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Conserved domains on  [gi|640581572|ref|WP_025011763|]
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MULTISPECIES: ribosome hibernation promoting factor [Shewanella]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RaiA super family cl00250
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 1-95 2.03e-39

RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).


The actual alignment was detected with superfamily member PRK10470:

Pssm-ID: 469687  Cd Length: 95  Bit Score: 126.18  E-value: 2.03e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572  1 MQINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQQIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:PRK10470  1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                        90
                ....*....|....*
gi 640581572 81 LDRQVIKHKEKLTKH 95
Cdd:PRK10470 81 LARQLTKHKDKLKQH 95
 
Name Accession Description Interval E-value
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-95 2.03e-39

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 126.18  E-value: 2.03e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572  1 MQINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQQIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:PRK10470  1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                        90
                ....*....|....*
gi 640581572 81 LDRQVIKHKEKLTKH 95
Cdd:PRK10470 81 LARQLTKHKDKLKQH 95
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-95 2.35e-36

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 118.35  E-value: 2.35e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572   2 QINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQ-QIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                         90
                 ....*....|....*
gi 640581572  81 LDRQVIKHKEKLTKH 95
Cdd:COG1544   81 LERQLRKYKEKLKDH 95
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-91 1.47e-34

RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).


Pssm-ID: 238308  Cd Length: 93  Bit Score: 113.76  E-value: 1.47e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572  2 QINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQK---LQQIAEAKIHLTGGEVYATSEHADMYAAIDVLI 78
Cdd:cd00552   1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                        90
                ....*....|...
gi 640581572 79 DKLDRQVIKHKEK 91
Cdd:cd00552  81 DKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 6.49e-34

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: 112.04  E-value: 6.49e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572   1 MQINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQQIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:TIGR00741  1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                         90
                 ....*....|....*
gi 640581572  81 LDRQVIKHKEKLTKH 95
Cdd:TIGR00741 81 LERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-92 1.78e-27

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: 95.65  E-value: 1.78e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572   3 INLTGHHIEITDSLRDYVESKFSKLERHFeqiNNVHVVLNVQKlQQIAEAKIHLTGGEVY-ATSEHADMYAAIDVLIDKL 81
Cdd:pfam02482  1 INITGRNIEVTDALREYVEKKLEKLEKYF---ISADVTLSVEK-RHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKL 76

                         90
                 ....*....|.
gi 640581572  82 DRQVIKHKEKL 92
Cdd:pfam02482 77 ERQLRKYKEKL 87
 
Name Accession Description Interval E-value
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-95 2.03e-39

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 126.18  E-value: 2.03e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572  1 MQINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQQIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:PRK10470  1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                        90
                ....*....|....*
gi 640581572 81 LDRQVIKHKEKLTKH 95
Cdd:PRK10470 81 LARQLTKHKDKLKQH 95
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-95 2.35e-36

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 118.35  E-value: 2.35e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572   2 QINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQ-QIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                         90
                 ....*....|....*
gi 640581572  81 LDRQVIKHKEKLTKH 95
Cdd:COG1544   81 LERQLRKYKEKLKDH 95
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-91 1.47e-34

RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).


Pssm-ID: 238308  Cd Length: 93  Bit Score: 113.76  E-value: 1.47e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572  2 QINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQK---LQQIAEAKIHLTGGEVYATSEHADMYAAIDVLI 78
Cdd:cd00552   1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                        90
                ....*....|...
gi 640581572 79 DKLDRQVIKHKEK 91
Cdd:cd00552  81 DKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 6.49e-34

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: 112.04  E-value: 6.49e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572   1 MQINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQQIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:TIGR00741  1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                         90
                 ....*....|....*
gi 640581572  81 LDRQVIKHKEKLTKH 95
Cdd:TIGR00741 81 LERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-92 1.78e-27

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: 95.65  E-value: 1.78e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572   3 INLTGHHIEITDSLRDYVESKFSKLERHFeqiNNVHVVLNVQKlQQIAEAKIHLTGGEVY-ATSEHADMYAAIDVLIDKL 81
Cdd:pfam02482  1 INITGRNIEVTDALREYVEKKLEKLEKYF---ISADVTLSVEK-RHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKL 76

                         90
                 ....*....|.
gi 640581572  82 DRQVIKHKEKL 92
Cdd:pfam02482 77 ERQLRKYKEKL 87
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-91 2.00e-15

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 65.89  E-value: 2.00e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640581572   1 MQINLTGHHIEITDSLRDYVESKFSKLERHFEQINNVHVVLNVQKLQQIAEAKIHLTGGEVYATSEHADMYAAIDVLIDK 80
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                         90
                 ....*....|.
gi 640581572  81 LDRQVIKHKEK 91
Cdd:PRK10324  81 LERQLNKLQHK 91
 
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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