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Conserved domains on  [gi|1931720860|ref|XP_037490990|]
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apicoplast ribosomal protein S4 (apicoplast) [Plasmodium vinckei vinckei]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
rps4 super family cl29646
ribosomal protein S4; Reviewed
1-148 5.18e-09

ribosomal protein S4; Reviewed


The actual alignment was detected with superfamily member CHL00113:

Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 53.68  E-value: 5.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931720860   1 MIKFLTPKIKILKKLNIpfLLYLSSKYN--YKLKINKYTYK--SYFDLKLKFVRYICYNYCITFKQYLYYLKKIKNYNEN 76
Cdd:CHL00113    1 MSRYRGPRLKIIRRLGA--LPGLTSKTPrpGSDLRNQSRSGkkSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGS 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1931720860  77 NlYFKLLNILESRLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDIIFFNSKIKYIILYN 148
Cdd:CHL00113   79 T-GQVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQ 149
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
1-148 5.18e-09

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 53.68  E-value: 5.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931720860   1 MIKFLTPKIKILKKLNIpfLLYLSSKYN--YKLKINKYTYK--SYFDLKLKFVRYICYNYCITFKQYLYYLKKIKNYNEN 76
Cdd:CHL00113    1 MSRYRGPRLKIIRRLGA--LPGLTSKTPrpGSDLRNQSRSGkkSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGS 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1931720860  77 NlYFKLLNILESRLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDIIFFNSKIKYIILYN 148
Cdd:CHL00113   79 T-GQVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQ 149
S4 smart00363
S4 RNA-binding domain;
88-146 7.05e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 47.59  E-value: 7.05e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1931720860   88 SRLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDIIFFNSKIKYIIL 146
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKRLK 59
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
89-135 9.15e-08

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: 47.10  E-value: 9.15e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1931720860  89 RLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDII 135
Cdd:pfam01479   2 RLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
1-135 8.28e-05

Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4 or related protein is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440288 [Multi-domain]  Cd Length: 204  Bit Score: 41.98  E-value: 8.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931720860   1 MIKFLTPKIKILKKLNIPflLYLSSKYnyKLKINKYTY-----------KSYFDLKL----KfVRYIcynYCITFKQY-L 64
Cdd:COG0522     1 MARYTGPKCKLCRREGVK--LFLKGER--KCALERRPYppgqhgqrrkkLSDYGLQLrekqK-LRRI---YGVLEKQFrR 72
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1931720860  65 YYLK--KIK-NYNENnlyfkLLNILESRLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDII 135
Cdd:COG0522    73 YFEEaaRRKgNTGEN-----LLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVI 141
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
89-148 2.63e-04

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: 38.00  E-value: 2.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931720860  89 RLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDIIFFNSKIKYIILYN 148
Cdd:cd00165     2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVY 61
 
Name Accession Description Interval E-value
rps4 CHL00113
ribosomal protein S4; Reviewed
1-148 5.18e-09

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 53.68  E-value: 5.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931720860   1 MIKFLTPKIKILKKLNIpfLLYLSSKYN--YKLKINKYTYK--SYFDLKLKFVRYICYNYCITFKQYLYYLKKIKNYNEN 76
Cdd:CHL00113    1 MSRYRGPRLKIIRRLGA--LPGLTSKTPrpGSDLRNQSRSGkkSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGS 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1931720860  77 NlYFKLLNILESRLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDIIFFNSKIKYIILYN 148
Cdd:CHL00113   79 T-GQVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQ 149
S4 smart00363
S4 RNA-binding domain;
88-146 7.05e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 47.59  E-value: 7.05e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1931720860   88 SRLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDIIFFNSKIKYIIL 146
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKRLK 59
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
89-135 9.15e-08

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: 47.10  E-value: 9.15e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1931720860  89 RLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDII 135
Cdd:pfam01479   2 RLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
1-135 8.28e-05

Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4 or related protein is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440288 [Multi-domain]  Cd Length: 204  Bit Score: 41.98  E-value: 8.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931720860   1 MIKFLTPKIKILKKLNIPflLYLSSKYnyKLKINKYTY-----------KSYFDLKL----KfVRYIcynYCITFKQY-L 64
Cdd:COG0522     1 MARYTGPKCKLCRREGVK--LFLKGER--KCALERRPYppgqhgqrrkkLSDYGLQLrekqK-LRRI---YGVLEKQFrR 72
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1931720860  65 YYLK--KIK-NYNENnlyfkLLNILESRLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDII 135
Cdd:COG0522    73 YFEEaaRRKgNTGEN-----LLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVI 141
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
89-148 2.63e-04

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: 38.00  E-value: 2.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931720860  89 RLDVFLVNIGFFKTILQSRYFIKYKYIYINNIYCNYYNIRLKSNDIIFFNSKIKYIILYN 148
Cdd:cd00165     2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVY 61
 
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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