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Conserved domains on  [gi|665410339|ref|NP_001287055|]
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ribosomal protein S4, isoform C [Drosophila melanogaster]

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
 1-258 5.65e-163

40S ribosomal protein S4; Provisional


:

Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 451.86  E-value: 5.65e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   1 MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDP 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  81 TYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVKKTQLGAKGVPFLVTHDGRTIRYPDPLIHANDSV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 161 QVDIASGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIGKGNKPYISLPK 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240

                        250
                 ....*....|....*...
gi 665410339 241 GKGVKLSIAEERDKRLAA 258
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAA 258
 
Name Accession Description Interval E-value
PLN00036 PLN00036
40S ribosomal protein S4; Provisional
 1-258 5.65e-163

40S ribosomal protein S4; Provisional


Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 451.86  E-value: 5.65e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   1 MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDP 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  81 TYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVKKTQLGAKGVPFLVTHDGRTIRYPDPLIHANDSV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 161 QVDIASGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIGKGNKPYISLPK 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240

                        250
                 ....*....|....*...
gi 665410339 241 GKGVKLSIAEERDKRLAA 258
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAA 258
RPS4A COG1471
Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E ...
 4-241 1.10e-78

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: 237.41  E-value: 1.10e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   4 GPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYP 83
Cdd:COG1471    1 GGSRHLKRLAAPKFWPISRKEYKWTVKPSPGPHPKERSIPLLVVLRDVLKYADTAREAKKIISEGKVLVDGRVRKDYKFP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  84 AGYMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVK--------KTQLGakgvpflvTHDGRTIRYPDPL-I 154
Cdd:COG1471   81 VGLMDVISIPKTGEYYRVVPDEKGRLKLIPISEEEAKLKLCKIEnkttvkggKIQLN--------LHDGRNILVDVENdY 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 155 HANDSVQVDIASGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSF-DIVHIKDSQGHVFATRLTNVFIIGKgNK 233
Cdd:COG1471  153 KTGDSLVISIPEQEILDHIPFEEGNLALIVGGKNAGEIGKIVEIKKGKGSKpNTVTIEDKDGEKFETIEDYVFVIGE-EK 231


                 ....*...
gi 665410339 234 PYISLPKG 241
Cdd:COG1471  232 PVIKLGEE 239
Ribosomal_S4e pfam00900
Ribosomal family S4e;
95-169 1.02e-40

Ribosomal family S4e;


Pssm-ID: 459988 [Multi-domain]  Cd Length: 75  Bit Score: 134.87  E-value: 1.02e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665410339   95 TGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVKKTQLGAKGVPFLVTHDGRTIRYPDPLIHANDSVQVDIASGKI 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 3.93e-29

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: 104.52  E-value: 3.93e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 665410339 175 FDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIG 229
Cdd:cd06087    1 FEEGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55
S4 smart00363
S4 RNA-binding domain;
51-99 3.50e-03

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 34.88  E-value: 3.50e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 665410339    51 RLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFF 99
Cdd:smart00363   9 RLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKR 57
 
Name Accession Description Interval E-value
PLN00036 PLN00036
40S ribosomal protein S4; Provisional
 1-258 5.65e-163

40S ribosomal protein S4; Provisional


Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 451.86  E-value: 5.65e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   1 MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDP 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  81 TYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVKKTQLGAKGVPFLVTHDGRTIRYPDPLIHANDSV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 161 QVDIASGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIGKGNKPYISLPK 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240

                        250
                 ....*....|....*...
gi 665410339 241 GKGVKLSIAEERDKRLAA 258
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAA 258
PTZ00118 PTZ00118
40S ribosomal protein S4; Provisional
 1-257 2.32e-131

40S ribosomal protein S4; Provisional


Pssm-ID: 240277 [Multi-domain]  Cd Length: 262  Bit Score: 371.90  E-value: 2.32e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   1 MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDP 80
Cdd:PTZ00118   1 MGKGIKKHMKRINAPSHWMLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  81 TYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVKKTQLGAKGVPFLVTHDGRTIRYPDPLIHANDSV 160
Cdd:PTZ00118  81 TYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 161 QVDIASGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIGKGNKPYISLPK 240
Cdd:PTZ00118 161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPR 240

                        250
                 ....*....|....*..
gi 665410339 241 GKGVKLSIAEERDKRLA 257
Cdd:PTZ00118 241 ERGIKKDIIEERRNRLA 257
PTZ00223 PTZ00223
40S ribosomal protein S4; Provisional
 6-258 2.36e-101

40S ribosomal protein S4; Provisional


Pssm-ID: 140250 [Multi-domain]  Cd Length: 273  Bit Score: 296.52  E-value: 2.36e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   6 KKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAG 85
Cdd:PTZ00223   3 KKHLKRLYAPKDWMLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  86 YMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVKKTQLGAKGVPFLVTHDGRTIRYPDPLIHANDSVQVDIA 165
Cdd:PTZ00223  83 FMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 166 SGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIGKG-NKPYISLPKGKGV 244
Cdd:PTZ00223 163 EKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDmNSVPVTLPKQQGL 242

                        250
                 ....*....|....
gi 665410339 245 KLSIAEERDKRLAA 258
Cdd:PTZ00223 243 RINVIQEREEKLIA 256
PRK04313 PRK04313
30S ribosomal protein S4e; Validated
 5-239 5.42e-80

30S ribosomal protein S4e; Validated


Pssm-ID: 179820 [Multi-domain]  Cd Length: 237  Bit Score: 240.50  E-value: 5.42e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   5 PKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPA 84
Cdd:PRK04313   1 MMRHLKRLAAPKSWPIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  85 GYMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVK--------KTQLGakgvpflvTHDGRTIRYPDPL-IH 155
Cdd:PRK04313  81 GLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIEnkttvkggKIQLN--------LHDGRNILVDVEDdYK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 156 ANDSVQVDIASGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSF-DIVHIKDSQGHVFATRLTNVFIIGKGnKP 234
Cdd:PRK04313 153 TGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKpNIVTLEDKDGEKFETILDYVFVIGKE-KP 231


                 ....*
gi 665410339 235 YISLP 239
Cdd:PRK04313 232 VIKLP 236
RPS4A COG1471
Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E ...
 4-241 1.10e-78

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: 237.41  E-value: 1.10e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339   4 GPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYP 83
Cdd:COG1471    1 GGSRHLKRLAAPKFWPISRKEYKWTVKPSPGPHPKERSIPLLVVLRDVLKYADTAREAKKIISEGKVLVDGRVRKDYKFP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339  84 AGYMDVITLEKTGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVK--------KTQLGakgvpflvTHDGRTIRYPDPL-I 154
Cdd:COG1471   81 VGLMDVISIPKTGEYYRVVPDEKGRLKLIPISEEEAKLKLCKIEnkttvkggKIQLN--------LHDGRNILVDVENdY 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410339 155 HANDSVQVDIASGKITDYIKFDSGNLCMITGGRNLGRVGTVVNRERHPGSF-DIVHIKDSQGHVFATRLTNVFIIGKgNK 233
Cdd:COG1471  153 KTGDSLVISIPEQEILDHIPFEEGNLALIVGGKNAGEIGKIVEIKKGKGSKpNTVTIEDKDGEKFETIEDYVFVIGE-EK 231


                 ....*...
gi 665410339 234 PYISLPKG 241
Cdd:COG1471  232 PVIKLGEE 239
Ribosomal_S4e pfam00900
Ribosomal family S4e;
95-169 1.02e-40

Ribosomal family S4e;


Pssm-ID: 459988 [Multi-domain]  Cd Length: 75  Bit Score: 134.87  E-value: 1.02e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665410339   95 TGEFFRLVYDVKGRFVIHRISAEEAKYKLCKVKKTQLGAKGVPFLVTHDGRTIRYPDPLIHANDSVQVDIASGKI 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 3.93e-29

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: 104.52  E-value: 3.93e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 665410339 175 FDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIG 229
Cdd:cd06087    1 FEEGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55
40S_S4_C pfam16121
40S ribosomal protein S4 C-terminus; This domain is found at the C-terminus of 40S ribosomal ...
 212-259 5.13e-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: 5.13e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 665410339  212 DSQGHVFATRLTNVFIIGKGNKPYISLPKGKGVKLSIAEERDKRLAAK 259
Cdd:pfam16121   1 DALGHTFATRLSNVFVIGKGNKPWISLPKGKGIKLTIAEERDKRLAAK 48
RS4NT pfam08071
RS4NT (NUC023) domain; This is the N-terminal domain of Ribosomal S4 / S4e proteins. This ...
 3-39 1.52e-19

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: 79.14  E-value: 1.52e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 665410339    3 RGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLR 39
Cdd:pfam08071   1 RGPKKHLKRLAAPKHWMLDKKGGVFAPKPSPGPHKLR 37
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 44-112 2.80e-05

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: 41.08  E-value: 2.80e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 665410339  44 LLIFLRnRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFFRLVYDVKGRFVIH 112
Cdd:cd00165    3 LDKILA-RLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVVN 70
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 42-90 2.76e-04

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: 37.86  E-value: 2.76e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 665410339   42 LPLLIFLRnRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVI 90
Cdd:pfam01479   1 RRLDKVLA-RLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
51-99 3.50e-03

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 34.88  E-value: 3.50e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 665410339    51 RLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFF 99
Cdd:smart00363   9 RLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKR 57
 
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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