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Conserved domains on  [gi|1596946263|gb|TDW02146|]
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sigma 54 modulation protein /SSU ribosomal protein S30P [Vibrio crassostreae]

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 ...
 2-101 1.52e-17

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 71.74  E-value: 1.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   2 KINVQTHHVSINDDSRKDIEGKFEKISNHFPSLISCDIIITKEHSQHQ-VEVFTNYEGVRVNAKATDDVMYPAIASALKK 80
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRFkVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                          90       100
                  ....*....|....*....|.
gi 1596946263  81 LEAGLSNRKGQLKADLHEKPT 101
Cdd:COG1544    81 LERQLRKYKEKLKDHRRRRAP 101
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-101 1.52e-17

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 71.74  E-value: 1.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   2 KINVQTHHVSINDDSRKDIEGKFEKISNHFPSLISCDIIITKEHSQHQ-VEVFTNYEGVRVNAKATDDVMYPAIASALKK 80
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRFkVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                          90       100
                  ....*....|....*....|.
gi 1596946263  81 LEAGLSNRKGQLKADLHEKPT 101
Cdd:COG1544    81 LERQLRKYKEKLKDHRRRRAP 101
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-97 1.27e-12

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: 58.88  E-value: 1.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   1 MKINVQTHHVSINDDSRKDIEGKFEKISNHFPSLISCDIIITKEHSQHQVEVFTNYEGVRVNAKATDDVMYPAIASALKK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*..
gi 1596946263  81 LEAGLsnRKGQLKADLH 97
Cdd:TIGR00741  81 LERQL--RKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-92 5.45e-11

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: 54.43  E-value: 5.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   3 INVQTHHVSINDDSRKDIEGKFEKISNHFpslISCDIIITKEHSqHQVEV-FTNYEGVRVNAKATDDVMYPAIASALKKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYF---ISADVTLSVEKR-HKVEVtIRLVPGVVLRAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|.
gi 1596946263  82 EAGLSNRKGQL 92
Cdd:pfam02482  77 ERQLRKYKEKL 87
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-93 9.72e-08

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 46.44  E-value: 9.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   1 MKINVQTHHVSINDDSRKDIEGKFEKISNHFPSLISCDIIITKEHSQHQVEVFTNYEGVRVNAKATDDVMYPAIASALKK 80
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                          90
                  ....*....|...
gi 1596946263  81 LEAGLSNRKGQLK 93
Cdd:PRK10470   81 LARQLTKHKDKLK 93
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-101 1.52e-17

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 71.74  E-value: 1.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   2 KINVQTHHVSINDDSRKDIEGKFEKISNHFPSLISCDIIITKEHSQHQ-VEVFTNYEGVRVNAKATDDVMYPAIASALKK 80
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRFkVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                          90       100
                  ....*....|....*....|.
gi 1596946263  81 LEAGLSNRKGQLKADLHEKPT 101
Cdd:COG1544    81 LERQLRKYKEKLKDHRRRRAP 101
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-97 1.27e-12

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: 58.88  E-value: 1.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   1 MKINVQTHHVSINDDSRKDIEGKFEKISNHFPSLISCDIIITKEHSQHQVEVFTNYEGVRVNAKATDDVMYPAIASALKK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*..
gi 1596946263  81 LEAGLsnRKGQLKADLH 97
Cdd:TIGR00741  81 LERQL--RKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-92 5.45e-11

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: 54.43  E-value: 5.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   3 INVQTHHVSINDDSRKDIEGKFEKISNHFpslISCDIIITKEHSqHQVEV-FTNYEGVRVNAKATDDVMYPAIASALKKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYF---ISADVTLSVEKR-HKVEVtIRLVPGVVLRAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|.
gi 1596946263  82 EAGLSNRKGQL 92
Cdd:pfam02482  77 ERQLRKYKEKL 87
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-93 9.72e-08

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 46.44  E-value: 9.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946263   1 MKINVQTHHVSINDDSRKDIEGKFEKISNHFPSLISCDIIITKEHSQHQVEVFTNYEGVRVNAKATDDVMYPAIASALKK 80
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                          90
                  ....*....|...
gi 1596946263  81 LEAGLSNRKGQLK 93
Cdd:PRK10470   81 LARQLTKHKDKLK 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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