NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|518172196|ref|WP_019342404|]
View 

ribosome hibernation-promoting factor, HPF/YfiA family [Stutzerimonas stutzeri]

Protein Classification

HPF/RaiA family ribosome-associated protein( domain architecture ID 10003959)

HPF/RaiA family ribosome-associated protein similar to ribosome-associated translation inhibitor RaiA, a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site, and 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 ...
 9-105 1.22e-09

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


:

Pssm-ID: 441153  Cd Length: 101  Bit Score: 50.94  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518172196   9 HSVDVTSNLEEHVKATVEsELERFDDQLTRVEVHLNDENSGKsgpqdKRCQMEARVKGHEpISTSHKADSLNLAIDGCAE 88
Cdd:COG1544    7 RNVEVTDALREYVEEKLE-KLEKYFDRIISADVTLSVEKNRR-----FKVEITLHVPGPV-LRAEAEAEDMYAAIDLAVD 79

                         90
                 ....*....|....*..
gi 518172196  89 KLSHALAHALDKKLNHH 105
Cdd:COG1544   80 KLERQLRKYKEKLKDHR 96
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 9-105 1.22e-09

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 50.94  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518172196   9 HSVDVTSNLEEHVKATVEsELERFDDQLTRVEVHLNDENSGKsgpqdKRCQMEARVKGHEpISTSHKADSLNLAIDGCAE 88
Cdd:COG1544    7 RNVEVTDALREYVEEKLE-KLEKYFDRIISADVTLSVEKNRR-----FKVEITLHVPGPV-LRAEAEAEDMYAAIDLAVD 79

                         90
                 ....*....|....*..
gi 518172196  89 KLSHALAHALDKKLNHH 105
Cdd:COG1544   80 KLERQLRKYKEKLKDHR 96
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-104 2.54e-08

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: 47.32  E-value: 2.54e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518172196    1 MQILVNSNHsVDVTSNLEEHVKATVEsELERFDDQLTRVEVHLNDEnsgksgPQDKRCQMEARVKGHEpISTSHKADSLN 80
Cdd:TIGR00741   1 MNINITGNN-VEITEALREYVEEKLA-RLERYFTRIINVDVVLSVE------RNRFKVEATLYVNGGV-IRASAESEDMY 71

                          90       100
                  ....*....|....*....|....
gi 518172196   81 LAIDGCAEKLSHALAHALDKKLNH 104
Cdd:TIGR00741  72 AAIDLAIDKLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 9-101 4.84e-07

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: 43.65  E-value: 4.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518172196    9 HSVDVTSNLEEHVkatvESELERFDDQLTRVEVHLNDENSgksgpqdKRCQMEARVKGHEPISTSHKADSLNLAIDGCAE 88
Cdd:pfam02482   6 RNIEVTDALREYV----EKKLEKLEKYFISADVTLSVEKR-------HKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVD 74

                          90
                  ....*....|...
gi 518172196   89 KLSHALAHALDKK 101
Cdd:pfam02482  75 KLERQLRKYKEKL 87
 
Name Accession Description Interval E-value
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 9-105 1.22e-09

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 50.94  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518172196   9 HSVDVTSNLEEHVKATVEsELERFDDQLTRVEVHLNDENSGKsgpqdKRCQMEARVKGHEpISTSHKADSLNLAIDGCAE 88
Cdd:COG1544    7 RNVEVTDALREYVEEKLE-KLEKYFDRIISADVTLSVEKNRR-----FKVEITLHVPGPV-LRAEAEAEDMYAAIDLAVD 79

                         90
                 ....*....|....*..
gi 518172196  89 KLSHALAHALDKKLNHH 105
Cdd:COG1544   80 KLERQLRKYKEKLKDHR 96
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-104 2.54e-08

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: 47.32  E-value: 2.54e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518172196    1 MQILVNSNHsVDVTSNLEEHVKATVEsELERFDDQLTRVEVHLNDEnsgksgPQDKRCQMEARVKGHEpISTSHKADSLN 80
Cdd:TIGR00741   1 MNINITGNN-VEITEALREYVEEKLA-RLERYFTRIINVDVVLSVE------RNRFKVEATLYVNGGV-IRASAESEDMY 71

                          90       100
                  ....*....|....*....|....
gi 518172196   81 LAIDGCAEKLSHALAHALDKKLNH 104
Cdd:TIGR00741  72 AAIDLAIDKLERQLRKLKEKRKEH 95
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 9-101 4.84e-07

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: 43.65  E-value: 4.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518172196    9 HSVDVTSNLEEHVkatvESELERFDDQLTRVEVHLNDENSgksgpqdKRCQMEARVKGHEPISTSHKADSLNLAIDGCAE 88
Cdd:pfam02482   6 RNIEVTDALREYV----EKKLEKLEKYFISADVTLSVEKR-------HKVEVTIRLVPGVVLRAEETAEDLYAAIDLAVD 74

                          90
                  ....*....|...
gi 518172196   89 KLSHALAHALDKK 101
Cdd:pfam02482  75 KLERQLRKYKEKL 87
 
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