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Conserved domains on  [gi|606215127|ref|NP_001278286|]
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U3 small nucleolar ribonucleoprotein protein IMP3 [Danio rerio]

Protein Classification

ribosomal protein uS4 family protein( domain architecture ID 1005891)

universal ribosomal protein uS4 family protein similar to Homo sapiens U3 small nucleolar ribonucleoprotein protein IMP3 that is required for the early cleavages during pre-18S ribosomal RNA processing

Gene Ontology:  GO:0015935|GO:0019843|GO:0003735
PubMed:  24524803

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 4-87 2.74e-16

Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.


:

Pssm-ID: 459696  Cd Length: 96  Bit Score: 70.27  E-value: 2.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127    4 KLKFHEQKLLKKVDFINWEVDNNIHEVKVLRkyhieKREDYTKYNKLSRNIRELAQKIRDLDAKDGFRSQ--STALFLEK 81
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGRCHRELKVAQ-----NRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKygLLEKQLRK 75


                  ....*.
gi 606215127   82 LYSVGL 87
Cdd:pfam00163  76 LYDMGL 81
uS4_arch super family cl29649
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 29-166 3.37e-13

ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


The actual alignment was detected with superfamily member TIGR01018:

Pssm-ID: 273397 [Multi-domain]  Cd Length: 162  Bit Score: 63.98  E-value: 3.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127   29 EVKVLRKYHIEKREDYTKYNKLSRNIRELAQKIRDLDAKDGfRSQSTALfLEKLYSVGLIP-TKQNLSLANEVSASAFCR 107
Cdd:TIGR01018  26 ELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLDDEQR-LFEGNQL-LRRLVRLGILDeENAKLDDVLGLTVEDFLE 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 606215127  108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNMEDFVTWVDSSKIK 166
Cdd:TIGR01018 104 RRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
 
Name Accession Description Interval E-value
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 4-87 2.74e-16

Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.


Pssm-ID: 459696  Cd Length: 96  Bit Score: 70.27  E-value: 2.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127    4 KLKFHEQKLLKKVDFINWEVDNNIHEVKVLRkyhieKREDYTKYNKLSRNIRELAQKIRDLDAKDGFRSQ--STALFLEK 81
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGRCHRELKVAQ-----NRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKygLLEKQLRK 75


                  ....*.
gi 606215127   82 LYSVGL 87
Cdd:pfam00163  76 LYDMGL 81
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 29-166 3.37e-13

ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273397 [Multi-domain]  Cd Length: 162  Bit Score: 63.98  E-value: 3.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127   29 EVKVLRKYHIEKREDYTKYNKLSRNIRELAQKIRDLDAKDGfRSQSTALfLEKLYSVGLIP-TKQNLSLANEVSASAFCR 107
Cdd:TIGR01018  26 ELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLDDEQR-LFEGNQL-LRRLVRLGILDeENAKLDDVLGLTVEDFLE 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 606215127  108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNMEDFVTWVDSSKIK 166
Cdd:TIGR01018 104 RRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 29-163 1.30e-11

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 60.53  E-value: 1.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127  29 EVKVLRKYHIE-KREDYTKYNKLSRnIRELAQKIRDLDAKDGFR-SQSTALfLEKLYSVGLIPTKQN-LSLANEVSASAF 105
Cdd:PLN00189  29 ELKLVGEYGLRnKRELWRVQYALSR-IRNAARMLLTLDEKNPRRiFEGEAL-LRRMNRYGLLDESQNkLDYVLALTVENF 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 606215127 106 CRRRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNMEDFVTWVDSS 163
Cdd:PLN00189 107 LERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTS 164
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 108-154 2.87e-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: 45.18  E-value: 2.87e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 606215127  108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNME 154
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDE 47
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 108-169 8.52e-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: 39.15  E-value: 8.52e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 606215127 108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNmeDFVTWVDSSKIKQHV 169
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPG--DVIEVDGKSIEEDIV 60
S4 smart00363
S4 RNA-binding domain;
108-164 7.40e-03

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 33.72  E-value: 7.40e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 606215127   108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVtrNMEDFVTWVDSSK 164
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIV--KPGDVISVRGKEL 55
 
Name Accession Description Interval E-value
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 4-87 2.74e-16

Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.


Pssm-ID: 459696  Cd Length: 96  Bit Score: 70.27  E-value: 2.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127    4 KLKFHEQKLLKKVDFINWEVDNNIHEVKVLRkyhieKREDYTKYNKLSRNIRELAQKIRDLDAKDGFRSQ--STALFLEK 81
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGRCHRELKVAQ-----NRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKygLLEKQLRK 75


                  ....*.
gi 606215127   82 LYSVGL 87
Cdd:pfam00163  76 LYDMGL 81
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 29-166 3.37e-13

ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273397 [Multi-domain]  Cd Length: 162  Bit Score: 63.98  E-value: 3.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127   29 EVKVLRKYHIEKREDYTKYNKLSRNIRELAQKIRDLDAKDGfRSQSTALfLEKLYSVGLIP-TKQNLSLANEVSASAFCR 107
Cdd:TIGR01018  26 ELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLDDEQR-LFEGNQL-LRRLVRLGILDeENAKLDDVLGLTVEDFLE 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 606215127  108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNMEDFVTWVDSSKIK 166
Cdd:TIGR01018 104 RRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 29-163 1.30e-11

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 60.53  E-value: 1.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127  29 EVKVLRKYHIE-KREDYTKYNKLSRnIRELAQKIRDLDAKDGFR-SQSTALfLEKLYSVGLIPTKQN-LSLANEVSASAF 105
Cdd:PLN00189  29 ELKLVGEYGLRnKRELWRVQYALSR-IRNAARMLLTLDEKNPRRiFEGEAL-LRRMNRYGLLDESQNkLDYVLALTVENF 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 606215127 106 CRRRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNMEDFVTWVDSS 163
Cdd:PLN00189 107 LERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTS 164
rps4p PRK04051
30S ribosomal protein S4P; Validated
 21-167 2.34e-11

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 59.50  E-value: 2.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127  21 WEVDNNIHEVKVLRKYHIEKREDYTKYNKLSRNIRELAQKIRDLDAKDgfRSQSTALFLEKLYSVGLIPTKQN----LSL 96
Cdd:PRK04051  18 WQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEE--RAKEEEQLLGKLKRYGILKENATlddvLSL 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 606215127  97 anevSASAFCRRRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNMEDFVTWVDSSKIKQ 167
Cdd:PRK04051  96 ----TVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLAD 162
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 29-163 2.24e-10

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 56.63  E-value: 2.24e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 606215127  29 EVKVLRKYHIE-KREDYTKYNKLSRnIRELAQKIRDLDAKDGFRSQSTALFLEKLYSVGLIP-TKQNLSLANEVSASAFC 106
Cdd:PTZ00155  27 ELKLCGEYGLKnKREIWRVQYTLAK-IRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDeDERKLDYVLGLTVEKLL 105

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 606215127 107 RRRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNMEDFVTWVDSS 163
Cdd:PTZ00155 106 ERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTS 162
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 108-154 2.87e-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: 45.18  E-value: 2.87e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 606215127  108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNME 154
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDE 47
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 108-169 8.52e-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: 39.15  E-value: 8.52e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 606215127 108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVTRNmeDFVTWVDSSKIKQHV 169
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPG--DVIEVDGKSIEEDIV 60
S4 smart00363
S4 RNA-binding domain;
108-164 7.40e-03

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 33.72  E-value: 7.40e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 606215127   108 RRLPTIMLKLRMAQNLRNAITFIEQGHIRVGPEVITDPAFLVtrNMEDFVTWVDSSK 164
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIV--KPGDVISVRGKEL 55
 
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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