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Conserved domains on  [gi|4506727|ref|NP_000999|]
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small ribosomal subunit protein eS4, Y isoform 1 [Homo sapiens]

Protein Classification

eS4 family ribosomal protein( domain architecture ID 11476322)

eS4 family ribosomal protein is the only ribosomal protein known to be encoded by more than one gene in the human genome, RPS4Y1 and RPS4X. The three functionally equivalent isoforms encoded by these genes are not identical.

Gene Ontology:  GO:0006412|GO:0031369|GO:0003735
PubMed:  24524803

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PLN00036 PLN00036
40S ribosomal protein S4; Provisional
1-260 5.61e-165

40S ribosomal protein S4; Provisional


:

Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 456.87  E-value: 5.61e-165
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727     1 MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDV 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    81 TYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727   161 QIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPR 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240
                        250       260
                 ....*....|....*....|
gi 4506727   241 GKGIRLTVAEERDKRLATKQ 260
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAAGQ 260
 
Name Accession Description Interval E-value
PLN00036 PLN00036
40S ribosomal protein S4; Provisional
1-260 5.61e-165

40S ribosomal protein S4; Provisional


Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 456.87  E-value: 5.61e-165
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727     1 MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDV 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    81 TYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727   161 QIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPR 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240
                        250       260
                 ....*....|....*....|
gi 4506727   241 GKGIRLTVAEERDKRLATKQ 260
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAAGQ 260
RPS4A COG1471
Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E ...
4-239 7.72e-73

Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441080  Cd Length: 239  Bit Score: 222.77  E-value: 7.72e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    4 GPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDVTYP 83
Cdd:COG1471   1 GGSRHLKRLAAPKFWPISRKEYKWTVKPSPGPHPKERSIPLLVVLRDVLKYADTAREAKKIISEGKVLVDGRVRKDYKFP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727   84 AGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVgVKG--IpHLVTHDARTIRY-PDPVIKVNDTV 160
Cdd:COG1471  81 VGLMDVISIPKTGEYYRVVPDEKGRLKLIPISEEEAKLKLCKIENKTT-VKGgkI-QLNLHDGRNILVdVENDYKTGDSL 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727  161 QIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSF-DVVHVKDANGNSFATRLSNIFVIGnGNKPWISLP 239
Cdd:COG1471 159 VISIPEQEILDHIPFEEGNLALIVGGKNAGEIGKIVEIKKGKGSKpNTVTIEDKDGEKFETIEDYVFVIG-EEKPVIKLG 237
Ribosomal_S4e pfam00900
Ribosomal family S4e;
95-169 6.97e-42

Ribosomal family S4e;


Pssm-ID: 459988 [Multi-domain]  Cd Length: 75  Bit Score: 137.95  E-value: 6.97e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4506727     95 TGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTVQIDLGTGKI 169
Cdd:pfam00900   1 TGEYYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKTTVKGGKPQLNLHDGRNILYPDPLIKTNDTVKIDLPTGKI 75
KOW_RPS4 cd06087
KOW motif of Ribosomal Protein S4 (RPS4); RPS4 plays a critical role in the core assembly of ...
175-229 6.31e-28

KOW motif of Ribosomal Protein S4 (RPS4); RPS4 plays a critical role in the core assembly of the small ribosomal subunit with a KOW motif at its C-terminal. RPS4 also acts as a general transcription antiterminator factor and regulates ribosomal RNA expression level. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPS4 deficiency in human has been associated with Turner syndrome. Archeae RPS4 (RPS4e) showed substantial identity to the eukaryotic equivalents RPS4, but the archaeal proteins formed a different complex from the eukaryotic proteins.


Pssm-ID: 240511 [Multi-domain]  Cd Length: 55  Bit Score: 101.44  E-value: 6.31e-28
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 4506727  175 FDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIG 229
Cdd:cd06087   1 FEEGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55
 
Name Accession Description Interval E-value
PLN00036 PLN00036
40S ribosomal protein S4; Provisional
1-260 5.61e-165

40S ribosomal protein S4; Provisional


Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 456.87  E-value: 5.61e-165
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727     1 MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDV 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    81 TYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727   161 QIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPR 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240
                        250       260
                 ....*....|....*....|
gi 4506727   241 GKGIRLTVAEERDKRLATKQ 260
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAAGQ 260
PTZ00118 PTZ00118
40S ribosomal protein S4; Provisional
1-260 5.21e-134

40S ribosomal protein S4; Provisional


Pssm-ID: 240277 [Multi-domain]  Cd Length: 262  Bit Score: 378.83  E-value: 5.21e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727     1 MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDV 80
Cdd:PTZ00118   1 MGKGIKKHMKRINAPSHWMLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDC 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    81 TYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTV 160
Cdd:PTZ00118  81 TYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727   161 QIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPR 240
Cdd:PTZ00118 161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPR 240
                        250       260
                 ....*....|....*....|
gi 4506727   241 GKGIRLTVAEERDKRLATKQ 260
Cdd:PTZ00118 241 ERGIKKDIIEERRNRLAKAL 260
PTZ00223 PTZ00223
40S ribosomal protein S4; Provisional
6-261 6.59e-99

40S ribosomal protein S4; Provisional


Pssm-ID: 140250 [Multi-domain]  Cd Length: 273  Bit Score: 290.36  E-value: 6.59e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727     6 KKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDVTYPAG 85
Cdd:PTZ00223   3 KKHLKRLYAPKDWMLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAG 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    86 FMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTVQIDLG 165
Cdd:PTZ00223  83 FMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVK 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727   166 TGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNG-NKPWISLPRGKGI 244
Cdd:PTZ00223 163 EKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDmNSVPVTLPKQQGL 242
                        250
                 ....*....|....*..
gi 4506727   245 RLTVAEERDKRLATKQS 261
Cdd:PTZ00223 243 RINVIQEREEKLIAAEA 259
PRK04313 PRK04313
30S ribosomal protein S4e; Validated
5-239 9.53e-75

30S ribosomal protein S4e; Validated


Pssm-ID: 179820 [Multi-domain]  Cd Length: 237  Bit Score: 227.40  E-value: 9.53e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727     5 PKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDVTYPA 84
Cdd:PRK04313   1 MMRHLKRLAAPKSWPIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    85 GFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVgVKG--IpHLVTHDARTIRYPDP-VIKVNDTVQ 161
Cdd:PRK04313  81 GLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTT-VKGgkI-QLNLHDGRNILVDVEdDYKTGDSLL 158
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4506727   162 IDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSF-DVVHVKDANGNSFATRLSNIFVIGNGnKPWISLP 239
Cdd:PRK04313 159 ISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKpNIVTLEDKDGEKFETILDYVFVIGKE-KPVIKLP 236
RPS4A COG1471
Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E ...
4-239 7.72e-73

Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441080  Cd Length: 239  Bit Score: 222.77  E-value: 7.72e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727    4 GPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDVTYP 83
Cdd:COG1471   1 GGSRHLKRLAAPKFWPISRKEYKWTVKPSPGPHPKERSIPLLVVLRDVLKYADTAREAKKIISEGKVLVDGRVRKDYKFP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727   84 AGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVgVKG--IpHLVTHDARTIRY-PDPVIKVNDTV 160
Cdd:COG1471  81 VGLMDVISIPKTGEYYRVVPDEKGRLKLIPISEEEAKLKLCKIENKTT-VKGgkI-QLNLHDGRNILVdVENDYKTGDSL 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506727  161 QIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSF-DVVHVKDANGNSFATRLSNIFVIGnGNKPWISLP 239
Cdd:COG1471 159 VISIPEQEILDHIPFEEGNLALIVGGKNAGEIGKIVEIKKGKGSKpNTVTIEDKDGEKFETIEDYVFVIG-EEKPVIKLG 237
Ribosomal_S4e pfam00900
Ribosomal family S4e;
95-169 6.97e-42

Ribosomal family S4e;


Pssm-ID: 459988 [Multi-domain]  Cd Length: 75  Bit Score: 137.95  E-value: 6.97e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4506727     95 TGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTVQIDLGTGKI 169
Cdd:pfam00900   1 TGEYYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKTTVKGGKPQLNLHDGRNILYPDPLIKTNDTVKIDLPTGKI 75
40S_S4_C pfam16121
40S ribosomal protein S4 C-terminus; This domain is found at the C-terminus of 40S ribosomal ...
212-259 6.05e-28

40S ribosomal protein S4 C-terminus; This domain is found at the C-terminus of 40S ribosomal protein S4.


Pssm-ID: 465028 [Multi-domain]  Cd Length: 48  Bit Score: 101.46  E-value: 6.05e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 4506727    212 DANGNSFATRLSNIFVIGNGNKPWISLPRGKGIRLTVAEERDKRLATK 259
Cdd:pfam16121   1 DALGHTFATRLSNVFVIGKGNKPWISLPKGKGIKLTIAEERDKRLAAK 48
KOW_RPS4 cd06087
KOW motif of Ribosomal Protein S4 (RPS4); RPS4 plays a critical role in the core assembly of ...
175-229 6.31e-28

KOW motif of Ribosomal Protein S4 (RPS4); RPS4 plays a critical role in the core assembly of the small ribosomal subunit with a KOW motif at its C-terminal. RPS4 also acts as a general transcription antiterminator factor and regulates ribosomal RNA expression level. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPS4 deficiency in human has been associated with Turner syndrome. Archeae RPS4 (RPS4e) showed substantial identity to the eukaryotic equivalents RPS4, but the archaeal proteins formed a different complex from the eukaryotic proteins.


Pssm-ID: 240511 [Multi-domain]  Cd Length: 55  Bit Score: 101.44  E-value: 6.31e-28
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 4506727  175 FDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIG 229
Cdd:cd06087   1 FEEGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55
RS4NT pfam08071
RS4NT (NUC023) domain; This is the N-terminal domain of Ribosomal S4 / S4e proteins. This ...
3-39 6.30e-21

RS4NT (NUC023) domain; This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains.


Pssm-ID: 429817 [Multi-domain]  Cd Length: 37  Bit Score: 82.61  E-value: 6.30e-21
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 4506727      3 RGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLR 39
Cdd:pfam08071   1 RGPKKHLKRLAAPKHWMLDKKGGVFAPKPSPGPHKLR 37
 
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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