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Conserved domains on  [gi|1788634556|ref|WP_158036158|]
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ribosome hibernation-promoting factor, HPF/YfiA family [Pseudoclavibacter caeni]

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
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 134-187 1.33e-23

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: 88.23  E-value: 1.33e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1788634556 134 PVVIRHKEFPAVELTPEQAVDRMELVGHDFFLFQNVETGRPSVVYRRKGWNYGV 187
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-86 4.37e-16

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 70.20  E-value: 4.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   2 QVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDVKVSnisdKTPDLGERVELTVVAPGPVVRAEAEGGDRFTAFDV 81
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLS----VEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDL 76


                  ....*
gi 1788634556  82 ALDKL 86
Cdd:COG1544    77 AVDKL 81
 
Name Accession Description Interval E-value
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 134-187 1.33e-23

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: 88.23  E-value: 1.33e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1788634556 134 PVVIRHKEFPAVELTPEQAVDRMELVGHDFFLFQNVETGRPSVVYRRKGWNYGV 187
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-86 4.37e-16

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 70.20  E-value: 4.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   2 QVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDVKVSnisdKTPDLGERVELTVVAPGPVVRAEAEGGDRFTAFDV 81
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLS----VEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDL 76


                  ....*
gi 1788634556  82 ALDKL 86
Cdd:COG1544    77 AVDKL 81
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-86 2.29e-15

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: 68.31  E-value: 2.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   2 QVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDVKVSniSDKTPDLGERVELTVVAPGPVVRAEAEGGDRFTAFDV 81
Cdd:cd00552     1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLS--VEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDL 78


                  ....*
gi 1788634556  82 ALDKL 86
Cdd:cd00552    79 AVDKL 83
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-86 2.09e-11

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: 57.72  E-value: 2.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   1 MQVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDVKVSNISdktpdLGERVELTVVAPGPVVRAEAEGGDRFTAFD 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVER-----NRFKVEATLYVNGGVIRASAESEDMYAAID 75


                  ....*.
gi 1788634556  81 VALDKL 86
Cdd:TIGR00741  76 LAIDKL 81
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-86 1.18e-08

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: 50.20  E-value: 1.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   3 VNVLARGVKKSQRFEDVVEQKSKRVEQLADRAqrfDVKVSNISDKtpdlgeRVELTV-VAPGPVVRAEAEGGDRFTAFDV 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFISA---DVTLSVEKRH------KVEVTIrLVPGVVLRAEETAEDLYAAIDL 71


                  ....*
gi 1788634556  82 ALDKL 86
Cdd:pfam02482  72 AVDKL 76
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-89 2.93e-04

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 38.74  E-value: 2.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   1 MQVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDV-----KVSNISDKTPDLGerveltvvapGPVVRAEAEGGDR 75
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVvlkveKVTHISDATLHVN----------GGEIHASAEGQDM 70

                          90
                  ....*....|....
gi 1788634556  76 FTAFDVALDKLTER 89
Cdd:PRK10470   71 YAAIDGLIDKLARQ 84
 
Name Accession Description Interval E-value
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 134-187 1.33e-23

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: 88.23  E-value: 1.33e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1788634556 134 PVVIRHKEFPAVELTPEQAVDRMELVGHDFFLFQNVETGRPSVVYRRKGWNYGV 187
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-86 4.37e-16

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 70.20  E-value: 4.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   2 QVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDVKVSnisdKTPDLGERVELTVVAPGPVVRAEAEGGDRFTAFDV 81
Cdd:COG1544     1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLS----VEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDL 76


                  ....*
gi 1788634556  82 ALDKL 86
Cdd:COG1544    77 AVDKL 81
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-86 2.29e-15

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: 68.31  E-value: 2.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   2 QVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDVKVSniSDKTPDLGERVELTVVAPGPVVRAEAEGGDRFTAFDV 81
Cdd:cd00552     1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLS--VEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDL 78


                  ....*
gi 1788634556  82 ALDKL 86
Cdd:cd00552    79 AVDKL 83
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-86 2.09e-11

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: 57.72  E-value: 2.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   1 MQVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDVKVSNISdktpdLGERVELTVVAPGPVVRAEAEGGDRFTAFD 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVER-----NRFKVEATLYVNGGVIRASAESEDMYAAID 75


                  ....*.
gi 1788634556  81 VALDKL 86
Cdd:TIGR00741  76 LAIDKL 81
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-86 1.18e-08

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: 50.20  E-value: 1.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   3 VNVLARGVKKSQRFEDVVEQKSKRVEQLADRAqrfDVKVSNISDKtpdlgeRVELTV-VAPGPVVRAEAEGGDRFTAFDV 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFISA---DVTLSVEKRH------KVEVTIrLVPGVVLRAEETAEDLYAAIDL 71


                  ....*
gi 1788634556  82 ALDKL 86
Cdd:pfam02482  72 AVDKL 76
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-89 2.93e-04

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 38.74  E-value: 2.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788634556   1 MQVNVLARGVKKSQRFEDVVEQKSKRVEQLADRAQRFDV-----KVSNISDKTPDLGerveltvvapGPVVRAEAEGGDR 75
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVvlkveKVTHISDATLHVN----------GGEIHASAEGQDM 70

                          90
                  ....*....|....
gi 1788634556  76 FTAFDVALDKLTER 89
Cdd:PRK10470   71 YAAIDGLIDKLARQ 84
 
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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