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Conserved domains on  [gi|19115815|ref|NP_594903|]
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U3 snoRNP-associated protein Imp3 [Schizosaccharomyces pombe]

Protein Classification

ribosomal protein uS4 family protein( domain architecture ID 11424867)

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

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 ...
 4-108 1.39e-21

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: 84.14  E-value: 1.39e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815     4 LKHHEQKLLRKVDFLNYKNDdNNHRDVMVMRryhisKREEYQKYNIICGKFRQLAHRLSLLDPTDPFRLQY--ENLLLEK 81
Cdd:pfam00163   2 YKGPEQKLLRRVGFKLWKKG-RCHRELKVAQ-----NRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYglLEKQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 19115815    82 LFDMGIlpsksKMSDIeNKANVSAICR 108
Cdd:pfam00163  76 LYDMGL-----KLKGV-TGENLLQLLE 96
rps4p super family cl29648
30S ribosomal protein S4P; Validated
 53-167 2.00e-11

30S ribosomal protein S4P; Validated


The actual alignment was detected with superfamily member PRK04051:

Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 59.50  E-value: 2.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815   53 KFRQLAHRLslLDPTDPFRLQYENLLLEKLFDMGILPSKSKMSDIENkANVSAICRRRLPVIMCKLRMSQVVSEATRLIE 132
Cdd:PRK04051  50 KYRRQARSL--LALPPEERAKEEEQLLGKLKRYGILKENATLDDVLS-LTVEDILERRLQTIVYRKGLARTPKQARQFIV 126

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 19115815  133 QGHVRVGPHVITDPAYLVTRSLEDFVTWTDTSKIK 167
Cdd:PRK04051 127 HGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLA 161
 
Name Accession Description Interval E-value
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 4-108 1.39e-21

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: 84.14  E-value: 1.39e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815     4 LKHHEQKLLRKVDFLNYKNDdNNHRDVMVMRryhisKREEYQKYNIICGKFRQLAHRLSLLDPTDPFRLQY--ENLLLEK 81
Cdd:pfam00163   2 YKGPEQKLLRRVGFKLWKKG-RCHRELKVAQ-----NRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYglLEKQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 19115815    82 LFDMGIlpsksKMSDIeNKANVSAICR 108
Cdd:pfam00163  76 LYDMGL-----KLKGV-TGENLLQLLE 96
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 28-167 7.83e-16

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: 70.92  E-value: 7.83e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815    28 RDVMVMRRYHISKREEYQKYNIICGKFRQLAHRLSLLDptDPFRLQYENLLLEKLFDMGILPS-KSKMSDIENkANVSAI 106
Cdd:TIGR01018  25 RELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGILDEeNAKLDDVLG-LTVEDF 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19115815   107 CRRRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRSLEDFVTWTDTSKIK 167
Cdd:TIGR01018 102 LERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 36-164 8.21e-12

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 60.48  E-value: 8.21e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815   36 YHISKREEYQKYNIICGKFRQLAHRLSLLDPTDPFRLQYENLLLEKLFDMGILPSKSKMSDIENKANVSAICRRRLPVIM 115
Cdd:PTZ00155  34 YGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDEDERKLDYVLGLTVEKLLERRLQTKV 113

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 19115815  116 CKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRSLEDFVTWTDTS 164
Cdd:PTZ00155 114 FKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTS 162
rps4p PRK04051
30S ribosomal protein S4P; Validated
 53-167 2.00e-11

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 59.50  E-value: 2.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815   53 KFRQLAHRLslLDPTDPFRLQYENLLLEKLFDMGILPSKSKMSDIENkANVSAICRRRLPVIMCKLRMSQVVSEATRLIE 132
Cdd:PRK04051  50 KYRRQARSL--LALPPEERAKEEEQLLGKLKRYGILKENATLDDVLS-LTVEDILERRLQTIVYRKGLARTPKQARQFIV 126

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 19115815  133 QGHVRVGPHVITDPAYLVTRSLEDFVTWTDTSKIK 167
Cdd:PRK04051 127 HGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLA 161
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 109-155 1.69e-08

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: 48.64  E-value: 1.69e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 19115815   109 RRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRSLE 155
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDE 47
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-178 2.93e-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: 40.31  E-value: 2.93e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815 109 RRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRslEDFVTWTDTSKIKRTIAKYNDKLD 178
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKP--GDVIEVDGKSIEEDIVYEDKKLLV 68
S4 smart00363
S4 RNA-binding domain;
109-165 6.95e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 36.42  E-value: 6.95e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115815    109 RRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVtrSLEDFVTWTDTSK 165
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 ...
 4-108 1.39e-21

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: 84.14  E-value: 1.39e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815     4 LKHHEQKLLRKVDFLNYKNDdNNHRDVMVMRryhisKREEYQKYNIICGKFRQLAHRLSLLDPTDPFRLQY--ENLLLEK 81
Cdd:pfam00163   2 YKGPEQKLLRRVGFKLWKKG-RCHRELKVAQ-----NRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYglLEKQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 19115815    82 LFDMGIlpsksKMSDIeNKANVSAICR 108
Cdd:pfam00163  76 LYDMGL-----KLKGV-TGENLLQLLE 96
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 28-167 7.83e-16

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: 70.92  E-value: 7.83e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815    28 RDVMVMRRYHISKREEYQKYNIICGKFRQLAHRLSLLDptDPFRLQYENLLLEKLFDMGILPS-KSKMSDIENkANVSAI 106
Cdd:TIGR01018  25 RELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGILDEeNAKLDDVLG-LTVEDF 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19115815   107 CRRRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRSLEDFVTWTDTSKIK 167
Cdd:TIGR01018 102 LERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 36-164 8.21e-12

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 60.48  E-value: 8.21e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815   36 YHISKREEYQKYNIICGKFRQLAHRLSLLDPTDPFRLQYENLLLEKLFDMGILPSKSKMSDIENKANVSAICRRRLPVIM 115
Cdd:PTZ00155  34 YGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDEDERKLDYVLGLTVEKLLERRLQTKV 113

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 19115815  116 CKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRSLEDFVTWTDTS 164
Cdd:PTZ00155 114 FKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTS 162
rps4p PRK04051
30S ribosomal protein S4P; Validated
 53-167 2.00e-11

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 59.50  E-value: 2.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815   53 KFRQLAHRLslLDPTDPFRLQYENLLLEKLFDMGILPSKSKMSDIENkANVSAICRRRLPVIMCKLRMSQVVSEATRLIE 132
Cdd:PRK04051  50 KYRRQARSL--LALPPEERAKEEEQLLGKLKRYGILKENATLDDVLS-LTVEDILERRLQTIVYRKGLARTPKQARQFIV 126

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 19115815  133 QGHVRVGPHVITDPAYLVTRSLEDFVTWTDTSKIK 167
Cdd:PRK04051 127 HGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLA 161
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 109-155 1.69e-08

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: 48.64  E-value: 1.69e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 19115815   109 RRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRSLE 155
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDE 47
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 53-164 2.54e-08

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 51.29  E-value: 2.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815   53 KFRQLAHRLSLLDPTDPFRLQYENLLLEKLFDMGILPSKSKMSDIENKANVSAICRRRLPVIMCKLRMSQVVSEATRLIE 132
Cdd:PLN00189  53 RIRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIR 132

                         90       100       110
                 ....*....|....*....|....*....|..
gi 19115815  133 QGHVRVGPHVITDPAYLVTRSLEDFVTWTDTS 164
Cdd:PLN00189 133 QRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTS 164
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-178 2.93e-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: 40.31  E-value: 2.93e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115815 109 RRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVTRslEDFVTWTDTSKIKRTIAKYNDKLD 178
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKP--GDVIEVDGKSIEEDIVYEDKKLLV 68
S4 smart00363
S4 RNA-binding domain;
109-165 6.95e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 36.42  E-value: 6.95e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115815    109 RRLPVIMCKLRMSQVVSEATRLIEQGHVRVGPHVITDPAYLVtrSLEDFVTWTDTSK 165
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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