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Conserved domains on  [gi|2467961990|gb|WEV61385|]
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ribosome-associated translation inhibitor RaiA [Streptococcaceae bacterium ESL0729]

Protein Classification

HPF/RaiA family ribosome-associated protein( domain architecture ID 10787768)

HPF/RaiA family ribosome-associated protein such as Bacillus subtilis 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 ...
 3-99 1.84e-34

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 117.19  E-value: 1.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   3 FNIRGENSEVTTALREYVENKIGKIEKYFKDSEDftAHVNLKVYSNKNAKVEVTIPMKHLTLRAEDTSQDMYGSIDLVVD 82
Cdd:COG1544     2 INITGRNVEVTDALREYVEEKLEKLEKYFDRIIS--ADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVD 79

                          90
                  ....*....|....*..
gi 2467961990  83 KLERQIRKYKTKTNRRK 99
Cdd:COG1544    80 KLERQLRKYKEKLKDHR 96
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 126-178 7.38e-27

Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the C-terminus of proteins containing pfam02482.


:

Pssm-ID: 435275  Cd Length: 54  Bit Score: 96.32  E-value: 7.38e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2467961990 126 KIVRTKEVGLKPMDAEEAVLQMEMLGHDFYLFTDADTDSASIVYRREDGDYGL 178
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-99 1.84e-34

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 117.19  E-value: 1.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   3 FNIRGENSEVTTALREYVENKIGKIEKYFKDSEDftAHVNLKVYSNKNAKVEVTIPMKHLTLRAEDTSQDMYGSIDLVVD 82
Cdd:COG1544     2 INITGRNVEVTDALREYVEEKLEKLEKYFDRIIS--ADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVD 79

                          90
                  ....*....|....*..
gi 2467961990  83 KLERQIRKYKTKTNRRK 99
Cdd:COG1544    80 KLERQLRKYKEKLKDHR 96
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-94 8.73e-33

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: 112.61  E-value: 8.73e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   3 FNIRGENSEVTTALREYVENKIGKIEKYFKDseDFTAHVNLKVYSN--KNAKVEVTIPMKHLTLRAEDTSQDMYGSIDLV 80
Cdd:cd00552     2 INITGRNIEVTDALREYVEEKLEKLEKYFDR--IISVDVVLSVEKNhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLA 79

                          90
                  ....*....|....
gi 2467961990  81 VDKLERQIRKYKTK 94
Cdd:cd00552    80 VDKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-98 4.21e-30

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: 105.87  E-value: 4.21e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   1 MSFNIRGENSEVTTALREYVENKIGKIEKYFKDSEDFTAHVNLKVYsnkNAKVEVTIPMKHLTLRAEDTSQDMYGSIDLV 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN---RFKVEATLYVNGGVIRASAESEDMYAAIDLA 77

                          90
                  ....*....|....*...
gi 2467961990  81 VDKLERQIRKYKTKTNRR 98
Cdd:TIGR00741  78 IDKLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-94 1.51e-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: 99.12  E-value: 1.51e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   3 FNIRGENSEVTTALREYVENKIGKIEKYFKDsedftAHVNLKVysNKNAKVEVTI-PMKHLTLRAEDTSQDMYGSIDLVV 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFIS-----ADVTLSV--EKRHKVEVTIrLVPGVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|...
gi 2467961990  82 DKLERQIRKYKTK 94
Cdd:pfam02482  74 DKLERQLRKYKEK 86
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 126-178 7.38e-27

Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the C-terminus of proteins containing pfam02482.


Pssm-ID: 435275  Cd Length: 54  Bit Score: 96.32  E-value: 7.38e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2467961990 126 KIVRTKEVGLKPMDAEEAVLQMEMLGHDFYLFTDADTDSASIVYRREDGDYGL 178
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-94 5.70e-14

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 64.16  E-value: 5.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   1 MSFNIRGENSEVTTALREYVENKIGKIEKYFkdseDFTAHVNLKVYSNKNAKV-EVTIPMKHLTLRAEDTSQDMYGSIDL 79
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYF----DRINQVYVVLKVEKVTHIsDATLHVNGGEIHASAEGQDMYAAIDG 76

                          90
                  ....*....|....*
gi 2467961990  80 VVDKLERQIRKYKTK 94
Cdd:PRK10470   77 LIDKLARQLTKHKDK 91
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-99 1.84e-34

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 117.19  E-value: 1.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   3 FNIRGENSEVTTALREYVENKIGKIEKYFKDSEDftAHVNLKVYSNKNAKVEVTIPMKHLTLRAEDTSQDMYGSIDLVVD 82
Cdd:COG1544     2 INITGRNVEVTDALREYVEEKLEKLEKYFDRIIS--ADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVD 79

                          90
                  ....*....|....*..
gi 2467961990  83 KLERQIRKYKTKTNRRK 99
Cdd:COG1544    80 KLERQLRKYKEKLKDHR 96
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-94 8.73e-33

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: 112.61  E-value: 8.73e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   3 FNIRGENSEVTTALREYVENKIGKIEKYFKDseDFTAHVNLKVYSN--KNAKVEVTIPMKHLTLRAEDTSQDMYGSIDLV 80
Cdd:cd00552     2 INITGRNIEVTDALREYVEEKLEKLEKYFDR--IISVDVVLSVEKNhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLA 79

                          90
                  ....*....|....
gi 2467961990  81 VDKLERQIRKYKTK 94
Cdd:cd00552    80 VDKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-98 4.21e-30

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: 105.87  E-value: 4.21e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   1 MSFNIRGENSEVTTALREYVENKIGKIEKYFKDSEDFTAHVNLKVYsnkNAKVEVTIPMKHLTLRAEDTSQDMYGSIDLV 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN---RFKVEATLYVNGGVIRASAESEDMYAAIDLA 77

                          90
                  ....*....|....*...
gi 2467961990  81 VDKLERQIRKYKTKTNRR 98
Cdd:TIGR00741  78 IDKLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-94 1.51e-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: 99.12  E-value: 1.51e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   3 FNIRGENSEVTTALREYVENKIGKIEKYFKDsedftAHVNLKVysNKNAKVEVTI-PMKHLTLRAEDTSQDMYGSIDLVV 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFIS-----ADVTLSV--EKRHKVEVTIrLVPGVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|...
gi 2467961990  82 DKLERQIRKYKTK 94
Cdd:pfam02482  74 DKLERQLRKYKEK 86
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 126-178 7.38e-27

Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the C-terminus of proteins containing pfam02482.


Pssm-ID: 435275  Cd Length: 54  Bit Score: 96.32  E-value: 7.38e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2467961990 126 KIVRTKEVGLKPMDAEEAVLQMEMLGHDFYLFTDADTDSASIVYRREDGDYGL 178
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-94 5.70e-14

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 64.16  E-value: 5.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   1 MSFNIRGENSEVTTALREYVENKIGKIEKYFkdseDFTAHVNLKVYSNKNAKV-EVTIPMKHLTLRAEDTSQDMYGSIDL 79
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYF----DRINQVYVVLKVEKVTHIsDATLHVNGGEIHASAEGQDMYAAIDG 76

                          90
                  ....*....|....*
gi 2467961990  80 VVDKLERQIRKYKTK 94
Cdd:PRK10470   77 LIDKLARQLTKHKDK 91
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-122 7.07e-11

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 56.64  E-value: 7.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2467961990   1 MSFNIRGENSEVTTALREYVENKIGKIEKYfkDSEDFTAHVNL-KVYSNKNAKVEVTIPMKHLTLRAEdtSQDMYGSIDL 79
Cdd:PRK10324    1 MTMNITSKQMEITPAIRQHVADRLAKLEKW--QTHLINPHIILsKEPQGFVADATINTPNGVLVASGK--HEDMYTAINE 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2467961990  80 VVDKLERQIRKYKTKTNRRKNVKGLKDlpledfSDFTISEEEE 122
Cdd:PRK10324   77 LINKLERQLNKLQHKGEARRAATSVKD------ANFVEEVEEE 113
 
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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