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Conserved domains on  [gi|567929594|ref|WP_024031994|]
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MULTISPECIES: RNA-binding S4 domain-containing protein [Pseudoalteromonas]

Protein Classification

RNA-binding S4 domain-containing protein( domain architecture ID 10594118)

RNA-binding S4 domain-containing protein, similar to \tBacillus subtilis ribosome maturation protein RlbA

Gene Ontology:  GO:0003723
PubMed:  10093218

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S4_2 pfam13275
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 17-72 8.86e-22

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4.


:

Pssm-ID: 433078 [Multi-domain]  Cd Length: 65  Bit Score: 81.72  E-value: 8.86e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 567929594   17 LCKLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQLT 72
Cdd:pfam13275  10 LGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEVV 65
 
Name Accession Description Interval E-value
S4_2 pfam13275
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 17-72 8.86e-22

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4.


Pssm-ID: 433078 [Multi-domain]  Cd Length: 65  Bit Score: 81.72  E-value: 8.86e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 567929594   17 LCKLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQLT 72
Cdd:pfam13275  10 LGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEVV 65
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 17-73 1.91e-20

Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 78.14  E-value: 1.91e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 567929594  17 LCKLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQLTL 73
Cdd:COG2501    5 LGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIRVVA 61
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 20-65 1.12e-09

S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274378 [Multi-domain]  Cd Length: 59  Bit Score: 50.63  E-value: 1.12e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 567929594   20 LLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFD 65
Cdd:TIGR02988  14 LLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
PRK11507 PRK11507
ribosome-associated protein YbcJ;
17-72 1.90e-08

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 47.58  E-value: 1.90e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 567929594  17 LCKLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQLT 72
Cdd:PRK11507  14 LCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV 69
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 19-70 1.46e-05

S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.


Pssm-ID: 238095 [Multi-domain]  Cd Length: 70  Bit Score: 40.31  E-value: 1.46e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 567929594  19 KLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQ 70
Cdd:cd00165    5 KILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIE 56
S4 smart00363
S4 RNA-binding domain;
32-67 2.77e-03

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 34.11  E-value: 2.77e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 567929594    32 QAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGE 67
Cdd:smart00363  18 QARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGK 53
 
Name Accession Description Interval E-value
S4_2 pfam13275
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 17-72 8.86e-22

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4.


Pssm-ID: 433078 [Multi-domain]  Cd Length: 65  Bit Score: 81.72  E-value: 8.86e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 567929594   17 LCKLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQLT 72
Cdd:pfam13275  10 LGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEVV 65
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 17-73 1.91e-20

Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 78.14  E-value: 1.91e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 567929594  17 LCKLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQLTL 73
Cdd:COG2501    5 LGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIRVVA 61
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 20-65 1.12e-09

S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274378 [Multi-domain]  Cd Length: 59  Bit Score: 50.63  E-value: 1.12e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 567929594   20 LLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFD 65
Cdd:TIGR02988  14 LLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
PRK11507 PRK11507
ribosome-associated protein YbcJ;
17-72 1.90e-08

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 47.58  E-value: 1.90e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 567929594  17 LCKLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQLT 72
Cdd:PRK11507  14 LCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV 69
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 19-70 1.46e-05

S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.


Pssm-ID: 238095 [Multi-domain]  Cd Length: 70  Bit Score: 40.31  E-value: 1.46e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 567929594  19 KLLKVLDLVEGGGQAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGELFQ 70
Cdd:cd00165    5 KILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIE 56
S4 smart00363
S4 RNA-binding domain;
32-67 2.77e-03

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 34.11  E-value: 2.77e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 567929594    32 QAKNLIAQGYVGVNHEICTIKRKKLYSGDVLEFDGE 67
Cdd:smart00363  18 QARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGK 53
 
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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