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Conserved domains on  [gi|446540389|ref|WP_000617735|]
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MULTISPECIES: ribosome hibernation-promoting factor, HPF/YfiA family [Staphylococcus]

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 8.77e-32

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 110.64  E-value: 8.77e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   3 RFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAvaHVKVKTYSNSATKIEVTIPLKNVTLRAEERNDDLYAGIDLIN 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISA--DVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 446540389  83 NKLERQVRKYKTRINRKSRDRG 104
Cdd:COG1544   79 DKLERQLRKYKEKLKDHRRRRA 100
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 132-184 1.59e-28

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: 100.56  E-value: 1.59e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446540389  132 EIIRSKEFSLKPMDSEEAVLQMNLLGHDFFVFTDRETDGTSIVYRRKDGKYGL 184
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-104 8.77e-32

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 110.64  E-value: 8.77e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   3 RFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAvaHVKVKTYSNSATKIEVTIPLKNVTLRAEERNDDLYAGIDLIN 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISA--DVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 446540389  83 NKLERQVRKYKTRINRKSRDRG 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 1.31e-31

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: 109.91  E-value: 1.31e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   3 RFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYSNSATKIEVTIPLKNVTLRAEERNDDLYAGIDLIN 82
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 446540389  83 NKLERQVRKYKTR 95
Cdd:cd00552   81 DKLERQLRKYKEK 93
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 132-184 1.59e-28

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: 100.56  E-value: 1.59e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446540389  132 EIIRSKEFSLKPMDSEEAVLQMNLLGHDFFVFTDRETDGTSIVYRRKDGKYGL 184
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 5-99 2.38e-25

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: 93.93  E-value: 2.38e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389    5 EIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYsnsATKIEVTIPLKNVTLRAEERNDDLYAGIDLINNK 84
Cdd:TIGR00741   4 NITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN---RFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 446540389   85 LERQVRKYKTRINRK 99
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-96 9.95e-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: 89.49  E-value: 9.95e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389    4 FEIHGDNLTITDAIRNYIEEKIGKLERYFNDVpnavaHVKVKTYSNSatKIEVTIPLKN-VTLRAEERNDDLYAGIDLIN 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFISA-----DVTLSVEKRH--KVEVTIRLVPgVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|....
gi 446540389   83 NKLERQVRKYKTRI 96
Cdd:pfam02482  74 DKLERQLRKYKEKL 87
PRK10470 PRK10470
ribosome hibernation promoting factor;
2-98 2.46e-10

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 54.91  E-value: 2.46e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   2 IRFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYSNSAtkiEVTIPLKNVTLRAEERNDDLYAGIDLI 81
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHIS---DATLHVNGGEIHASAEGQDMYAAIDGL 77

                         90
                 ....*....|....*..
gi 446540389  82 NNKLERQVRKYKTRINR 98
Cdd:PRK10470  78 IDKLARQLTKHKDKLKQ 94
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-104 8.77e-32

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 110.64  E-value: 8.77e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   3 RFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAvaHVKVKTYSNSATKIEVTIPLKNVTLRAEERNDDLYAGIDLIN 82
Cdd:COG1544    1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISA--DVTLSVEKNRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAV 78

                         90       100
                 ....*....|....*....|..
gi 446540389  83 NKLERQVRKYKTRINRKSRDRG 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 1.31e-31

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: 109.91  E-value: 1.31e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   3 RFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYSNSATKIEVTIPLKNVTLRAEERNDDLYAGIDLIN 82
Cdd:cd00552    1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                         90
                 ....*....|...
gi 446540389  83 NKLERQVRKYKTR 95
Cdd:cd00552   81 DKLERQLRKYKEK 93
Ribosom_S30AE_C pfam16321
Sigma 54 modulation/S30EA ribosomal protein C terminus; This domain often occurs at the ...
 132-184 1.59e-28

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: 100.56  E-value: 1.59e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446540389  132 EIIRSKEFSLKPMDSEEAVLQMNLLGHDFFVFTDRETDGTSIVYRRKDGKYGL 184
Cdd:pfam16321   2 EIVRTKRFPLKPMSVEEAVLQMELLGHDFFVFRNAETGEVNVVYRRKDGNYGL 54
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 5-99 2.38e-25

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: 93.93  E-value: 2.38e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389    5 EIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYsnsATKIEVTIPLKNVTLRAEERNDDLYAGIDLINNK 84
Cdd:TIGR00741   4 NITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERN---RFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 446540389   85 LERQVRKYKTRINRK 99
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-96 9.95e-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: 89.49  E-value: 9.95e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389    4 FEIHGDNLTITDAIRNYIEEKIGKLERYFNDVpnavaHVKVKTYSNSatKIEVTIPLKN-VTLRAEERNDDLYAGIDLIN 82
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYFISA-----DVTLSVEKRH--KVEVTIRLVPgVVLRAEETAEDLYAAIDLAV 73

                          90
                  ....*....|....
gi 446540389   83 NKLERQVRKYKTRI 96
Cdd:pfam02482  74 DKLERQLRKYKEKL 87
PRK10470 PRK10470
ribosome hibernation promoting factor;
2-98 2.46e-10

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 54.91  E-value: 2.46e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   2 IRFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYSNSAtkiEVTIPLKNVTLRAEERNDDLYAGIDLI 81
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHIS---DATLHVNGGEIHASAEGQDMYAAIDGL 77

                         90
                 ....*....|....*..
gi 446540389  82 NNKLERQVRKYKTRINR 98
Cdd:PRK10470  78 IDKLARQLTKHKDKLKQ 94
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
6-115 8.22e-06

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 43.16  E-value: 8.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446540389   6 IHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAvaHVKVKTYSNSATKiEVTIPLKNVTLRAEERNDDLYAGIDLINNKL 85
Cdd:PRK10324   5 ITSKQMEITPAIRQHVADRLAKLEKWQTHLINP--HIILSKEPQGFVA-DATINTPNGVLVASGKHEDMYTAINELINKL 81

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446540389  86 ERQVRK--YKTRINRKSRDRGDQEvFVAELQE 115
Cdd:PRK10324  82 ERQLNKlqHKGEARRAATSVKDAN-FVEEVEE 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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