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Conserved domains on  [gi|768520782|gb|AJU33846|]
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Rps4bp [Saccharomyces cerevisiae YJM981]

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
 1-259 1.14e-155

40S ribosomal protein S4; Provisional


:

Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 433.37  E-value: 1.14e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   1 MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDT 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  81 TYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 161 KIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240

                        250
                 ....*....|....*....
gi 768520782 241 GKGIKLSIAEERDRRRAQQ 259
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAAG 259
 
Name Accession Description Interval E-value
PLN00036 PLN00036
40S ribosomal protein S4; Provisional
 1-259 1.14e-155

40S ribosomal protein S4; Provisional


Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 433.37  E-value: 1.14e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   1 MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDT 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  81 TYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 161 KIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240

                        250
                 ....*....|....*....
gi 768520782 241 GKGIKLSIAEERDRRRAQQ 259
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAAG 259
RPS4A COG1471
Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E ...
 4-241 3.60e-74

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: 225.85  E-value: 3.60e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   4 GPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYP 83
Cdd:COG1471    1 GGSRHLKRLAAPKFWPISRKEYKWTVKPSPGPHPKERSIPLLVVLRDVLKYADTAREAKKIISEGKVLVDGRVRKDYKFP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  84 AGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPN-IKVNDTVKI 162
Cdd:COG1471   81 VGLMDVISIPKTGEYYRVVPDEKGRLKLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVENdYKTGDSLVI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 163 DLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIvhKERHDGGF---DLVHIKDSLDNTFVTRLNNVFVIGEQgKPYISLP 239
Cdd:COG1471  161 SIPEQEILDHIPFEEGNLALIVGGKNAGEIGKI--VEIKKGKGskpNTVTIEDKDGEKFETIEDYVFVIGEE-KPVIKLG 237


                 ..
gi 768520782 240 KG 241
Cdd:COG1471  238 EE 239
Ribosomal_S4e pfam00900
Ribosomal family S4e;
95-169 9.29e-42

Ribosomal family S4e;


Pssm-ID: 459988 [Multi-domain]  Cd Length: 75  Bit Score: 137.57  E-value: 9.29e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768520782   95 TNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKI 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 2.09e-25

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: 94.89  E-value: 2.09e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 768520782 175 FDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIG 229
Cdd:cd06087    1 FEEGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55
S4 smart00363
S4 RNA-binding domain;
44-93 5.32e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.19  E-value: 5.32e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 768520782    44 LIVFLRnRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVITLD 93
Cdd:smart00363   3 LDKFLA-RLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVR 51
 
Name Accession Description Interval E-value
PLN00036 PLN00036
40S ribosomal protein S4; Provisional
 1-259 1.14e-155

40S ribosomal protein S4; Provisional


Pssm-ID: 177670 [Multi-domain]  Cd Length: 261  Bit Score: 433.37  E-value: 1.14e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   1 MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDT 80
Cdd:PLN00036   1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  81 TYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTV 160
Cdd:PLN00036  81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 161 KIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK 240
Cdd:PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240

                        250
                 ....*....|....*....
gi 768520782 241 GKGIKLSIAEERDRRRAQQ 259
Cdd:PLN00036 241 GKGIKLSIIEEARKRLAAG 259
PTZ00118 PTZ00118
40S ribosomal protein S4; Provisional
 1-258 8.82e-131

40S ribosomal protein S4; Provisional


Pssm-ID: 240277 [Multi-domain]  Cd Length: 262  Bit Score: 370.36  E-value: 8.82e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   1 MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDT 80
Cdd:PTZ00118   1 MGKGIKKHMKRINAPSHWMLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  81 TYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTV 160
Cdd:PTZ00118  81 TYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 161 KIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK 240
Cdd:PTZ00118 161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPR 240

                        250
                 ....*....|....*...
gi 768520782 241 GKGIKLSIAEERDRRRAQ 258
Cdd:PTZ00118 241 ERGIKKDIIEERRNRLAK 258
PTZ00223 PTZ00223
40S ribosomal protein S4; Provisional
 6-255 5.81e-94

40S ribosomal protein S4; Provisional


Pssm-ID: 140250 [Multi-domain]  Cd Length: 273  Bit Score: 277.65  E-value: 5.81e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   6 KKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAG 85
Cdd:PTZ00223   3 KKHLKRLYAPKDWMLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  86 FMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLA 165
Cdd:PTZ00223  83 FMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 166 SGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPY-ISLPKGKGI 244
Cdd:PTZ00223 163 EKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVpVTLPKQQGL 242

                        250
                 ....*....|.
gi 768520782 245 KLSIAEERDRR 255
Cdd:PTZ00223 243 RINVIQEREEK 253
PRK04313 PRK04313
30S ribosomal protein S4e; Validated
 5-239 5.29e-76

30S ribosomal protein S4e; Validated


Pssm-ID: 179820 [Multi-domain]  Cd Length: 237  Bit Score: 230.48  E-value: 5.29e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   5 PKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPA 84
Cdd:PRK04313   1 MMRHLKRLAAPKSWPIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  85 GFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVK--------KVQLGkkgvpyvvTHDGRTIRYPDPN-IK 155
Cdd:PRK04313  81 GLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIEnkttvkggKIQLN--------LHDGRNILVDVEDdYK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 156 VNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGF-DLVHIKDSLDNTFVTRLNNVFVIGEqGKP 234
Cdd:PRK04313 153 TGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKpNIVTLEDKDGEKFETILDYVFVIGK-EKP 231


                 ....*
gi 768520782 235 YISLP 239
Cdd:PRK04313 232 VIKLP 236
RPS4A COG1471
Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4E ...
 4-241 3.60e-74

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: 225.85  E-value: 3.60e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782   4 GPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYP 83
Cdd:COG1471    1 GGSRHLKRLAAPKFWPISRKEYKWTVKPSPGPHPKERSIPLLVVLRDVLKYADTAREAKKIISEGKVLVDGRVRKDYKFP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782  84 AGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPN-IKVNDTVKI 162
Cdd:COG1471   81 VGLMDVISIPKTGEYYRVVPDEKGRLKLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVENdYKTGDSLVI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768520782 163 DLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIvhKERHDGGF---DLVHIKDSLDNTFVTRLNNVFVIGEQgKPYISLP 239
Cdd:COG1471  161 SIPEQEILDHIPFEEGNLALIVGGKNAGEIGKI--VEIKKGKGskpNTVTIEDKDGEKFETIEDYVFVIGEE-KPVIKLG 237


                 ..
gi 768520782 240 KG 241
Cdd:COG1471  238 EE 239
Ribosomal_S4e pfam00900
Ribosomal family S4e;
95-169 9.29e-42

Ribosomal family S4e;


Pssm-ID: 459988 [Multi-domain]  Cd Length: 75  Bit Score: 137.57  E-value: 9.29e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768520782   95 TNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKI 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 2.43e-26

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: 97.22  E-value: 2.43e-26
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 768520782  212 DSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEERDRRRAQQ 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 2.09e-25

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: 94.89  E-value: 2.09e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 768520782 175 FDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIG 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 3.26e-18

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: 75.67  E-value: 3.26e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 768520782    3 RGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLR 39
Cdd:pfam08071   1 RGPKKHLKRLAAPKHWMLDKKGGVFAPKPSPGPHKLR 37
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 44-112 1.09e-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: 39.54  E-value: 1.09e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 768520782  44 LIVFLRnRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVH 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 1.97e-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: 38.24  E-value: 1.97e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 768520782   42 LPLIVFLRnRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVI 90
Cdd:pfam01479   1 RRLDKVLA-RLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
44-93 5.32e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.19  E-value: 5.32e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 768520782    44 LIVFLRnRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVITLD 93
Cdd:smart00363   3 LDKFLA-RLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVR 51
 
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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