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Conserved domains on  [gi|446593847|ref|WP_000671193|]
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MULTISPECIES: ribosome hibernation-promoting factor, HPF/YfiA family [Bacillus]

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 ...
 2-101 1.62e-37

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 124.89  E-value: 1.62e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   2 KFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDK-QRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                         90       100
                 ....*....|....*....|.
gi 446593847  81 LERQIRKHKTKVNRKLREKGS 101
Cdd:COG1544   81 LERQLRKYKEKLKDHRRRRAP 101
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 124-176 1.69e-29

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: 102.87  E-value: 1.69e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446593847  124 ELVRTKRFDLKPMDVEEAILQMDMLGHNFFVFTNADTNETNVVYGRKDGKYGL 176
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-101 1.62e-37

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 124.89  E-value: 1.62e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   2 KFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDK-QRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                         90       100
                 ....*....|....*....|.
gi 446593847  81 LERQIRKHKTKVNRKLREKGS 101
Cdd:COG1544   81 LERQLRKYKEKLKDHRRRRAP 101
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-91 1.25e-36

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: 122.24  E-value: 1.25e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   2 KFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVY---SDKQRVEVTIPFTDLLLRAEETNSDMYAAIDLVV 78
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEknhGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 446593847  79 DKLERQIRKHKTK 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 1.97e-36

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: 121.67  E-value: 1.97e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847    1 MKFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDKQRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 446593847   81 LERQIRKHKTKVNRK 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 1.56e-30

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: 106.43  E-value: 1.56e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847    3 FNIRGENIEVTPALKEYVEKKLSKLERYFDtfpEIKVNLKVySDKQRVEVTIPFTD-LLLRAEETNSDMYAAIDLVVDKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFI---SADVTLSV-EKRHKVEVTIRLVPgVVLRAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|.
gi 446593847   82 ERQIRKHKTKV 92
Cdd:pfam02482  77 ERQLRKYKEKL 87
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 124-176 1.69e-29

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: 102.87  E-value: 1.69e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446593847  124 ELVRTKRFDLKPMDVEEAILQMDMLGHNFFVFTNADTNETNVVYGRKDGKYGL 176
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-94 6.41e-22

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 84.96  E-value: 6.41e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   1 MKFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDKQRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                         90
                 ....*....|....
gi 446593847  81 LERQIRKHKTKVNR 94
Cdd:PRK10470  81 LARQLTKHKDKLKQ 94
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-101 1.62e-37

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 124.89  E-value: 1.62e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   2 KFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDK-QRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                         90       100
                 ....*....|....*....|.
gi 446593847  81 LERQIRKHKTKVNRKLREKGS 101
Cdd:COG1544   81 LERQLRKYKEKLKDHRRRRAP 101
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-91 1.25e-36

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: 122.24  E-value: 1.25e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   2 KFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVY---SDKQRVEVTIPFTDLLLRAEETNSDMYAAIDLVV 78
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEknhGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 446593847  79 DKLERQIRKHKTK 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 1.97e-36

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: 121.67  E-value: 1.97e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847    1 MKFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDKQRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 446593847   81 LERQIRKHKTKVNRK 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 1.56e-30

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: 106.43  E-value: 1.56e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847    3 FNIRGENIEVTPALKEYVEKKLSKLERYFDtfpEIKVNLKVySDKQRVEVTIPFTD-LLLRAEETNSDMYAAIDLVVDKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFI---SADVTLSV-EKRHKVEVTIRLVPgVVLRAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|.
gi 446593847   82 ERQIRKHKTKV 92
Cdd:pfam02482  77 ERQLRKYKEKL 87
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 124-176 1.69e-29

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: 102.87  E-value: 1.69e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446593847  124 ELVRTKRFDLKPMDVEEAILQMDMLGHNFFVFTNADTNETNVVYGRKDGKYGL 176
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-94 6.41e-22

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 84.96  E-value: 6.41e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   1 MKFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDKQRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                         90
                 ....*....|....
gi 446593847  81 LERQIRKHKTKVNR 94
Cdd:PRK10470  81 LARQLTKHKDKLKQ 94
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-103 5.42e-10

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 54.33  E-value: 5.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446593847   1 MKFNIRGENIEVTPALKEYVEKKLSKLERYFDTFPEIKVNLKVYSDKQRVEVTIPFTDLLLRAEETNSDMYAAIDLVVDK 80
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                         90       100
                 ....*....|....*....|...
gi 446593847  81 LERQIRKHKTKVNRKlREKGSVK 103
Cdd:PRK10324  81 LERQLNKLQHKGEAR-RAATSVK 102
 
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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