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Conserved domains on  [gi|306869117|gb|EFN00919|]
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Ribosome-associated inhibitor A [Actinobacillus pleuropneumoniae serovar 12 str. 1096]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RaiA super family cl00250
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 1-103 1.12e-39

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).


The actual alignment was detected with superfamily member PRK10324:

Pssm-ID: 469687  Cd Length: 113  Bit Score: 127.91  E-value: 1.12e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   1 MTINISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMIHKLPNSYEVEASIGTPVGELFAKANNEDLYLAINEVETK 80
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                         90       100
                 ....*....|....*....|...
gi 306869117  81 LETQLNKLVHKNEARRTDSTLKN 103
Cdd:PRK10324  81 LERQLNKLQHKGEARRAATSVKD 103
 
Name Accession Description Interval E-value
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-103 1.12e-39

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 127.91  E-value: 1.12e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   1 MTINISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMIHKLPNSYEVEASIGTPVGELFAKANNEDLYLAINEVETK 80
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                         90       100
                 ....*....|....*....|...
gi 306869117  81 LETQLNKLVHKNEARRTDSTLKN 103
Cdd:PRK10324  81 LERQLNKLQHKGEARRAATSVKD 103
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 2.84e-32

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: 108.19  E-value: 2.84e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117    1 MTINISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMIHKLPNSYEVEASIGTPVGELFAKANNEDLYLAINEVETK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 306869117   81 LETQLNKLVHKNEAR 95
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-91 1.28e-27

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: 96.43  E-value: 1.28e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   3 INISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMI---HKLPNSYEVEASIGTPVGELFAKANNEDLYLAINEVET 79
Cdd:cd00552    2 INITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLsveKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAVD 81

                         90
                 ....*....|..
gi 306869117  80 KLETQLNKLVHK 91
Cdd:cd00552   82 KLERQLRKYKEK 93
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-100 2.29e-25

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 91.00  E-value: 2.29e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   3 INISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMIHKLPN-SYEVEASIGTPVGELFAKANNEDLYLAINEVETKL 81
Cdd:COG1544    2 INITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNrRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDKL 81

                         90
                 ....*....|....*....
gi 306869117  82 ETQLNKLVHKNEARRTDST 100
Cdd:COG1544   82 ERQLRKYKEKLKDHRRRRA 100
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-91 2.54e-18

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: 72.54  E-value: 2.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117    3 INISSKQMDVTPAIRTHIEERLAKLEKWqtqLINPHFMIhKLPNSYEVEASIGTPVGE-LFAKANNEDLYLAINEVETKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKY---FISADVTL-SVEKRHKVEVTIRLVPGVvLRAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|
gi 306869117   82 ETQLNKLVHK 91
Cdd:pfam02482  77 ERQLRKYKEK 86
 
Name Accession Description Interval E-value
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-103 1.12e-39

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 127.91  E-value: 1.12e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   1 MTINISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMIHKLPNSYEVEASIGTPVGELFAKANNEDLYLAINEVETK 80
Cdd:PRK10324   1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                         90       100
                 ....*....|....*....|...
gi 306869117  81 LETQLNKLVHKNEARRTDSTLKN 103
Cdd:PRK10324  81 LERQLNKLQHKGEARRAATSVKD 103
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 2.84e-32

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: 108.19  E-value: 2.84e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117    1 MTINISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMIHKLPNSYEVEASIGTPVGELFAKANNEDLYLAINEVETK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 306869117   81 LETQLNKLVHKNEAR 95
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 3-91 1.28e-27

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: 96.43  E-value: 1.28e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   3 INISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMI---HKLPNSYEVEASIGTPVGELFAKANNEDLYLAINEVET 79
Cdd:cd00552    2 INITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLsveKNHGKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAVD 81

                         90
                 ....*....|..
gi 306869117  80 KLETQLNKLVHK 91
Cdd:cd00552   82 KLERQLRKYKEK 93
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 3-100 2.29e-25

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 91.00  E-value: 2.29e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   3 INISSKQMDVTPAIRTHIEERLAKLEKWQTQLINPHFMIHKLPN-SYEVEASIGTPVGELFAKANNEDLYLAINEVETKL 81
Cdd:COG1544    2 INITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKNrRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDKL 81

                         90
                 ....*....|....*....
gi 306869117  82 ETQLNKLVHKNEARRTDST 100
Cdd:COG1544   82 ERQLRKYKEKLKDHRRRRA 100
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 3-91 2.54e-18

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: 72.54  E-value: 2.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117    3 INISSKQMDVTPAIRTHIEERLAKLEKWqtqLINPHFMIhKLPNSYEVEASIGTPVGE-LFAKANNEDLYLAINEVETKL 81
Cdd:pfam02482   1 INITGRNIEVTDALREYVEKKLEKLEKY---FISADVTL-SVEKRHKVEVTIRLVPGVvLRAEETAEDLYAAIDLAVDKL 76

                          90
                  ....*....|
gi 306869117   82 ETQLNKLVHK 91
Cdd:pfam02482  77 ERQLRKYKEK 86
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-96 1.33e-08

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 47.98  E-value: 1.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306869117   1 MTINISSKQMDVTPAIRTHIEERLAKLEKWQTQlINPHFMIHKLPNSYEV-EASIGTPVGELFAKANNEDLYLAINEVET 79
Cdd:PRK10470   1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDR-INQVYVVLKVEKVTHIsDATLHVNGGEIHASAEGQDMYAAIDGLID 79

                         90
                 ....*....|....*..
gi 306869117  80 KLETQLNKlvHKNEARR 96
Cdd:PRK10470  80 KLARQLTK--HKDKLKQ 94
 
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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