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Conserved domains on  [gi|38683855|ref|NP_060422|]
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small ribosomal subunit protein mS39 precursor [Homo sapiens]

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 ...
 319-379 1.11e-06

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: 46.20  E-value: 1.11e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 38683855   319 LLRHMVAQKVKPNLQTFNTILkclrrfHVFARSP----ALQVLREMKAIGIEPSLATYHHIIRLF 379
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLL------HAYANVGnlklALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 254-300 4.79e-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: 43.89  E-value: 4.79e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 38683855   254 KNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEA 300
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 ...
 319-379 1.11e-06

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: 46.20  E-value: 1.11e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 38683855   319 LLRHMVAQKVKPNLQTFNTILkclrrfHVFARSP----ALQVLREMKAIGIEPSLATYHHIIRLF 379
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLL------HAYANVGnlklALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 254-300 4.79e-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: 43.89  E-value: 4.79e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 38683855   254 KNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEA 300
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03077 PLN03077
Protein ECB2; Provisional
 233-294 8.02e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 46.00  E-value: 8.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 38683855  233 QFGVTWraknNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTF 294
Cdd:PLN03077 133 RFGELV----HAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTF 190
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 272-378 1.35e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 42.17  E-value: 1.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38683855   272 YEQALNLYTELLNNRLHADVYTFNALIEAtVCAINEkfeekWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVFarS 351
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITA-LCEGNQ-----LPKALEVLSEMKRLGLCPNTITYSILLVASERKDDA--D 771

                          90       100
                  ....*....|....*....|....*..
gi 38683855   352 PALQVLREMKAIGIEPSLATYHHIIRL 378
Cdd:PLN03218  772 VGLDLLSQAKEDGIKPNLVMCRCITGL 798
 
Name Accession Description Interval E-value
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 319-379 1.11e-06

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: 46.20  E-value: 1.11e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 38683855   319 LLRHMVAQKVKPNLQTFNTILkclrrfHVFARSP----ALQVLREMKAIGIEPSLATYHHIIRLF 379
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLL------HAYANVGnlklALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 254-300 4.79e-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: 43.89  E-value: 4.79e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 38683855   254 KNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEA 300
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 ...
 290-342 3.59e-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: 41.58  E-value: 3.59e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 38683855   290 DVYTFNALIEAtvCAINEKFEEkwskILELLRHMVAQKVKPNLQTFNTILKCL 342
Cdd:pfam13041   2 DVVTYNTLING--YCKKGKVEE----AFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03077 PLN03077
Protein ECB2; Provisional
 233-294 8.02e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 46.00  E-value: 8.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 38683855  233 QFGVTWraknNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTF 294
Cdd:PLN03077 133 RFGELV----HAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTF 190
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 290-340 6.05e-04

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: 38.49  E-value: 6.05e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 38683855   290 DVYTFNALIEATVCAINEKFeekwskILELLRHMVAQKVKPNLQTFNTILK 340
Cdd:pfam13812  14 NVNTYTHLLHAYANVGNLKL------ALEIFERMKKKGIKPTLDTYNAILG 58
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 243-301 6.61e-04

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 42.94  E-value: 6.61e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 38683855  243 NAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEAT 301
Cdd:PLN03081 176 DARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRAS 234
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 272-378 1.35e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 42.17  E-value: 1.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38683855   272 YEQALNLYTELLNNRLHADVYTFNALIEAtVCAINEkfeekWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVFarS 351
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITA-LCEGNQ-----LPKALEVLSEMKRLGLCPNTITYSILLVASERKDDA--D 771

                          90       100
                  ....*....|....*....|....*..
gi 38683855   352 PALQVLREMKAIGIEPSLATYHHIIRL 378
Cdd:PLN03218  772 VGLDLLSQAKEDGIKPNLVMCRCITGL 798
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 243-298 2.23e-03

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 41.39  E-value: 2.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 38683855  243 NAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALI 298
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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