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Conserved domains on  [gi|524044696|emb|CCY26513|]
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s4 domain protein [Firmicutes bacterium CAG:114]

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 ...
 6-69 1.83e-28

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: 96.35  E-value: 1.83e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 524044696   6 VSITTEYIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTV 69
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEV 64
 
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 ...
 6-69 1.83e-28

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: 96.35  E-value: 1.83e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 524044696   6 VSITTEYIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTV 69
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEV 64
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 11-70 4.80e-27

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


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 92.39  E-value: 4.80e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 524044696 11 EYIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTVQ 70
Cdd:COG2501   1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIRVV 60
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 6-63 6.64e-22

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: 79.51  E-value: 6.64e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 524044696   6 VSITTEYIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFA 63
Cdd:TIGR02988  2 IKIFTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 15-69 2.37e-08

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: 45.32  E-value: 2.37e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 524044696 15 LEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTV 69
Cdd:cd00165   3 LDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57
PRK11507 PRK11507
ribosome-associated protein YbcJ;
12-70 8.83e-08

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 44.11  E-value: 8.83e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 524044696 12 YIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTVQ 70
Cdd:PRK11507 11 HVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV 69
S4 smart00363
S4 RNA-binding domain;
15-69 9.28e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 43.74  E-value: 9.28e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 524044696   15 LEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTV 69
Cdd:smart00363  3 LDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKR 57
 
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 ...
 6-69 1.83e-28

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: 96.35  E-value: 1.83e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 524044696   6 VSITTEYIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTV 69
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDGETIEV 64
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 11-70 4.80e-27

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


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 92.39  E-value: 4.80e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 524044696 11 EYIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTVQ 70
Cdd:COG2501   1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGETIRVV 60
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 6-63 6.64e-22

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: 79.51  E-value: 6.64e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 524044696   6 VSITTEYIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFA 63
Cdd:TIGR02988  2 IKIFTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 15-69 2.37e-08

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: 45.32  E-value: 2.37e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 524044696 15 LEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTV 69
Cdd:cd00165   3 LDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57
PRK11507 PRK11507
ribosome-associated protein YbcJ;
12-70 8.83e-08

ribosome-associated protein YbcJ;


Pssm-ID: 183166  Cd Length: 70  Bit Score: 44.11  E-value: 8.83e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 524044696 12 YIKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTVQ 70
Cdd:PRK11507 11 HVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV 69
S4 smart00363
S4 RNA-binding domain;
15-69 9.28e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 43.74  E-value: 9.28e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 524044696   15 LEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQVAFAGRELTV 69
Cdd:smart00363  3 LDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKR 57
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 15-60 2.54e-06

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, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.


Pssm-ID: 396182 [Multi-domain]  Cd Length: 48  Bit Score: 39.78  E-value: 2.54e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 524044696  15 LEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDQV 60
Cdd:pfam01479  3 LDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
TyrS COG0162
Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Tyrosyl-tRNA ...
 13-70 7.21e-06

Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Tyrosyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 439932 [Multi-domain]  Cd Length: 409  Bit Score: 41.17  E-value: 7.21e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 524044696  13 IKLEALLKLANLVSSGGEAKCLIQDGQVSVNGQVCRMRGKKLRPGDqvAFAGRELTVQ 70
Cdd:COG0162  342 IPLVDLLVEAGLAASKSEARRLIKQGGVSVNGEKVTDPDAVLTAGD--LLHGGYLVLR 397
 
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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