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Conserved domains on  [gi|1002258299|ref|XP_015633480|]
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large ribosomal RNA subunit accumulation protein YCED homolog 1, chloroplastic isoform X1 [Oryza sativa Japonica Group]

Protein Classification

DUF177 domain-containing protein( domain architecture ID 10495743)

uncharacterized DUF177 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YceD pfam02620
Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally ...
 166-294 2.81e-19

Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally conserved in bacteria and plants except the Chlorophyceae algae. Thus far, mutantional analysis in bacteria have not established a function. In contrast, mutants have embryo lethal phenotypes in maize and Arabidopsis. In maize, the mutant embryos arrest at an early transition stage.It has been suggested that family members specifically affect 23S rRNA accumulation in plastids as well as bacteria.


:

Pssm-ID: 460623  Cd Length: 119  Bit Score: 81.65  E-value: 2.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002258299 166 VRTVITLGCYGCAEPAPQGIFANFSLLLTEGRVEEPDVVDLGtifEEEqtkapvltgsqedgddedidwddrLHFPAGEK 245
Cdd:pfam02620   5 VEGTVTLPCDRCLEPVELPLDVDFTELFVPEEEEAEEEELEE---EDE------------------------EEILYEGD 57

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002258299 246 EVDISKHIRDIIHLEITLDALCSPTCKG--LCVGCGENLNTSSCSCNTEKQ 294
Cdd:pfam02620  58 EIDLEELIEEELLLALPMKPLCSEDCKGemLCPVCGANLNEEPCDCEEEKV 108
 
Name Accession Description Interval E-value
YceD pfam02620
Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally ...
 166-294 2.81e-19

Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally conserved in bacteria and plants except the Chlorophyceae algae. Thus far, mutantional analysis in bacteria have not established a function. In contrast, mutants have embryo lethal phenotypes in maize and Arabidopsis. In maize, the mutant embryos arrest at an early transition stage.It has been suggested that family members specifically affect 23S rRNA accumulation in plastids as well as bacteria.


Pssm-ID: 460623  Cd Length: 119  Bit Score: 81.65  E-value: 2.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002258299 166 VRTVITLGCYGCAEPAPQGIFANFSLLLTEGRVEEPDVVDLGtifEEEqtkapvltgsqedgddedidwddrLHFPAGEK 245
Cdd:pfam02620   5 VEGTVTLPCDRCLEPVELPLDVDFTELFVPEEEEAEEEELEE---EDE------------------------EEILYEGD 57

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002258299 246 EVDISKHIRDIIHLEITLDALCSPTCKG--LCVGCGENLNTSSCSCNTEKQ 294
Cdd:pfam02620  58 EIDLEELIEEELLLALPMKPLCSEDCKGemLCPVCGANLNEEPCDCEEEKV 108
YceD COG1399
23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) ...
 136-293 1.81e-06

23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441009  Cd Length: 169  Bit Score: 47.26  E-value: 1.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002258299 136 PNLTGTKDETPVLVSLDVARRRGRLRLDGIVRTVITLGCYGCAEPAPQGIFANFSLLLTEGRVEEPDvvdlgtifEEEQt 215
Cdd:COG1399    31 ERLADLPALGPVRVDLRLEKVGGGVLLTGTVEGTVTLPCDRCLEPFEYPLDVEFEELFVFDEEEAEE--------EDEV- 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002258299 216 kapvltgsqedgddedidwddrlhFPAGEKEVDISKHIRDIIHLEITLDALCSPTCKGLCVgcGENLNTSSCSCNTEK 293
Cdd:COG1399   102 ------------------------ILLEGDEIDLEELIEEELLLALPMKPLCPEDCKGLCE--GANLNEGECGCEEEK 153
 
Name Accession Description Interval E-value
YceD pfam02620
Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally ...
 166-294 2.81e-19

Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally conserved in bacteria and plants except the Chlorophyceae algae. Thus far, mutantional analysis in bacteria have not established a function. In contrast, mutants have embryo lethal phenotypes in maize and Arabidopsis. In maize, the mutant embryos arrest at an early transition stage.It has been suggested that family members specifically affect 23S rRNA accumulation in plastids as well as bacteria.


Pssm-ID: 460623  Cd Length: 119  Bit Score: 81.65  E-value: 2.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002258299 166 VRTVITLGCYGCAEPAPQGIFANFSLLLTEGRVEEPDVVDLGtifEEEqtkapvltgsqedgddedidwddrLHFPAGEK 245
Cdd:pfam02620   5 VEGTVTLPCDRCLEPVELPLDVDFTELFVPEEEEAEEEELEE---EDE------------------------EEILYEGD 57

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002258299 246 EVDISKHIRDIIHLEITLDALCSPTCKG--LCVGCGENLNTSSCSCNTEKQ 294
Cdd:pfam02620  58 EIDLEELIEEELLLALPMKPLCSEDCKGemLCPVCGANLNEEPCDCEEEKV 108
YceD COG1399
23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) ...
 136-293 1.81e-06

23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441009  Cd Length: 169  Bit Score: 47.26  E-value: 1.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002258299 136 PNLTGTKDETPVLVSLDVARRRGRLRLDGIVRTVITLGCYGCAEPAPQGIFANFSLLLTEGRVEEPDvvdlgtifEEEQt 215
Cdd:COG1399    31 ERLADLPALGPVRVDLRLEKVGGGVLLTGTVEGTVTLPCDRCLEPFEYPLDVEFEELFVFDEEEAEE--------EDEV- 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002258299 216 kapvltgsqedgddedidwddrlhFPAGEKEVDISKHIRDIIHLEITLDALCSPTCKGLCVgcGENLNTSSCSCNTEK 293
Cdd:COG1399   102 ------------------------ILLEGDEIDLEELIEEELLLALPMKPLCPEDCKGLCE--GANLNEGECGCEEEK 153
 
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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