual alignment was detected with superfamily member pfam13812:

Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 42.35  E-value: 2.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958770926 217 LLRHMVAQKVKPNLQTFNTTLkclRKFHSLGRLP-ALQILREMKHIGIEPSLATYHHIIHLFYPR 280
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLL---HAYANVGNLKlALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 152-198 4.80e-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: 4.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958770926 152 KNARSYCTMIRGMVKHRAYAQALNLYTELLNNRLSADVYTFNALIEA 198
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
 
Name Accession Description Interval E-value
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 217-280 2.77e-05

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: 42.35  E-value: 2.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958770926 217 LLRHMVAQKVKPNLQTFNTTLkclRKFHSLGRLP-ALQILREMKHIGIEPSLATYHHIIHLFYPR 280
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLL---HAYANVGNLKlALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 152-198 4.80e-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: 4.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958770926 152 KNARSYCTMIRGMVKHRAYAQALNLYTELLNNRLSADVYTFNALIEA 198
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03077 PLN03077
Protein ECB2; Provisional
 141-204 9.64e-04

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 42.14  E-value: 9.64e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958770926 141 NAERIFALMPEKNARSYCTMIRGMVKHRAYAQALNLYTELLNNRLSADVYTFNALIEAKTFIPN 204
Cdd:PLN03077  139 HAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPD 202
 
Name Accession Description Interval E-value
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 217-280 2.77e-05

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: 42.35  E-value: 2.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958770926 217 LLRHMVAQKVKPNLQTFNTTLkclRKFHSLGRLP-ALQILREMKHIGIEPSLATYHHIIHLFYPR 280
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLL---HAYANVGNLKlALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 152-198 4.80e-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: 4.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958770926 152 KNARSYCTMIRGMVKHRAYAQALNLYTELLNNRLSADVYTFNALIEA 198
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 188-242 4.98e-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: 4.98e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958770926 188 DVYTFNALIEA--KtfipnekfEEKWNDILDLLRHMVAQKVKPNLQTFNTTLKCLRK 242
Cdd:pfam13041   2 DVVTYNTLINGycK--------KGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 141-204 9.64e-04

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 42.14  E-value: 9.64e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958770926 141 NAERIFALMPEKNARSYCTMIRGMVKHRAYAQALNLYTELLNNRLSADVYTFNALIEAKTFIPN 204
Cdd:PLN03077  139 HAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPD 202
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 141-200 3.15e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 40.62  E-value: 3.15e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958770926 141 NAERIFALMPEKNARSYCTMIRGMVKHRAYAQALNLYTELLNNRLSADVYTFNALIEAKT 200
Cdd:PLN03081  176 DARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASA 235
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 141-196 3.62e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 40.24  E-value: 3.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958770926 141 NAERIFALMPEKNARSYCTMIRGMVKHRAYAQALNLYTELLNNRLSADVYTFNALI 196
Cdd:PLN03081  277 DARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMI 332
 
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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