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Conserved domains on  [gi|499795468|ref|WP_011476202|]
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ribosome hibernation-promoting factor, HPF/YfiA family [Ligilactobacillus salivarius]

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 1.34e-38

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 127.59  E-value: 1.34e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   3 KINVRGENIEVTGAIREYVEKRLAKLEKFFDNTADstAHVNLKVYSDKTAKVEVTIPLPYLVLRAEETSPDMYASIDLVT 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIIS--ADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 499795468  83 DKLERQIRKYKTKVNRKSREKG 104
Cdd:COG1544   79 DKLERQLRKYKEKLKDHRRRRA 100
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 125-178 8.00e-25

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: 90.93  E-value: 8.00e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 499795468  125 FEIVRTKRLSLKPMDSEEAVLQMDMLGHDFFIYEDAENGGIYIVYRRRDGRYGL 178
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-104 1.34e-38

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 127.59  E-value: 1.34e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   3 KINVRGENIEVTGAIREYVEKRLAKLEKFFDNTADstAHVNLKVYSDKTAKVEVTIPLPYLVLRAEETSPDMYASIDLVT 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIIS--ADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 499795468  83 DKLERQIRKYKTKVNRKSREKG 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 1.64e-35

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: 119.54  E-value: 1.64e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   3 KINVRGENIEVTGAIREYVEKRLAKLEKFFDNTADSTAHVNLKVYSDKTAKVEVTIPLPYLVLRAEETSPDMYASIDLVT 82
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 499795468  83 DKLERQIRKYKTK 95
Cdd:cd00552   81 DKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 2-99 3.68e-30

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: 105.87  E-value: 3.68e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468    2 LKINVRGENIEVTGAIREYVEKRLAKLEKFFDNTADSTAHVNLKVYsdkTAKVEVTIPLPYLVLRAEETSPDMYASIDLV 81
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN---RFKVEATLYVNGGVIRASAESEDMYAAIDLA 77

                          90
                  ....*....|....*...
gi 499795468   82 TDKLERQIRKYKTKVNRK 99
Cdd:TIGR00741  78 IDKLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-96 1.82e-29

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: 103.74  E-value: 1.82e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468    4 INVRGENIEVTGAIREYVEKRLAKLEKFFDNtadstAHVNLKVysDKTAKVEVTIPL-PYLVLRAEETSPDMYASIDLVT 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFIS-----ADVTLSV--EKRHKVEVTIRLvPGVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|....
gi 499795468   83 DKLERQIRKYKTKV 96
Cdd:pfam02482  74 DKLERQLRKYKEKL 87
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 125-178 8.00e-25

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: 90.93  E-value: 8.00e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 499795468  125 FEIVRTKRLSLKPMDSEEAVLQMDMLGHDFFIYEDAENGGIYIVYRRRDGRYGL 178
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
2-98 1.38e-14

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 66.09  E-value: 1.38e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   2 LKINVRGENIEVTGAIREYVEKRLAKLEKFFDNTadSTAHVNLKVysDKTAKV-EVTIPLPYLVLRAEETSPDMYASIDL 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRI--NQVYVVLKV--EKVTHIsDATLHVNGGEIHASAEGQDMYAAIDG 76

                         90
                 ....*....|....*...
gi 499795468  81 VTDKLERQIRKYKTKVNR 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 1.34e-38

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 127.59  E-value: 1.34e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   3 KINVRGENIEVTGAIREYVEKRLAKLEKFFDNTADstAHVNLKVYSDKTAKVEVTIPLPYLVLRAEETSPDMYASIDLVT 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIIS--ADVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 499795468  83 DKLERQIRKYKTKVNRKSREKG 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 1.64e-35

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: 119.54  E-value: 1.64e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   3 KINVRGENIEVTGAIREYVEKRLAKLEKFFDNTADSTAHVNLKVYSDKTAKVEVTIPLPYLVLRAEETSPDMYASIDLVT 82
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 499795468  83 DKLERQIRKYKTK 95
Cdd:cd00552   81 DKLERQLRKYKEK 93
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 2-99 3.68e-30

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: 105.87  E-value: 3.68e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468    2 LKINVRGENIEVTGAIREYVEKRLAKLEKFFDNTADSTAHVNLKVYsdkTAKVEVTIPLPYLVLRAEETSPDMYASIDLV 81
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN---RFKVEATLYVNGGVIRASAESEDMYAAIDLA 77

                          90
                  ....*....|....*...
gi 499795468   82 TDKLERQIRKYKTKVNRK 99
Cdd:TIGR00741  78 IDKLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-96 1.82e-29

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: 103.74  E-value: 1.82e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468    4 INVRGENIEVTGAIREYVEKRLAKLEKFFDNtadstAHVNLKVysDKTAKVEVTIPL-PYLVLRAEETSPDMYASIDLVT 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFIS-----ADVTLSV--EKRHKVEVTIRLvPGVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|....
gi 499795468   83 DKLERQIRKYKTKV 96
Cdd:pfam02482  74 DKLERQLRKYKEKL 87
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 125-178 8.00e-25

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: 90.93  E-value: 8.00e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 499795468  125 FEIVRTKRLSLKPMDSEEAVLQMDMLGHDFFIYEDAENGGIYIVYRRRDGRYGL 178
Cdd:pfam16321   1 PEIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
PRK10470 PRK10470
ribosome hibernation promoting factor;
2-98 1.38e-14

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 66.09  E-value: 1.38e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   2 LKINVRGENIEVTGAIREYVEKRLAKLEKFFDNTadSTAHVNLKVysDKTAKV-EVTIPLPYLVLRAEETSPDMYASIDL 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRI--NQVYVVLKV--EKVTHIsDATLHVNGGEIHASAEGQDMYAAIDG 76

                         90
                 ....*....|....*...
gi 499795468  81 VTDKLERQIRKYKTKVNR 98
Cdd:PRK10470  77 LIDKLARQLTKHKDKLKQ 94
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
2-116 3.36e-11

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 57.42  E-value: 3.36e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499795468   2 LKINVRGENIEVTGAIREYVEKRLAKLEKFfdntadSTAHVNLKVYSDKTAK---VEVTIPLPYLVLRAEETSPDMYASI 78
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKW------QTHLINPHIILSKEPQgfvADATINTPNGVLVASGKHEDMYTAI 74

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 499795468  79 DLVTDKLERQIRKYKTKVNRKSREKGFKNFEFAPVADE 116
Cdd:PRK10324  75 NELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEE 112
 
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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