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Conserved domains on  [gi|492743122|ref|WP_005945285|]
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MULTISPECIES: rRNA maturation RNase YbeY [Phocaeicola]

Protein Classification

rRNA maturation RNAse YbeY( domain architecture ID 10001064)

rRNA maturation RNAse YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of 16S rRNA

Gene Symbol:  ybeY
Gene Ontology:  GO:0006364|GO:0004222|GO:0004521

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 13-138 8.82e-46

ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and biogenesis]; ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme is part of the Pathway/BioSystem: 16S rRNA modification


:

Pssm-ID: 440088  Cd Length: 144  Bit Score: 145.69  E-value: 8.82e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122  13 AIKKRETTEWIKKVAADYGK-RVGEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYCA----GNRLSGDLFISLDTVRT 87
Cdd:COG0319   12 ELDEALLERWLEAALEAEGLaEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDElpedGPPLLGDIVISVETAAR 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 492743122  88 NAEQFNQPYERELHRVIIHGILHLCGINDKGPGEREIMEAAENKALEMLSI 138
Cdd:COG0319   92 EAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGI 142
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 13-138 8.82e-46

ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and biogenesis]; ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440088  Cd Length: 144  Bit Score: 145.69  E-value: 8.82e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122  13 AIKKRETTEWIKKVAADYGK-RVGEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYCA----GNRLSGDLFISLDTVRT 87
Cdd:COG0319   12 ELDEALLERWLEAALEAEGLaEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDElpedGPPLLGDIVISVETAAR 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 492743122  88 NAEQFNQPYERELHRVIIHGILHLCGINDKGPGEREIMEAAENKALEMLSI 138
Cdd:COG0319   92 EAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGI 142
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 35-136 1.10e-34

rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrated metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and more recently it was shown that mutants have a ribosomal RNA processing defect. [Protein synthesis, Other]


Pssm-ID: 272871 [Multi-domain]  Cd Length: 110  Bit Score: 116.21  E-value: 1.10e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122   35 GEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYCAGNRLS-------GDLFISLDTVRTNAEQFNQPYERELHRVIIHG 107
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGgfpeevlGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80

                          90       100
                  ....*....|....*....|....*....
gi 492743122  108 ILHLCGINDKGPGEREIMEAAENKALEML 136
Cdd:TIGR00043  81 LLHLLGYDHETEDEEKEMFALEEEILALL 109
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 16-136 8.80e-28

Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices.


Pssm-ID: 460455  Cd Length: 125  Bit Score: 99.08  E-value: 8.80e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122   16 KRETTEWIKKVAADYG-KRVGEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYCAGNRLSGDLFISLDTVRTNAEQFNQ 94
Cdd:pfam02130   4 EKLIKLVLEAALDEEKvPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEPLGDIVISPEKAKEQAEEYGH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 492743122   95 PYERELHRVIIHGILHLCGINDKGPGEREIMEAAENKALEML 136
Cdd:pfam02130  84 SLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
PRK13963 PRK13963
rRNA maturation RNase YbeY;
15-136 2.17e-10

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 56.32  E-value: 2.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122  15 KKRETTEWIK-KVAADygkrvGEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYC--AGNRLSGDLFISLDTVRTNAEQ 91
Cdd:PRK13963 132 KRKLIAEWIEpALFAD-----AQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYAeePDGPVIGDLVLCCPVVEKEARE 206

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 492743122  92 FNQPYERELHRVIIHGILHLCGINDKGPGEREIMEAAENKALEML 136
Cdd:PRK13963 207 QGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKL 251
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 13-138 8.82e-46

ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and biogenesis]; ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440088  Cd Length: 144  Bit Score: 145.69  E-value: 8.82e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122  13 AIKKRETTEWIKKVAADYGK-RVGEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYCA----GNRLSGDLFISLDTVRT 87
Cdd:COG0319   12 ELDEALLERWLEAALEAEGLaEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDElpedGPPLLGDIVISVETAAR 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 492743122  88 NAEQFNQPYERELHRVIIHGILHLCGINDKGPGEREIMEAAENKALEMLSI 138
Cdd:COG0319   92 EAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGI 142
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 35-136 1.10e-34

rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrated metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and more recently it was shown that mutants have a ribosomal RNA processing defect. [Protein synthesis, Other]


Pssm-ID: 272871 [Multi-domain]  Cd Length: 110  Bit Score: 116.21  E-value: 1.10e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122   35 GEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYCAGNRLS-------GDLFISLDTVRTNAEQFNQPYERELHRVIIHG 107
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGgfpeevlGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80

                          90       100
                  ....*....|....*....|....*....
gi 492743122  108 ILHLCGINDKGPGEREIMEAAENKALEML 136
Cdd:TIGR00043  81 LLHLLGYDHETEDEEKEMFALEEEILALL 109
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 16-136 8.80e-28

Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices.


Pssm-ID: 460455  Cd Length: 125  Bit Score: 99.08  E-value: 8.80e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122   16 KRETTEWIKKVAADYG-KRVGEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYCAGNRLSGDLFISLDTVRTNAEQFNQ 94
Cdd:pfam02130   4 EKLIKLVLEAALDEEKvPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEPLGDIVISPEKAKEQAEEYGH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 492743122   95 PYERELHRVIIHGILHLCGINDKGPGEREIMEAAENKALEML 136
Cdd:pfam02130  84 SLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
PRK13963 PRK13963
rRNA maturation RNase YbeY;
15-136 2.17e-10

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 56.32  E-value: 2.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122  15 KKRETTEWIK-KVAADygkrvGEIAYIFCSDEKILEVNRQYLQHDYYTDIITFDYC--AGNRLSGDLFISLDTVRTNAEQ 91
Cdd:PRK13963 132 KRKLIAEWIEpALFAD-----AQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYAeePDGPVIGDLVLCCPVVEKEARE 206

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 492743122  92 FNQPYERELHRVIIHGILHLCGINDKGPGEREIMEAAENKALEML 136
Cdd:PRK13963 207 QGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKL 251
PLN02887 PLN02887
hydrolase family protein
 36-136 6.57e-07

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 47.18  E-value: 6.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492743122  36 EIAYIFCSDEKILEVNRQYLQHDYYTDIITFD-YCAGNRLS----GDLFISLDTVRTNAEQFNQPYERELHRVIIHGILH 110
Cdd:PLN02887 161 ELSVMLCNDDFIRKLNKEWRGEDHATDVLSMSqHVPGLKLPvlmlGDIVISVETAARQAEERGHTLLDEIRILVVHGLLH 240

                         90       100
                 ....*....|....*....|....*..
gi 492743122 111 LCGINDKGPGEREI-MEAAENKALEML 136
Cdd:PLN02887 241 LLGFDHEISNEAEAeMEKEEELLLKSL 267
 
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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