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Conserved domains on  [gi|15599659|ref|NP_253153|]
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hypothetical protein PA4463 [Pseudomonas aeruginosa PAO1]

Protein Classification

ribosome-associated translation inhibitor RaiA( domain architecture ID 10794665)

ribosome-associated translation inhibitor RaiA, such as Pseudomonas putida ribosome hibernation promoting factor (HPF), which promotes and stabilizes dimerization of 70S ribosomes by the ribosome modulation factor (RMF), leading to the formation of inactive 100S ribosomes, during stationary phase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 6.00e-40

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: 127.45  E-value: 6.00e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659     1 MQVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLKQKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 15599659    81 LDRQLIKHKEKYLER 95
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
 
Name Accession Description Interval E-value
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 6.00e-40

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: 127.45  E-value: 6.00e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659     1 MQVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLKQKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 15599659    81 LDRQLIKHKEKYLER 95
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-91 5.40e-39

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 125.28  E-value: 5.40e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659   2 QVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLK-QKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:COG1544   1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                        90
                ....*....|.
gi 15599659  81 LDRQLIKHKEK 91
Cdd:COG1544  81 LERQLRKYKEK 91
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-91 8.25e-38

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: 122.24  E-value: 8.25e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659   2 QVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEK---LKQKIEATLRIAGGEIVANAEHEDMYAAIDLLI 78
Cdd:cd00552   1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                        90
                ....*....|...
gi 15599659  79 DKLDRQLIKHKEK 91
Cdd:cd00552  81 DKLERQLRKYKEK 93
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-91 4.91e-33

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 110.38  E-value: 4.91e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659    1 MQVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLKQKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                         90
                 ....*....|.
gi 15599659   81 LDRQLIKHKEK 91
Cdd:PRK10470  81 LARQLTKHKDK 91
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-91 1.47e-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: 101.04  E-value: 1.47e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659     3 VNISGHQLDVTDALRDYVGEKLSRLERHFdkiTNVQVIMEVEKlKQKIEATLRIAGGEIV-ANAEHEDMYAAIDLLIDKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYF---ISADVTLSVEK-RHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|
gi 15599659    82 DRQLIKHKEK 91
Cdd:pfam02482  77 ERQLRKYKEK 86
 
Name Accession Description Interval E-value
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 6.00e-40

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: 127.45  E-value: 6.00e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659     1 MQVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLKQKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 15599659    81 LDRQLIKHKEKYLER 95
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 2-91 5.40e-39

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 125.28  E-value: 5.40e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659   2 QVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLK-QKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:COG1544   1 KINITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNRrFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDK 80

                        90
                ....*....|.
gi 15599659  81 LDRQLIKHKEK 91
Cdd:COG1544  81 LERQLRKYKEK 91
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 2-91 8.25e-38

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: 122.24  E-value: 8.25e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659   2 QVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEK---LKQKIEATLRIAGGEIVANAEHEDMYAAIDLLI 78
Cdd:cd00552   1 NINITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAV 80

                        90
                ....*....|...
gi 15599659  79 DKLDRQLIKHKEK 91
Cdd:cd00552  81 DKLERQLRKYKEK 93
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-91 4.91e-33

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 110.38  E-value: 4.91e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659    1 MQVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLKQKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                         90
                 ....*....|.
gi 15599659   81 LDRQLIKHKEK 91
Cdd:PRK10470  81 LARQLTKHKDK 91
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-91 1.47e-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: 101.04  E-value: 1.47e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659     3 VNISGHQLDVTDALRDYVGEKLSRLERHFdkiTNVQVIMEVEKlKQKIEATLRIAGGEIV-ANAEHEDMYAAIDLLIDKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKYF---ISADVTLSVEK-RHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|
gi 15599659    82 DRQLIKHKEK 91
Cdd:pfam02482  77 ERQLRKYKEK 86
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-91 5.95e-18

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 72.44  E-value: 5.95e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599659    1 MQVNISGHQLDVTDALRDYVGEKLSRLERHFDKITNVQVIMEVEKLKQKIEATLRIAGGEIVANAEHEDMYAAIDLLIDK 80
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                         90
                 ....*....|.
gi 15599659   81 LDRQLIKHKEK 91
Cdd:PRK10324  81 LERQLNKLQHK 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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