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Conserved domains on  [gi|1376744931|gb|PTP39915|]
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ribosomal subunit interface protein [Vibrio splendidus]

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 1.79e-29

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 101.78  E-value: 1.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   2 KMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNKKKKFEAVLTVPKGQLVASSIHDDLYVAINEVEQK 81
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                          90       100
                  ....*....|....*....|
gi 1376744931  82 LERQLNKLRHKPEARRAEKP 101
Cdd:COG1544    81 LERQLRKYKEKLKDHRRRRA 100
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-101 1.79e-29

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 101.78  E-value: 1.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   2 KMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNKKKKFEAVLTVPKGQLVASSIHDDLYVAINEVEQK 81
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                          90       100
                  ....*....|....*....|
gi 1376744931  82 LERQLNKLRHKPEARRAEKP 101
Cdd:COG1544    81 LERQLRKYKEKLKDHRRRRA 100
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-98 1.91e-29

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 102.10  E-value: 1.91e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   1 MKMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPnKKKKFEAVLTVPKGQLVASSIHDDLYVAINEVEQ 80
Cdd:PRK10324    1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEP-QGFVADATINTPNGVLVASGKHEDMYTAINELIN 79

                          90
                  ....*....|....*...
gi 1376744931  81 KLERQLNKLRHKPEARRA 98
Cdd:PRK10324   80 KLERQLNKLQHKGEARRA 97
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-92 4.28e-29

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: 100.28  E-value: 4.28e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   2 KMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNKKKKF--EAVLTVPKGQLVASSIHDDLYVAINEVE 79
Cdd:cd00552     1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFkvEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                          90
                  ....*....|...
gi 1376744931  80 QKLERQLNKLRHK 92
Cdd:cd00552    81 DKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-96 4.20e-27

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: 95.47  E-value: 4.20e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   1 MKMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNkKKKFEAVLTVPKGQLVASSIHDDLYVAINEVEQ 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN-RFKVEATLYVNGGVIRASAESEDMYAAIDLAID 79

                          90
                  ....*....|....*.
gi 1376744931  81 KLERQLNKLRHKPEAR 96
Cdd:TIGR00741  80 KLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-92 6.21e-20

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: 77.16  E-value: 6.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   4 NITGKNIDITSAIRDHIESKFKKLDKWqvdIIGCQASFSEEpnKKKKFEAVLTVPKGQLV-ASSIHDDLYVAINEVEQKL 82
Cdd:pfam02482   2 NITGRNIEVTDALREYVEKKLEKLEKY---FISADVTLSVE--KRHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|
gi 1376744931  83 ERQLNKLRHK 92
Cdd:pfam02482  77 ERQLRKYKEK 86
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-101 1.79e-29

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 101.78  E-value: 1.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   2 KMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNKKKKFEAVLTVPKGQLVASSIHDDLYVAINEVEQK 81
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                          90       100
                  ....*....|....*....|
gi 1376744931  82 LERQLNKLRHKPEARRAEKP 101
Cdd:COG1544    81 LERQLRKYKEKLKDHRRRRA 100
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-98 1.91e-29

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 102.10  E-value: 1.91e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   1 MKMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPnKKKKFEAVLTVPKGQLVASSIHDDLYVAINEVEQ 80
Cdd:PRK10324    1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEP-QGFVADATINTPNGVLVASGKHEDMYTAINELIN 79

                          90
                  ....*....|....*...
gi 1376744931  81 KLERQLNKLRHKPEARRA 98
Cdd:PRK10324   80 KLERQLNKLQHKGEARRA 97
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-92 4.28e-29

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: 100.28  E-value: 4.28e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   2 KMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNKKKKF--EAVLTVPKGQLVASSIHDDLYVAINEVE 79
Cdd:cd00552     1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFkvEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                          90
                  ....*....|...
gi 1376744931  80 QKLERQLNKLRHK 92
Cdd:cd00552    81 DKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-96 4.20e-27

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: 95.47  E-value: 4.20e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   1 MKMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNkKKKFEAVLTVPKGQLVASSIHDDLYVAINEVEQ 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN-RFKVEATLYVNGGVIRASAESEDMYAAIDLAID 79

                          90
                  ....*....|....*.
gi 1376744931  81 KLERQLNKLRHKPEAR 96
Cdd:TIGR00741  80 KLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-92 6.21e-20

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: 77.16  E-value: 6.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   4 NITGKNIDITSAIRDHIESKFKKLDKWqvdIIGCQASFSEEpnKKKKFEAVLTVPKGQLV-ASSIHDDLYVAINEVEQKL 82
Cdd:pfam02482   2 NITGRNIEVTDALREYVEKKLEKLEKY---FISADVTLSVE--KRHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|
gi 1376744931  83 ERQLNKLRHK 92
Cdd:pfam02482  77 ERQLRKYKEK 86
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-92 7.57e-13

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 59.15  E-value: 7.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1376744931   1 MKMNITGKNIDITSAIRDHIESKFKKLDKWQVDIIGCQASFSEEPNKKKKfEAVLTVPKGQLVASSIHDDLYVAINEVEQ 80
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHIS-DATLHVNGGEIHASAEGQDMYAAIDGLID 79

                          90
                  ....*....|..
gi 1376744931  81 KLERQLNKLRHK 92
Cdd:PRK10470   80 KLARQLTKHKDK 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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