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Conserved domains on  [gi|1779141484|ref|WP_155190744|]
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ribosome hibernation-promoting factor, HPF/YfiA family [Roseibium denhamense]

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 ...
 3-103 1.36e-29

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 105.25  E-value: 1.36e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   3 LRISGKNVDVGEALRTHITDRIEdAVSKYFAGGFTGHVTLSREGTG-FKSECSLHLDtGVVLQVSAQDQDPRNSFDLASD 81
Cdd:COG1544     2 INITGRNVEVTDALREYVEEKLE-KLEKYFDRIISADVTLSVEKNRrFKVEITLHVP-GPVLRAEAEAEDMYAAIDLAVD 79

                          90       100
                  ....*....|....*....|..
gi 1779141484  82 KIEKRLRRYKRKLKDHHSHNGS 103
Cdd:COG1544    80 KLERQLRKYKEKLKDHRRRRAP 101
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 130-182 1.21e-15

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: 67.81  E-value: 1.21e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1779141484 130 PLVIAETSAKVKTMTVGMAVMELDLTEAPVVLFKNAANGGVNVVYRRSDGNIG 182
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYG 53
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-103 1.36e-29

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 105.25  E-value: 1.36e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   3 LRISGKNVDVGEALRTHITDRIEdAVSKYFAGGFTGHVTLSREGTG-FKSECSLHLDtGVVLQVSAQDQDPRNSFDLASD 81
Cdd:COG1544     2 INITGRNVEVTDALREYVEEKLE-KLEKYFDRIISADVTLSVEKNRrFKVEITLHVP-GPVLRAEAEAEDMYAAIDLAVD 79

                          90       100
                  ....*....|....*....|..
gi 1779141484  82 KIEKRLRRYKRKLKDHHSHNGS 103
Cdd:COG1544    80 KLERQLRKYKEKLKDHRRRRAP 101
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-93 2.90e-24

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: 91.04  E-value: 2.90e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   3 LRISGKNVDVGEALRTHITDRIEDaVSKYFAGGFTGHVTLSRE---GTGFKSECSLHLDtGVVLQVSAQDQDPRNSFDLA 79
Cdd:cd00552     2 INITGRNIEVTDALREYVEEKLEK-LEKYFDRIISVDVVLSVEknhGKRFKVEITIHLP-GGVLRAEASAEDLYAAIDLA 79

                          90
                  ....*....|....
gi 1779141484  80 SDKIEKRLRRYKRK 93
Cdd:cd00552    80 VDKLERQLRKYKEK 93
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-94 6.20e-22

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: 84.86  E-value: 6.20e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   3 LRISGKNVDVGEALRTHITDRIEdAVSKYFAGGftgHVTLSREgTGFKSECSLHLDTGVVLQVSAQDQDPRNSFDLASDK 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLE-KLEKYFISA---DVTLSVE-KRHKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVDK 75

                          90
                  ....*....|..
gi 1779141484  83 IEKRLRRYKRKL 94
Cdd:pfam02482  76 LERQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-97 1.94e-20

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: 81.22  E-value: 1.94e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   1 MALRISGKNVDVGEALRTHITDRIEDAVsKYFAGGFTGHVTLSREGTGFKSECSLHLDTGVVLQvSAQDQDPRNSFDLAS 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLE-RYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRA-SAESEDMYAAIDLAI 78

                          90
                  ....*....|....*..
gi 1779141484  81 DKIEKRLRRYKRKLKDH 97
Cdd:TIGR00741  79 DKLERQLRKLKEKRKEH 95
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 130-182 1.21e-15

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: 67.81  E-value: 1.21e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1779141484 130 PLVIAETSAKVKTMTVGMAVMELDLTEAPVVLFKNAANGGVNVVYRRSDGNIG 182
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYG 53
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-97 4.89e-09

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 51.45  E-value: 4.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   1 MALRISGKNVDVGEALRTHITDRIEDaVSKYFAGGFTGHVTLSREGTGFKSECSLHLDTGVvLQVSAQDQDPRNSFDLAS 80
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAK-LEQYFDRINQVYVVLKVEKVTHISDATLHVNGGE-IHASAEGQDMYAAIDGLI 78

                          90
                  ....*....|....*..
gi 1779141484  81 DKIEKRLRRYKRKLKDH 97
Cdd:PRK10470   79 DKLARQLTKHKDKLKQH 95
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-103 1.36e-29

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 105.25  E-value: 1.36e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   3 LRISGKNVDVGEALRTHITDRIEdAVSKYFAGGFTGHVTLSREGTG-FKSECSLHLDtGVVLQVSAQDQDPRNSFDLASD 81
Cdd:COG1544     2 INITGRNVEVTDALREYVEEKLE-KLEKYFDRIISADVTLSVEKNRrFKVEITLHVP-GPVLRAEAEAEDMYAAIDLAVD 79

                          90       100
                  ....*....|....*....|..
gi 1779141484  82 KIEKRLRRYKRKLKDHHSHNGS 103
Cdd:COG1544    80 KLERQLRKYKEKLKDHRRRRAP 101
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-93 2.90e-24

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: 91.04  E-value: 2.90e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   3 LRISGKNVDVGEALRTHITDRIEDaVSKYFAGGFTGHVTLSRE---GTGFKSECSLHLDtGVVLQVSAQDQDPRNSFDLA 79
Cdd:cd00552     2 INITGRNIEVTDALREYVEEKLEK-LEKYFDRIISVDVVLSVEknhGKRFKVEITIHLP-GGVLRAEASAEDLYAAIDLA 79

                          90
                  ....*....|....
gi 1779141484  80 SDKIEKRLRRYKRK 93
Cdd:cd00552    80 VDKLERQLRKYKEK 93
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-94 6.20e-22

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: 84.86  E-value: 6.20e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   3 LRISGKNVDVGEALRTHITDRIEdAVSKYFAGGftgHVTLSREgTGFKSECSLHLDTGVVLQVSAQDQDPRNSFDLASDK 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLE-KLEKYFISA---DVTLSVE-KRHKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVDK 75

                          90
                  ....*....|..
gi 1779141484  83 IEKRLRRYKRKL 94
Cdd:pfam02482  76 LERQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-97 1.94e-20

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: 81.22  E-value: 1.94e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   1 MALRISGKNVDVGEALRTHITDRIEDAVsKYFAGGFTGHVTLSREGTGFKSECSLHLDTGVVLQvSAQDQDPRNSFDLAS 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLE-RYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRA-SAESEDMYAAIDLAI 78

                          90
                  ....*....|....*..
gi 1779141484  81 DKIEKRLRRYKRKLKDH 97
Cdd:TIGR00741  79 DKLERQLRKLKEKRKEH 95
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 130-182 1.21e-15

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: 67.81  E-value: 1.21e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1779141484 130 PLVIAETSAKVKTMTVGMAVMELDLTEAPVVLFKNAANGGVNVVYRRSDGNIG 182
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYG 53
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-97 4.89e-09

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 51.45  E-value: 4.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   1 MALRISGKNVDVGEALRTHITDRIEDaVSKYFAGGFTGHVTLSREGTGFKSECSLHLDTGVvLQVSAQDQDPRNSFDLAS 80
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAK-LEQYFDRINQVYVVLKVEKVTHISDATLHVNGGE-IHASAEGQDMYAAIDGLI 78

                          90
                  ....*....|....*..
gi 1779141484  81 DKIEKRLRRYKRKLKDH 97
Cdd:PRK10470   79 DKLARQLTKHKDKLKQH 95
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-123 7.66e-08

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 48.94  E-value: 7.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1779141484   1 MALRISGKNVDVGEALRTHITDRIEDaVSKYFAGGFTGHVTLSREGTGFKSECSLHLDTGvVLQVSAQDQDPRNSFDLAS 80
Cdd:PRK10324    1 MTMNITSKQMEITPAIRQHVADRLAK-LEKWQTHLINPHIILSKEPQGFVADATINTPNG-VLVASGKHEDMYTAINELI 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1779141484  81 DKIEKRLRRYKrklkdhhsHNGSGREAieAASYVLASPDEEEE 123
Cdd:PRK10324   79 NKLERQLNKLQ--------HKGEARRA--ATSVKDANFVEEVE 111
 
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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