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Conserved domains on  [gi|2563316464|gb|WLS85660|]
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S4 domain-containing protein YaaA [Lactobacillus apis]

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 ...
 9-71 2.13e-29

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: 98.67  E-value: 2.13e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2563316464  9 FKVKGEYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVDHETYQ 71
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIE 63
 
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 ...
 9-71 2.13e-29

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: 98.67  E-value: 2.13e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2563316464  9 FKVKGEYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVDHETYQ 71
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIE 63
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 8-66 4.21e-29

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: 97.62  E-value: 4.21e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 2563316464  8 EFKVKGEYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVD 66
Cdd:TIGR02988  1 EIKIFTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 14-71 4.37e-26

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


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 90.08  E-value: 4.37e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2563316464 14 EYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVDHETYQ 71
Cdd:COG2501    1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIR 58
PRK11507 PRK11507
ribosome-associated protein YbcJ;
12-69 2.51e-03

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 32.94  E-value: 2.51e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2563316464 12 KGEYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVDHET 69
Cdd:PRK11507   8 KHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHS 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 ...
 9-71 2.13e-29

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: 98.67  E-value: 2.13e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2563316464  9 FKVKGEYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVDHETYQ 71
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIE 63
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 8-66 4.21e-29

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: 97.62  E-value: 4.21e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 2563316464  8 EFKVKGEYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVD 66
Cdd:TIGR02988  1 EIKIFTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 14-71 4.37e-26

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


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 90.08  E-value: 4.37e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2563316464 14 EYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVDHETYQ 71
Cdd:COG2501    1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIR 58
PRK11507 PRK11507
ribosome-associated protein YbcJ;
12-69 2.51e-03

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 32.94  E-value: 2.51e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2563316464 12 KGEYVTLSQFLKEESIISSGGQAKWYLQDNPVLFNGAKENRRGKKIRPGDQIEVDHET 69
Cdd:PRK11507   8 KHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHS 65
 
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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