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Conserved domains on  [gi|1030991025|emb|SBK36117|]
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sigma-54 modulation protein [Klebsiella variicola]

Protein Classification

ribosome-associated translation inhibitor RaiA( domain architecture ID 10793375)

ribosome-associated translation inhibitor RaiA 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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-111 1.62e-74

ribosome-associated translation inhibitor RaiA;


:

Pssm-ID: 182378  Cd Length: 113  Bit Score: 216.12  E-value: 1.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   1 MTMNITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:PRK10324    1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1030991025  81 LERQLNKVQHKGEARRAATSVKEAGFVEEEE 111
Cdd:PRK10324   81 LERQLNKLQHKGEARRAATSVKDANFVEEVE 111
 
Name Accession Description Interval E-value
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-111 1.62e-74

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 216.12  E-value: 1.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   1 MTMNITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:PRK10324    1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1030991025  81 LERQLNKVQHKGEARRAATSVKEAGFVEEEE 111
Cdd:PRK10324   81 LERQLNKLQHKGEARRAATSVKDANFVEEVE 111
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 1.28e-41

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: 132.07  E-value: 1.28e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   1 MTMNITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 1030991025  81 LERQLNKVQHKGEAR 95
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 4-91 1.03e-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: 107.22  E-value: 1.03e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   4 NITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEP---QGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:cd00552     3 NITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAVDK 82

                          90
                  ....*....|.
gi 1030991025  81 LERQLNKVQHK 91
Cdd:cd00552    83 LERQLRKYKEK 93
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 4-97 2.12e-31

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 106.40  E-value: 2.12e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   4 NITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEP-QGFIADATINTPNGHLVASARHEDMYAAINELINKLE 82
Cdd:COG1544     3 NITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKnRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDKLE 82

                          90
                  ....*....|....*
gi 1030991025  83 RQLNKVQHKGEARRA 97
Cdd:COG1544    83 RQLRKYKEKLKDHRR 97
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-91 3.33e-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: 87.94  E-value: 3.33e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   4 NITSKQMEITPAIRQHVADRLAKLDKwqtHLINPHIILSKEpQGFIADATINTPNGHLV-ASARHEDMYAAINELINKLE 82
Cdd:pfam02482   2 NITGRNIEVTDALREYVEKKLEKLEK---YFISADVTLSVE-KRHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKLE 77


                  ....*....
gi 1030991025  83 RQLNKVQHK 91
Cdd:pfam02482  78 RQLRKYKEK 86
 
Name Accession Description Interval E-value
PRK10324 PRK10324
ribosome-associated translation inhibitor RaiA;
1-111 1.62e-74

ribosome-associated translation inhibitor RaiA;


Pssm-ID: 182378  Cd Length: 113  Bit Score: 216.12  E-value: 1.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   1 MTMNITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:PRK10324    1 MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINK 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1030991025  81 LERQLNKVQHKGEARRAATSVKEAGFVEEEE 111
Cdd:PRK10324   81 LERQLNKLQHKGEARRAATSVKDANFVEEVE 111
yfiA TIGR00741
ribosomal subunit interface protein; This model includes a small protein encoded by one of two ...
 1-95 1.28e-41

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: 132.07  E-value: 1.28e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   1 MTMNITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:TIGR00741   1 MNINITGNNVEITEALREYVEEKLARLERYFTRIINVDVVLSVERNRFKVEATLYVNGGVIRASAESEDMYAAIDLAIDK 80

                          90
                  ....*....|....*
gi 1030991025  81 LERQLNKVQHKGEAR 95
Cdd:TIGR00741  81 LERQLRKLKEKRKEH 95
RaiA cd00552
RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a ...
 4-91 1.03e-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: 107.22  E-value: 1.03e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   4 NITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEP---QGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:cd00552     3 NITGRNIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKnhgKRFKVEITIHLPGGVLRAEASAEDLYAAIDLAVDK 82

                          90
                  ....*....|.
gi 1030991025  81 LERQLNKVQHK 91
Cdd:cd00552    83 LERQLRKYKEK 93
RaiA COG1544
Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and ...
 4-97 2.12e-31

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


Pssm-ID: 441153  Cd Length: 101  Bit Score: 106.40  E-value: 2.12e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   4 NITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEP-QGFIADATINTPNGHLVASARHEDMYAAINELINKLE 82
Cdd:COG1544     3 NITGRNVEVTDALREYVEEKLEKLEKYFDRIISADVTLSVEKnRRFKVEITLHVPGPVLRAEAEAEDMYAAIDLAVDKLE 82

                          90
                  ....*....|....*
gi 1030991025  83 RQLNKVQHKGEARRA 97
Cdd:COG1544    83 RQLRKYKEKLKDHRR 97
Ribosomal_S30AE pfam02482
Sigma 54 modulation protein / S30EA ribosomal protein; This Pfam family contains the sigma-54 ...
 4-91 3.33e-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: 87.94  E-value: 3.33e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   4 NITSKQMEITPAIRQHVADRLAKLDKwqtHLINPHIILSKEpQGFIADATINTPNGHLV-ASARHEDMYAAINELINKLE 82
Cdd:pfam02482   2 NITGRNIEVTDALREYVEKKLEKLEK---YFISADVTLSVE-KRHKVEVTIRLVPGVVLrAEETAEDLYAAIDLAVDKLE 77


                  ....*....
gi 1030991025  83 RQLNKVQHK 91
Cdd:pfam02482  78 RQLRKYKEK 86
PRK10470 PRK10470
ribosome hibernation promoting factor;
1-91 4.85e-19

ribosome hibernation promoting factor;


Pssm-ID: 182484  Cd Length: 95  Bit Score: 74.95  E-value: 4.85e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1030991025   1 MTMNITSKQMEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASARHEDMYAAINELINK 80
Cdd:PRK10470    1 MQLNITGHNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHISDATLHVNGGEIHASAEGQDMYAAIDGLIDK 80

                          90
                  ....*....|.
gi 1030991025  81 LERQLNKVQHK 91
Cdd:PRK10470   81 LARQLTKHKDK 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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