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Conserved domains on  [gi|501167612|ref|WP_012211611|]
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ribosome hibernation-promoting factor, HPF/YfiA family [Lactobacillus helveticus]

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 ...
 3-104 7.83e-36

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 120.66  E-value: 7.83e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   3 KYNVRGENIEVTDALRSYVEKRLNKLEKYFElnQDVIAHVNLRVYRDHSAKVEVTIPLPYLVLRAEETTDDMYRSIDFVS 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFD--RIISADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 501167612  83 EKLERQIRKYKTRVNRKSREKG 104
Cdd:COG1544   79 DKLERQLRKYKEKLKDHRRRRA 100
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 125-176 5.16e-26

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: 94.01  E-value: 5.16e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 501167612  125 IVRNKRVSLKPMDPEEAILQMDMMEHDFFVFEDAETNGISVVYRRNDGRYGL 176
Cdd:pfam16321   3 IVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-104 7.83e-36

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 120.66  E-value: 7.83e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   3 KYNVRGENIEVTDALRSYVEKRLNKLEKYFElnQDVIAHVNLRVYRDHSAKVEVTIPLPYLVLRAEETTDDMYRSIDFVS 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFD--RIISADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 501167612  83 EKLERQIRKYKTRVNRKSREKG 104
Cdd:COG1544   79 DKLERQLRKYKEKLKDHRRRRA 100
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-95 1.21e-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: 114.53  E-value: 1.21e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   3 KYNVRGENIEVTDALRSYVEKRLNKLEKYFELNQDVIAHVNLRVYRDHSAKVEVTIPLPYLVLRAEETTDDMYRSIDFVS 82
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 501167612  83 EKLERQIRKYKTR 95
Cdd:cd00552   81 DKLERQLRKYKEK 93
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-96 6.48e-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: 97.19  E-value: 6.48e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612    4 YNVRGENIEVTDALRSYVEKRLNKLEKYFelnqdVIAHVNLRVYRDHsaKVEVTIPL-PYLVLRAEETTDDMYRSIDFVS 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYF-----ISADVTLSVEKRH--KVEVTIRLvPGVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|....
gi 501167612   83 EKLERQIRKYKTRV 96
Cdd:pfam02482  74 DKLERQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 2-99 1.30e-26

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: 97.02  E-value: 1.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612    2 LKYNVRGENIEVTDALRSYVEKRLNKLEKYFELNQDVIAHVNLRVYRdhsAKVEVTIPLPYLVLRAEETTDDMYRSIDFV 81
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNR---FKVEATLYVNGGVIRASAESEDMYAAIDLA 77

                          90
                  ....*....|....*...
gi 501167612   82 SEKLERQIRKYKTRVNRK 99
Cdd:TIGR00741  78 IDKLERQLRKLKEKRKEH 95
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 125-176 5.16e-26

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: 94.01  E-value: 5.16e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 501167612  125 IVRNKRVSLKPMDPEEAILQMDMMEHDFFVFEDAETNGISVVYRRNDGRYGL 176
Cdd:pfam16321   3 IVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
2-98 1.16e-10

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 55.69  E-value: 1.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   2 LKYNVRGENIEVTDALRSYVEKRLNKLEKYFE-LNQdviAHVNLRVYRDHSAkVEVTIPLPYLVLRAEETTDDMYRSIDF 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDrINQ---VYVVLKVEKVTHI-SDATLHVNGGEIHASAEGQDMYAAIDG 76

                         90
                 ....*....|....*...
gi 501167612  81 VSEKLERQIRKYKTRVNR 98
Cdd:PRK10470  77 LIDKLARQLTKHKDKLKQ 94
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-104 7.83e-36

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 120.66  E-value: 7.83e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   3 KYNVRGENIEVTDALRSYVEKRLNKLEKYFElnQDVIAHVNLRVYRDHSAKVEVTIPLPYLVLRAEETTDDMYRSIDFVS 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFD--RIISADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 501167612  83 EKLERQIRKYKTRVNRKSREKG 104
Cdd:COG1544   79 DKLERQLRKYKEKLKDHRRRRA 100
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-95 1.21e-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: 114.53  E-value: 1.21e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   3 KYNVRGENIEVTDALRSYVEKRLNKLEKYFELNQDVIAHVNLRVYRDHSAKVEVTIPLPYLVLRAEETTDDMYRSIDFVS 82
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 501167612  83 EKLERQIRKYKTR 95
Cdd:cd00552   81 DKLERQLRKYKEK 93
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-96 6.48e-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: 97.19  E-value: 6.48e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612    4 YNVRGENIEVTDALRSYVEKRLNKLEKYFelnqdVIAHVNLRVYRDHsaKVEVTIPL-PYLVLRAEETTDDMYRSIDFVS 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYF-----ISADVTLSVEKRH--KVEVTIRLvPGVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|....
gi 501167612   83 EKLERQIRKYKTRV 96
Cdd:pfam02482  74 DKLERQLRKYKEKL 87
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 2-99 1.30e-26

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: 97.02  E-value: 1.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612    2 LKYNVRGENIEVTDALRSYVEKRLNKLEKYFELNQDVIAHVNLRVYRdhsAKVEVTIPLPYLVLRAEETTDDMYRSIDFV 81
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNR---FKVEATLYVNGGVIRASAESEDMYAAIDLA 77

                          90
                  ....*....|....*...
gi 501167612   82 SEKLERQIRKYKTRVNRK 99
Cdd:TIGR00741  78 IDKLERQLRKLKEKRKEH 95
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 125-176 5.16e-26

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: 94.01  E-value: 5.16e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 501167612  125 IVRNKRVSLKPMDPEEAILQMDMMEHDFFVFEDAETNGISVVYRRNDGRYGL 176
Cdd:pfam16321   3 IVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
2-98 1.16e-10

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 55.69  E-value: 1.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   2 LKYNVRGENIEVTDALRSYVEKRLNKLEKYFE-LNQdviAHVNLRVYRDHSAkVEVTIPLPYLVLRAEETTDDMYRSIDF 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDrINQ---VYVVLKVEKVTHI-SDATLHVNGGEIHASAEGQDMYAAIDG 76

                         90
                 ....*....|....*...
gi 501167612  81 VSEKLERQIRKYKTRVNR 98
Cdd:PRK10470  77 LIDKLARQLTKHKDKLKQ 94
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
5-95 1.88e-06

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 44.70  E-value: 1.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501167612   5 NVRGENIEVTDALRSYVEKRLNKLEKYfelnQDVIAHVNLRVYRDHSAKV-EVTIPLPYLVLRAEETTDDMYRSIDFVSE 83
Cdd:PRK10324   4 NITSKQMEITPAIRQHVADRLAKLEKW----QTHLINPHIILSKEPQGFVaDATINTPNGVLVASGKHEDMYTAINELIN 79

                         90
                 ....*....|..
gi 501167612  84 KLERQIRKYKTR 95
Cdd:PRK10324  80 KLERQLNKLQHK 91
 
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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