NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2486357049|ref|WP_279073309|]
View 

DUF177 domain-containing protein, partial [Microbacterium lacticum]

Protein Classification

YceD family protein( domain architecture ID 10003643)

YceD family protein is an uncharacterized DUF177 domain-containing protein similar to the large ribosomal RNA subunit accumulation protein YceD

PubMed:  27574185

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YceD COG1399
23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) ...
 1-135 1.04e-31

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


:

Pssm-ID: 441009  Cd Length: 169  Bit Score: 110.43  E-value: 1.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486357049   1 MNGPFSFPVRDILhrSGDMREFEIDTPAPEkwGEGLVSVAEGEPVEASVRLEAVHEGILVTADVATRYTGVCGRCLTDVA 80
Cdd:COG1399     2 SKLKMKIDLAELK--AGKGLEFEGEVDLAE--LERLADLPALGPVRVDLRLEKVGGGVLLTGTVEGTVTLPCDRCLEPFE 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2486357049  81 EPVEVEIQELFGYSGDEAAD----FEVQDDHVDLETLVRDSIVLSLPFQPVCQPDCPGL 135
Cdd:COG1399    78 YPLDVEFEELFVFDEEEAEEedevILLEGDEIDLEELIEEELLLALPMKPLCPEDCKGL 136
 
Name Accession Description Interval E-value
YceD COG1399
23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) ...
 1-135 1.04e-31

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


Pssm-ID: 441009  Cd Length: 169  Bit Score: 110.43  E-value: 1.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486357049   1 MNGPFSFPVRDILhrSGDMREFEIDTPAPEkwGEGLVSVAEGEPVEASVRLEAVHEGILVTADVATRYTGVCGRCLTDVA 80
Cdd:COG1399     2 SKLKMKIDLAELK--AGKGLEFEGEVDLAE--LERLADLPALGPVRVDLRLEKVGGGVLLTGTVEGTVTLPCDRCLEPFE 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2486357049  81 EPVEVEIQELFGYSGDEAAD----FEVQDDHVDLETLVRDSIVLSLPFQPVCQPDCPGL 135
Cdd:COG1399    78 YPLDVEFEELFVFDEEEAEEedevILLEGDEIDLEELIEEELLLALPMKPLCPEDCKGL 136
YceD pfam02620
Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally ...
 60-134 2.66e-17

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: 72.02  E-value: 2.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486357049  60 VTADVATRYTGVCGRCLTDVAEPVEVEIQELFGYSGDEAADFE----------VQDDHVDLETLVRDSIVLSLPFQPVCQ 129
Cdd:pfam02620   1 LDGHVEGTVTLPCDRCLEPVELPLDVDFTELFVPEEEEAEEEEleeedeeeilYEGDEIDLEELIEEELLLALPMKPLCS 80


                  ....*
gi 2486357049 130 PDCPG 134
Cdd:pfam02620  81 EDCKG 85
 
Name Accession Description Interval E-value
YceD COG1399
23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) ...
 1-135 1.04e-31

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


Pssm-ID: 441009  Cd Length: 169  Bit Score: 110.43  E-value: 1.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486357049   1 MNGPFSFPVRDILhrSGDMREFEIDTPAPEkwGEGLVSVAEGEPVEASVRLEAVHEGILVTADVATRYTGVCGRCLTDVA 80
Cdd:COG1399     2 SKLKMKIDLAELK--AGKGLEFEGEVDLAE--LERLADLPALGPVRVDLRLEKVGGGVLLTGTVEGTVTLPCDRCLEPFE 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2486357049  81 EPVEVEIQELFGYSGDEAAD----FEVQDDHVDLETLVRDSIVLSLPFQPVCQPDCPGL 135
Cdd:COG1399    78 YPLDVEFEELFVFDEEEAEEedevILLEGDEIDLEELIEEELLLALPMKPLCPEDCKGL 136
YceD pfam02620
Large ribosomal RNA subunit accumulation protein YceD; This family is nearly universally ...
 60-134 2.66e-17

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: 72.02  E-value: 2.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2486357049  60 VTADVATRYTGVCGRCLTDVAEPVEVEIQELFGYSGDEAADFE----------VQDDHVDLETLVRDSIVLSLPFQPVCQ 129
Cdd:pfam02620   1 LDGHVEGTVTLPCDRCLEPVELPLDVDFTELFVPEEEEAEEEEleeedeeeilYEGDEIDLEELIEEELLLALPMKPLCS 80


                  ....*
gi 2486357049 130 PDCPG 134
Cdd:pfam02620  81 EDCKG 85
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH