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Conserved domains on  [gi|1823214496|ref|WP_166297727|]
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ribosome assembly RNA-binding protein YhbY [Lysobacter sp. HDW10]

Protein Classification

YhbY family RNA-binding protein( domain architecture ID 10003947)

YhbY family RNA-binding protein similar to ribosome assembly RNA-binding protein YhbY that adopts a fold resembling that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YhbY COG1534
RNA-binding protein YhbY [Translation, ribosomal structure and biogenesis];
4-98 1.02e-45

RNA-binding protein YhbY [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 441143  Cd Length: 95  Bit Score: 142.15  E-value: 1.02e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   4 TLSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHT 83
Cdd:COG1534     1 MLTGKQRRYLRALAHHLKPVVQIGKNGLTEAVLAEIDRALEAHELIKVKVLQNDREDRKEIAEEIAEATGAELVQVIGKT 80

                          90
                  ....*....|....*
gi 1823214496  84 AVLYRPSKDKRTIVL 98
Cdd:COG1534    81 LVLYRPSPEKKKIEL 95
 
Name Accession Description Interval E-value
YhbY COG1534
RNA-binding protein YhbY [Translation, ribosomal structure and biogenesis];
4-98 1.02e-45

RNA-binding protein YhbY [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441143  Cd Length: 95  Bit Score: 142.15  E-value: 1.02e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   4 TLSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHT 83
Cdd:COG1534     1 MLTGKQRRYLRALAHHLKPVVQIGKNGLTEAVLAEIDRALEAHELIKVKVLQNDREDRKEIAEEIAEATGAELVQVIGKT 80

                          90
                  ....*....|....*
gi 1823214496  84 AVLYRPSKDKRTIVL 98
Cdd:COG1534    81 LVLYRPSPEKKKIEL 95
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 5-88 1.83e-34

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 113.33  E-value: 1.83e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496    5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 1823214496   85 VLYR 88
Cdd:smart01103  81 VLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 5-88 1.41e-33

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 110.95  E-value: 1.41e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQVIGRTI 80


                  ....
gi 1823214496  85 VLYR 88
Cdd:pfam01985  81 VLYR 84
RNA_bind_YhbY TIGR00253
putative RNA-binding protein, YhbY family; A combination of crystal structure, molecular ...
 5-99 6.89e-29

putative RNA-binding protein, YhbY family; A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins. [Unknown function, General]


Pssm-ID: 129355  Cd Length: 95  Bit Score: 99.59  E-value: 6.89e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:TIGR00253   1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80

                          90
                  ....*....|....*
gi 1823214496  85 VLYRPSKDKRTIVLP 99
Cdd:TIGR00253  81 VLYRPTKERKIIELP 95
PRK10343 PRK10343
ribosome assembly RNA-binding protein YhbY;
5-100 3.16e-25

ribosome assembly RNA-binding protein YhbY;


Pssm-ID: 182393  Cd Length: 97  Bit Score: 90.56  E-value: 3.16e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:PRK10343    3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTL 82

                          90
                  ....*....|....*.
gi 1823214496  85 VLYRPSKDkRTIVLPR 100
Cdd:PRK10343   83 VLYRPTKE-RKISLPR 97
 
Name Accession Description Interval E-value
YhbY COG1534
RNA-binding protein YhbY [Translation, ribosomal structure and biogenesis];
4-98 1.02e-45

RNA-binding protein YhbY [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441143  Cd Length: 95  Bit Score: 142.15  E-value: 1.02e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   4 TLSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHT 83
Cdd:COG1534     1 MLTGKQRRYLRALAHHLKPVVQIGKNGLTEAVLAEIDRALEAHELIKVKVLQNDREDRKEIAEEIAEATGAELVQVIGKT 80

                          90
                  ....*....|....*
gi 1823214496  84 AVLYRPSKDKRTIVL 98
Cdd:COG1534    81 LVLYRPSPEKKKIEL 95
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 5-88 1.83e-34

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 113.33  E-value: 1.83e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496    5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 1823214496   85 VLYR 88
Cdd:smart01103  81 VLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 5-88 1.41e-33

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 110.95  E-value: 1.41e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQVIGRTI 80


                  ....
gi 1823214496  85 VLYR 88
Cdd:pfam01985  81 VLYR 84
RNA_bind_YhbY TIGR00253
putative RNA-binding protein, YhbY family; A combination of crystal structure, molecular ...
 5-99 6.89e-29

putative RNA-binding protein, YhbY family; A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins. [Unknown function, General]


Pssm-ID: 129355  Cd Length: 95  Bit Score: 99.59  E-value: 6.89e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:TIGR00253   1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80

                          90
                  ....*....|....*
gi 1823214496  85 VLYRPSKDKRTIVLP 99
Cdd:TIGR00253  81 VLYRPTKERKIIELP 95
PRK10343 PRK10343
ribosome assembly RNA-binding protein YhbY;
5-100 3.16e-25

ribosome assembly RNA-binding protein YhbY;


Pssm-ID: 182393  Cd Length: 97  Bit Score: 90.56  E-value: 3.16e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1823214496   5 LSNSQIRFLRGMAHDLKPLMQIGNKGLTPAFSAELDAALEHHELVKVKVGGDDREARDQVIHAMADALRAHLVQRIGHTA 84
Cdd:PRK10343    3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTL 82

                          90
                  ....*....|....*.
gi 1823214496  85 VLYRPSKDkRTIVLPR 100
Cdd:PRK10343   83 VLYRPTKE-RKISLPR 97
 
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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