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Conserved domains on  [gi|609247995|ref|WP_024269526|]
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ribosome-associated translation inhibitor RaiA [Salinispira pacifica]

Protein Classification

HPF/RaiA family ribosome-associated protein( domain architecture ID 10003959)

HPF/RaiA family ribosome-associated protein similar to ribosome-associated translation inhibitor RaiA, a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site, and ribosome hibernation promotion factor (HPF), which is required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-98 5.06e-14

Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 61.72  E-value: 5.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995   2 RVDIKGVHYQITDVTRNFLESKLEKINYAEDYIVDLMFTLAKDHDAW-IAEVNVNFRwGVTAHLKEDTFNLHESIEKLVD 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRfKVEITLHVP-GPVLRAEAEAEDMYAAIDLAVD 79

                         90
                 ....*....|....*...
gi 609247995  81 RLDQKIRKEKEKVQDKHR 98
Cdd:COG1544   80 KLERQLRKYKEKLKDHRR 97
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-98 5.06e-14

Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441153  Cd Length: 101  Bit Score: 61.72  E-value: 5.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995   2 RVDIKGVHYQITDVTRNFLESKLEKINYAEDYIVDLMFTLAKDHDAW-IAEVNVNFRwGVTAHLKEDTFNLHESIEKLVD 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRfKVEITLHVP-GPVLRAEAEAEDMYAAIDLAVD 79

                         90
                 ....*....|....*...
gi 609247995  81 RLDQKIRKEKEKVQDKHR 98
Cdd:COG1544   80 KLERQLRKYKEKLKDHRR 97
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-93 6.62e-13

Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 modulation protein family and the S30AE family of ribosomal proteins which includes the light- repressed protein (lrtA).


Pssm-ID: 460569  Cd Length: 87  Bit Score: 58.67  E-value: 6.62e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995   3 VDIKGVHYQITDVTRNFLESKLEKInyaEDYIVDLMFTLaKDHDAWIAEVNVNFRWGVTAHLKEDTFNLHESIEKLVDRL 82
Cdd:pfam02482  1 INITGRNIEVTDALREYVEKKLEKL---EKYFISADVTL-SVEKRHKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVDKL 76

                         90
                 ....*....|.
gi 609247995  83 DQKIRKEKEKV 93
Cdd:pfam02482 77 ERQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-96 3.40e-08

ribosomal subunit interface protein; This model includes a small protein encoded by one of two genes, both downstream of the gene rpoN for sigma 54, whose deletion leads to increased expression from sigma 54-dependent promoters. It also includes the N-terminal half of a light-repressed protein LtrA of Synechococcus PCC 7002 and the N-terminal region (after removal of the transit peptide) of a larger plastid-specific ribosomal protein of spinach. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes. [Protein synthesis, Translation factors]


Pssm-ID: 129824 [Multi-domain]  Cd Length: 95  Bit Score: 46.94  E-value: 3.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995   1 MRVDIKGVHYQITDVTRNFLESKLEKINYAEDYIVDLMFTLAKDHDAWIAEVNVNFRWGVTaHLKEDTFNLHESIEKLVD 80
Cdd:TIGR00741  1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVI-RASAESEDMYAAIDLAID 79

                         90
                 ....*....|....*.
gi 609247995  81 RLDQKIRKEKEKVQDK 96
Cdd:TIGR00741 80 KLERQLRKLKEKRKEH 95
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-94 1.80e-05

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 39.89  E-value: 1.80e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995  1 MRVDIKGVHYQITDVTRNFLESKLEKINYAEDYIVDLMFTLAKDHDAWIAEVNVNFRWGvTAHLKEDTFNLHESIEKLVD 80
Cdd:PRK10470  1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGG-EIHASAEGQDMYAAIDGLID 79

                        90
                ....*....|....
gi 609247995 81 RLDQKIRKEKEKVQ 94
Cdd:PRK10470 80 KLARQLTKHKDKLK 93
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-98 5.06e-14

Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441153  Cd Length: 101  Bit Score: 61.72  E-value: 5.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995   2 RVDIKGVHYQITDVTRNFLESKLEKINYAEDYIVDLMFTLAKDHDAW-IAEVNVNFRwGVTAHLKEDTFNLHESIEKLVD 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRfKVEITLHVP-GPVLRAEAEAEDMYAAIDLAVD 79

                         90
                 ....*....|....*...
gi 609247995  81 RLDQKIRKEKEKVQDKHR 98
Cdd:COG1544   80 KLERQLRKYKEKLKDHRR 97
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-93 6.62e-13

Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 modulation protein family and the S30AE family of ribosomal proteins which includes the light- repressed protein (lrtA).


Pssm-ID: 460569  Cd Length: 87  Bit Score: 58.67  E-value: 6.62e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995   3 VDIKGVHYQITDVTRNFLESKLEKInyaEDYIVDLMFTLaKDHDAWIAEVNVNFRWGVTAHLKEDTFNLHESIEKLVDRL 82
Cdd:pfam02482  1 INITGRNIEVTDALREYVEKKLEKL---EKYFISADVTL-SVEKRHKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVDKL 76

                         90
                 ....*....|.
gi 609247995  83 DQKIRKEKEKV 93
Cdd:pfam02482 77 ERQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-96 3.40e-08

ribosomal subunit interface protein; This model includes a small protein encoded by one of two genes, both downstream of the gene rpoN for sigma 54, whose deletion leads to increased expression from sigma 54-dependent promoters. It also includes the N-terminal half of a light-repressed protein LtrA of Synechococcus PCC 7002 and the N-terminal region (after removal of the transit peptide) of a larger plastid-specific ribosomal protein of spinach. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes. [Protein synthesis, Translation factors]


Pssm-ID: 129824 [Multi-domain]  Cd Length: 95  Bit Score: 46.94  E-value: 3.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995   1 MRVDIKGVHYQITDVTRNFLESKLEKINYAEDYIVDLMFTLAKDHDAWIAEVNVNFRWGVTaHLKEDTFNLHESIEKLVD 80
Cdd:TIGR00741  1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVI-RASAESEDMYAAIDLAID 79

                         90
                 ....*....|....*.
gi 609247995  81 RLDQKIRKEKEKVQDK 96
Cdd:TIGR00741 80 KLERQLRKLKEKRKEH 95
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-94 1.80e-05

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 39.89  E-value: 1.80e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 609247995  1 MRVDIKGVHYQITDVTRNFLESKLEKINYAEDYIVDLMFTLAKDHDAWIAEVNVNFRWGvTAHLKEDTFNLHESIEKLVD 80
Cdd:PRK10470  1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGG-EIHASAEGQDMYAAIDGLID 79

                        90
                ....*....|....
gi 609247995 81 RLDQKIRKEKEKVQ 94
Cdd:PRK10470 80 KLARQLTKHKDKLK 93
 
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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