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Conserved domains on  [gi|1228174521|gb|OXY60519|]
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metal-binding heat shock protein [Salmonella enterica subsp. enterica serovar Enteritidis str. SHSE004]

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 ...
20-148 3.24e-63

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: 190.37  E-value: 3.24e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  20 DEAQFQRWLDGVIPQ--FQEEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPFEAPPGIEMPLLGDLIICRQVVEQEA 97
Cdd:COG0319    14 DEALLERWLEAALEAegLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLLGDIVISVETAAREA 93
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1228174521  98 QEQSKPLEAHWAHMVVHGSLHLLGYDHIDDDEAEEMESLETEIMLAMGYED 148
Cdd:COG0319    94 KEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
20-148 3.24e-63

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: 190.37  E-value: 3.24e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  20 DEAQFQRWLDGVIPQ--FQEEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPFEAPPGIEMPLLGDLIICRQVVEQEA 97
Cdd:COG0319    14 DEALLERWLEAALEAegLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLLGDIVISVETAAREA 93
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1228174521  98 QEQSKPLEAHWAHMVVHGSLHLLGYDHIDDDEAEEMESLETEIMLAMGYED 148
Cdd:COG0319    94 KEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
6-150 6.13e-56

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 176.12  E-value: 6.13e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521   6 LDLQ----LACENHAGLPDEAQFQRWLDgviPQFQEEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPF-EAPPGiem 80
Cdd:PRK13963  114 LTVQygdeIGGAQRKALPKRKLIAEWIE---PALFADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYaEEPDG--- 187
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  81 PLLGDLIICRQVVEQEAQEQSKPLEAHWAHMVVHGSLHLLGYDHIDDDEAEEMESLETEIMLAMGYEDPY 150
Cdd:PRK13963  188 PVIGDLVLCCPVVEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
21-144 1.37e-47

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: 150.31  E-value: 1.37e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  21 EAQFQRWLDGVI--PQFQEEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPFEAPPGIemplLGDLIICRQVVEQEAQ 98
Cdd:pfam02130   4 EKLIKLVLEAALdeEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----LGDIVISPEKAKEQAE 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1228174521  99 EQSKPLEAHWAHMVVHGSLHLLGYDHIDDDEAEEMESLETEIMLAM 144
Cdd:pfam02130  80 EYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
39-145 5.00e-45

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: 143.17  E-value: 5.00e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  39 AEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPFE---APPGIEMPLLGDLIICRQVVEQEAQEQSKPLEAHWAHMVVHG 115
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEeeePPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80
                          90       100       110
                  ....*....|....*....|....*....|
gi 1228174521 116 SLHLLGYDHIDDDEAEEMESLETEIMLAMG 145
Cdd:TIGR00043  81 LLHLLGYDHETEDEEKEMFALEEEILALLG 110
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
20-148 3.24e-63

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: 190.37  E-value: 3.24e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  20 DEAQFQRWLDGVIPQ--FQEEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPFEAPPGIEMPLLGDLIICRQVVEQEA 97
Cdd:COG0319    14 DEALLERWLEAALEAegLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLLGDIVISVETAAREA 93
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1228174521  98 QEQSKPLEAHWAHMVVHGSLHLLGYDHIDDDEAEEMESLETEIMLAMGYED 148
Cdd:COG0319    94 KEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
6-150 6.13e-56

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 176.12  E-value: 6.13e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521   6 LDLQ----LACENHAGLPDEAQFQRWLDgviPQFQEEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPF-EAPPGiem 80
Cdd:PRK13963  114 LTVQygdeIGGAQRKALPKRKLIAEWIE---PALFADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYaEEPDG--- 187
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  81 PLLGDLIICRQVVEQEAQEQSKPLEAHWAHMVVHGSLHLLGYDHIDDDEAEEMESLETEIMLAMGYEDPY 150
Cdd:PRK13963  188 PVIGDLVLCCPVVEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
21-144 1.37e-47

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: 150.31  E-value: 1.37e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  21 EAQFQRWLDGVI--PQFQEEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPFEAPPGIemplLGDLIICRQVVEQEAQ 98
Cdd:pfam02130   4 EKLIKLVLEAALdeEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----LGDIVISPEKAKEQAE 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1228174521  99 EQSKPLEAHWAHMVVHGSLHLLGYDHIDDDEAEEMESLETEIMLAM 144
Cdd:pfam02130  80 EYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
39-145 5.00e-45

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: 143.17  E-value: 5.00e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  39 AEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPFE---APPGIEMPLLGDLIICRQVVEQEAQEQSKPLEAHWAHMVVHG 115
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEeeePPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80
                          90       100       110
                  ....*....|....*....|....*....|
gi 1228174521 116 SLHLLGYDHIDDDEAEEMESLETEIMLAMG 145
Cdd:TIGR00043  81 LLHLLGYDHETEDEEKEMFALEEEILALLG 110
PLN02887 PLN02887
hydrolase family protein
37-147 8.44e-13

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 64.90  E-value: 8.44e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228174521  37 EEAEVTIRLVDEAESHNLNLTYRGKDKPTNVLSFPfEAPPGIEMP--LLGDLIICRQVVEQEAQEQSKPLEAHWAHMVVH 114
Cdd:PLN02887  158 DSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMS-QHVPGLKLPvlMLGDIVISVETAARQAEERGHTLLDEIRILVVH 236
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1228174521 115 GSLHLLGYDHIDDDEAE-EMESLETEIMLAMGYE 147
Cdd:PLN02887  237 GLLHLLGFDHEISNEAEaEMEKEEELLLKSLGWK 270
 
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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