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Conserved domains on  [gi|15226130|ref|NP_178806|]
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Alpha-L RNA-binding motif/Ribosomal protein S4 family protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpsD_bact super family cl29645
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 52-191 2.59e-11

ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


The actual alignment was detected with superfamily member TIGR01017:

Pssm-ID: 200066 [Multi-domain]  Cd Length: 200  Bit Score: 62.32  E-value: 2.59e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130    52 IKKRKIYP------KKYLTSY-IQLQTTRKLPLFHG--DLPITEMHRGTKRT---SYIPFPLNPETRFDVIPLRLHFLET 119
Cdd:TIGR01017  25 LLKRKYPPgqhgqrRKKLSDYgLQLQEKQKLKFMYGitEKQFRKYFKEAKKLkgnTGENLLRLLESRLDNVVYRLGFAPT 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130   120 IPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQE---NNAIIRG--EEIRRSF---YKEISVEKIIGKLLHQPLRMW 191
Cdd:TIGR01017 105 RFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEkskKIPLVKEnlETNGQRNipsWLEVDKKTLEGKVLRVPERSQ 184
 
Name Accession Description Interval E-value
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 52-191 2.59e-11

ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 200066 [Multi-domain]  Cd Length: 200  Bit Score: 62.32  E-value: 2.59e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130    52 IKKRKIYP------KKYLTSY-IQLQTTRKLPLFHG--DLPITEMHRGTKRT---SYIPFPLNPETRFDVIPLRLHFLET 119
Cdd:TIGR01017  25 LLKRKYPPgqhgqrRKKLSDYgLQLQEKQKLKFMYGitEKQFRKYFKEAKKLkgnTGENLLRLLESRLDNVVYRLGFAPT 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130   120 IPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQE---NNAIIRG--EEIRRSF---YKEISVEKIIGKLLHQPLRMW 191
Cdd:TIGR01017 105 RFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEkskKIPLVKEnlETNGQRNipsWLEVDKKTLEGKVLRVPERSQ 184
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 106-157 1.95e-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: 50.71  E-value: 1.95e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15226130 106 RFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQEN 157
Cdd:cd00165   2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGK 53
S4 smart00363
S4 RNA-binding domain;
105-157 8.90e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 48.36  E-value: 8.90e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 15226130    105 TRFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQEN 157
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGK 53
rps4 CHL00113
ribosomal protein S4; Reviewed
 104-153 1.29e-07

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 51.37  E-value: 1.29e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 15226130  104 ETRFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIIS 153
Cdd:CHL00113  88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIIT 137
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 106-152 3.77e-07

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: 46.33  E-value: 3.77e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15226130   106 RFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDII 152
Cdd:pfam01479   2 RLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 104-189 4.44e-06

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: 46.99  E-value: 4.44e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130 104 ETRFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQE---NNAIIRG--EEI-RRSFYKEISV- 176
Cdd:COG0522  93 ERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREkskKLPRIKEalESAeQRGVPEWLEVd 172

                        90
                ....*....|....
gi 15226130 177 -EKIIGKLLHQPLR 189
Cdd:COG0522 173 aEKLSGTVVRLPER 186
 
Name Accession Description Interval E-value
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 52-191 2.59e-11

ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 200066 [Multi-domain]  Cd Length: 200  Bit Score: 62.32  E-value: 2.59e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130    52 IKKRKIYP------KKYLTSY-IQLQTTRKLPLFHG--DLPITEMHRGTKRT---SYIPFPLNPETRFDVIPLRLHFLET 119
Cdd:TIGR01017  25 LLKRKYPPgqhgqrRKKLSDYgLQLQEKQKLKFMYGitEKQFRKYFKEAKKLkgnTGENLLRLLESRLDNVVYRLGFAPT 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130   120 IPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQE---NNAIIRG--EEIRRSF---YKEISVEKIIGKLLHQPLRMW 191
Cdd:TIGR01017 105 RFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEkskKIPLVKEnlETNGQRNipsWLEVDKKTLEGKVLRVPERSQ 184
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 106-157 1.95e-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: 50.71  E-value: 1.95e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15226130 106 RFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQEN 157
Cdd:cd00165   2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGK 53
S4 smart00363
S4 RNA-binding domain;
105-157 8.90e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 48.36  E-value: 8.90e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 15226130    105 TRFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQEN 157
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGK 53
rps4 CHL00113
ribosomal protein S4; Reviewed
 104-153 1.29e-07

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 51.37  E-value: 1.29e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 15226130  104 ETRFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIIS 153
Cdd:CHL00113  88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIIT 137
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 106-152 3.77e-07

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: 46.33  E-value: 3.77e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15226130   106 RFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDII 152
Cdd:pfam01479   2 RLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 104-189 4.44e-06

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: 46.99  E-value: 4.44e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226130 104 ETRFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQE---NNAIIRG--EEI-RRSFYKEISV- 176
Cdd:COG0522  93 ERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREkskKLPRIKEalESAeQRGVPEWLEVd 172

                        90
                ....*....|....
gi 15226130 177 -EKIIGKLLHQPLR 189
Cdd:COG0522 173 aEKLSGTVVRLPER 186
 
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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