NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|770221244|ref|WP_045115904|]
View 

ribosome hibernation-promoting factor, HPF/YfiA family [Plesiocystis pacifica]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-102 2.72e-28

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 102.17  E-value: 2.72e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   2 QTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKIN-HIAQFDVTLrNGLQLHSSEKTESMYSSIDMALA 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHV-PGPVLRAEAEAEDMYAAIDLAVD 79

                         90       100
                 ....*....|....*....|..
gi 770221244  81 KMERQVRRYKDRITNHKPHKGK 102
Cdd:COG1544   80 KLERQLRKYKEKLKDHRRRRAP 101
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 146-199 5.68e-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: 66.27  E-value: 5.68e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 770221244  146 TIIRETEFQAGRLKVREAVMQLNLAHKQFLVFTNTETGDINVIYRLEDeGSYGL 199
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKD-GNYGL 54
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-102 2.72e-28

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 102.17  E-value: 2.72e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   2 QTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKIN-HIAQFDVTLrNGLQLHSSEKTESMYSSIDMALA 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHV-PGPVLRAEAEAEDMYAAIDLAVD 79

                         90       100
                 ....*....|....*....|..
gi 770221244  81 KMERQVRRYKDRITNHKPHKGK 102
Cdd:COG1544   80 KLERQLRKYKEKLKDHRRRRAP 101
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 4-92 1.56e-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: 92.19  E-value: 1.56e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   4 QFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEK---INHIAQFDVTLrNGLQLHSSEKTESMYSSIDMALA 80
Cdd:cd00552    3 NITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHL-PGGVLRAEASAEDLYAAIDLAVD 81

                         90
                 ....*....|..
gi 770221244  81 KMERQVRRYKDR 92
Cdd:cd00552   82 KLERQLRKYKEK 93
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-93 2.54e-24

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: 91.41  E-value: 2.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244    4 QFVFRHMESSDALRNYAEDRLAKIKRYFSDplkVNCTFSVEKInHIAQFDVTLRNGLQLHSSEKTESMYSSIDMALAKME 83
Cdd:pfam02482   2 NITGRNIEVTDALREYVEKKLEKLEKYFIS---ADVTLSVEKR-HKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVDKLE 77

                          90
                  ....*....|
gi 770221244   84 RQVRRYKDRI 93
Cdd:pfam02482  78 RQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-96 7.24e-21

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: 82.76  E-value: 7.24e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244    1 MQTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKINHIAqfDVTLR-NGLQLHSSEKTESMYSSIDMAL 79
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKV--EATLYvNGGVIRASAESEDMYAAIDLAI 78

                          90
                  ....*....|....*..
gi 770221244   80 AKMERQVRRYKDRITNH 96
Cdd:TIGR00741  79 DKLERQLRKLKEKRKEH 95
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-96 2.28e-15

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 68.78  E-value: 2.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   1 MQTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKINHIAqfDVTLR-NGLQLHSSEKTESMYSSIDMAL 79
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHIS--DATLHvNGGEIHASAEGQDMYAAIDGLI 78

                         90
                 ....*....|....*..
gi 770221244  80 AKMERQVRRYKDRITNH 96
Cdd:PRK10470  79 DKLARQLTKHKDKLKQH 95
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 146-199 5.68e-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: 66.27  E-value: 5.68e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 770221244  146 TIIRETEFQAGRLKVREAVMQLNLAHKQFLVFTNTETGDINVIYRLEDeGSYGL 199
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKD-GNYGL 54
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-102 2.72e-28

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 102.17  E-value: 2.72e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   2 QTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKIN-HIAQFDVTLrNGLQLHSSEKTESMYSSIDMALA 80
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHV-PGPVLRAEAEAEDMYAAIDLAVD 79

                         90       100
                 ....*....|....*....|..
gi 770221244  81 KMERQVRRYKDRITNHKPHKGK 102
Cdd:COG1544   80 KLERQLRKYKEKLKDHRRRRAP 101
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 4-92 1.56e-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: 92.19  E-value: 1.56e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   4 QFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEK---INHIAQFDVTLrNGLQLHSSEKTESMYSSIDMALA 80
Cdd:cd00552    3 NITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHL-PGGVLRAEASAEDLYAAIDLAVD 81

                         90
                 ....*....|..
gi 770221244  81 KMERQVRRYKDR 92
Cdd:cd00552   82 KLERQLRKYKEK 93
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-93 2.54e-24

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: 91.41  E-value: 2.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244    4 QFVFRHMESSDALRNYAEDRLAKIKRYFSDplkVNCTFSVEKInHIAQFDVTLRNGLQLHSSEKTESMYSSIDMALAKME 83
Cdd:pfam02482   2 NITGRNIEVTDALREYVEKKLEKLEKYFIS---ADVTLSVEKR-HKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVDKLE 77

                          90
                  ....*....|
gi 770221244   84 RQVRRYKDRI 93
Cdd:pfam02482  78 RQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-96 7.24e-21

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: 82.76  E-value: 7.24e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244    1 MQTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKINHIAqfDVTLR-NGLQLHSSEKTESMYSSIDMAL 79
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKV--EATLYvNGGVIRASAESEDMYAAIDLAI 78

                          90
                  ....*....|....*..
gi 770221244   80 AKMERQVRRYKDRITNH 96
Cdd:TIGR00741  79 DKLERQLRKLKEKRKEH 95
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-96 2.28e-15

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 68.78  E-value: 2.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   1 MQTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKINHIAqfDVTLR-NGLQLHSSEKTESMYSSIDMAL 79
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHIS--DATLHvNGGEIHASAEGQDMYAAIDGLI 78

                         90
                 ....*....|....*..
gi 770221244  80 AKMERQVRRYKDRITNH 96
Cdd:PRK10470  79 DKLARQLTKHKDKLKQH 95
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 146-199 5.68e-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: 66.27  E-value: 5.68e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 770221244  146 TIIRETEFQAGRLKVREAVMQLNLAHKQFLVFTNTETGDINVIYRLEDeGSYGL 199
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKD-GNYGL 54
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-120 4.23e-08

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 49.71  E-value: 4.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 770221244   1 MQTQFVFRHMESSDALRNYAEDRLAKIKRYFSDPLKVNCTFSVEKINHIAQFDVTLRNGlQLHSSEKTESMYSSIDMALA 80
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNG-VLVASGKHEDMYTAINELIN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 770221244  81 KMERQVRRYKdritnhkpHKGKAARVRQVVFSLDGQEEPE 120
Cdd:PRK10324  80 KLERQLNKLQ--------HKGEARRAATSVKDANFVEEVE 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH