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Conserved domains on  [gi|640723878|ref|WP_025146931|]
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MULTISPECIES: S4 domain-containing protein YaaA [Bacillus]

Protein Classification

RNA-binding S4 domain-containing protein( domain architecture ID 10021620)

RNA-binding S4 domain-containing protein

Gene Ontology:  GO:0003723
PubMed:  10093218

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 4-61 1.77e-32

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: 106.09  E-value: 1.77e-32
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 640723878   4 IKISTEYITLGQFLKLADVIDTGGAVKWFLQEYEVYVNQELENRRGRKLYANDIVEIP 61
Cdd:TIGR02988  2 IKIFTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
 
Name Accession Description Interval E-value
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 4-61 1.77e-32

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: 106.09  E-value: 1.77e-32
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 640723878   4 IKISTEYITLGQFLKLADVIDTGGAVKWFLQEYEVYVNQELENRRGRKLYANDIVEIP 61
Cdd:TIGR02988  2 IKIFTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
S4_2 pfam13275
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 4-68 3.78e-31

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: 102.90  E-value: 3.78e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640723878   4 IKISTEYITLGQFLKLADVIDTGGAVKWFLQEYEVYVNQELENRRGRKLYANDIVEIPGsGTFQV 68
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDG-ETIEV 64
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 9-70 1.72e-28

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


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 96.24  E-value: 1.72e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 640723878  9 EYITLGQFLKLADVIDTGGAVKWFLQEYEVYVNQELENRRGRKLYANDIVEIPGSgTFQVQS 70
Cdd:COG2501   1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGE-TIRVVA 61
AARP2CN smart00785
AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to ...
 48-68 3.89e-03

AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU.


Pssm-ID: 129021 [Multi-domain]  Cd Length: 83  Bit Score: 32.53  E-value: 3.89e-03
                          10        20
                  ....*....|....*....|.
gi 640723878   48 RGRKLYANDIVEIPGSGTFQV 68
Cdd:smart00785 53 RGTGLNANQLVHIPGLGDFQI 73
 
Name Accession Description Interval E-value
YaaA_near_RecF TIGR02988
S4 domain protein YaaA; This small protein has a single S4 domain (pfam01479), as do bacterial ...
 4-61 1.77e-32

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: 106.09  E-value: 1.77e-32
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 640723878   4 IKISTEYITLGQFLKLADVIDTGGAVKWFLQEYEVYVNQELENRRGRKLYANDIVEIP 61
Cdd:TIGR02988  2 IKIFTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59
S4_2 pfam13275
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 4-68 3.78e-31

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: 102.90  E-value: 3.78e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640723878   4 IKISTEYITLGQFLKLADVIDTGGAVKWFLQEYEVYVNQELENRRGRKLYANDIVEIPGsGTFQV 68
Cdd:pfam13275  1 IKIRGEYITLGQLLKLAGLVESGGEAKWFIAEGEVLVNGEVETRRGKKLRAGDVVEFDG-ETIEV 64
YbcJ COG2501
Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal ...
 9-70 1.72e-28

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


Pssm-ID: 441995 [Multi-domain]  Cd Length: 61  Bit Score: 96.24  E-value: 1.72e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 640723878  9 EYITLGQFLKLADVIDTGGAVKWFLQEYEVYVNQELENRRGRKLYANDIVEIPGSgTFQVQS 70
Cdd:COG2501   1 EYITLGQLLKLAGLVESGGEAKALIAEGEVKVNGEVETRRGRKLRPGDVVEVGGE-TIRVVA 61
AARP2CN pfam08142
AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to ...
 48-70 1.14e-03

AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU.


Pssm-ID: 462369  Cd Length: 86  Bit Score: 34.02  E-value: 1.14e-03
                         10        20
                 ....*....|....*....|...
gi 640723878  48 RGRKLYANDIVEIPGSGTFQVQS 70
Cdd:pfam08142 57 RGTPLKVNQLVHIPGLGDFQISK 79
AARP2CN smart00785
AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to ...
 48-68 3.89e-03

AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU.


Pssm-ID: 129021 [Multi-domain]  Cd Length: 83  Bit Score: 32.53  E-value: 3.89e-03
                          10        20
                  ....*....|....*....|.
gi 640723878   48 RGRKLYANDIVEIPGSGTFQV 68
Cdd:smart00785 53 RGTGLNANQLVHIPGLGDFQI 73
 
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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