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Conserved domains on  [gi|6321942|ref|NP_012018|]
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snoRNA-binding rRNA-processing protein IMP3 [Saccharomyces cerevisiae S288C]

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 2.24e-22

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: 86.06  E-value: 2.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942      4 KLKHHEQKLLKKVDFLEWKQDQGHRDTQVMrtyhiQNREDYHKYNRICGDIRRLANKLSLLPPTDPFRRKHEQL--LLDK 81
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGLLekQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 6321942     82 LYAMGvlttkSKISDLeNKVTVSAICR 108
Cdd:pfam00163  76 LYDMG-----LKLKGV-TGENLLQLLE 96
PLN00189 super family cl29650
40S ribosomal protein S9; Provisional
 54-164 1.09e-10

40S ribosomal protein S9; Provisional


The actual alignment was detected with superfamily member PLN00189:

Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 57.84  E-value: 1.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942    54 IRRLANKLSLLPPTDPFRRKHEQLLLDKLYAMGVLTTKSKISDLENKVTVSAICRRRLPVIMHRLKMAETIQDAVKFIEQ 133
Cdd:PLN00189  54 IRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQ 133

                         90       100       110
                 ....*....|....*....|....*....|.
gi 6321942   134 GHVRVGPNLINDPAYLVTRNMEDYVTWVDNS 164
Cdd:PLN00189 134 RHIRVGKQIVNVPSFMVRVDSQKHIDFSLTS 164
 
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 2.24e-22

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: 86.06  E-value: 2.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942      4 KLKHHEQKLLKKVDFLEWKQDQGHRDTQVMrtyhiQNREDYHKYNRICGDIRRLANKLSLLPPTDPFRRKHEQL--LLDK 81
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGLLekQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 6321942     82 LYAMGvlttkSKISDLeNKVTVSAICR 108
Cdd:pfam00163  76 LYDMG-----LKLKGV-TGENLLQLLE 96
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 21-167 2.46e-17

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: 74.77  E-value: 2.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942     21 WKQDQGHRDTQVMRTYHIQNREDYHKYNRICGDIRRLANKLSLLPptDPFRRKHEQLLLDKLYAMGVL-TTKSKISDLEN 99
Cdd:TIGR01018  18 WIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGILdEENAKLDDVLG 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6321942    100 kVTVSAICRRRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNMEDYVTWVDNSKIK 167
Cdd:TIGR01018  96 -LTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
rps4p PRK04051
30S ribosomal protein S4P; Validated
 28-177 3.63e-17

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 74.91  E-value: 3.63e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942    28 RDTQVMRTYHIQNREDYHKYNRICGDIRRLANKLSLLPPTDpfRRKHEQLLLDKLYAMGVLTTKSKISDLENkVTVSAIC 107
Cdd:PRK04051  25 EERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEE--RAKEEEQLLGKLKRYGILKENATLDDVLS-LTVEDIL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942   108 RRRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNMEDYVTWVDNSKIKKTLLRYRNQI 177
Cdd:PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLADELHPERAEA 171
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 54-164 1.09e-10

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 57.84  E-value: 1.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942    54 IRRLANKLSLLPPTDPFRRKHEQLLLDKLYAMGVLTTKSKISDLENKVTVSAICRRRLPVIMHRLKMAETIQDAVKFIEQ 133
Cdd:PLN00189  54 IRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQ 133

                         90       100       110
                 ....*....|....*....|....*....|.
gi 6321942   134 GHVRVGPNLINDPAYLVTRNMEDYVTWVDNS 164
Cdd:PLN00189 134 RHIRVGKQIVNVPSFMVRVDSQKHIDFSLTS 164
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 109-155 8.56e-09

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: 49.41  E-value: 8.56e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 6321942    109 RRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNME 155
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDE 47
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-170 3.48e-07

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: 45.70  E-value: 3.48e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6321942  109 RRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNmeDYVTWVDNSKIKKTL 170
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPG--DVIEVDGKSIEEDIV 60
S4 smart00363
S4 RNA-binding domain;
109-165 5.02e-07

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 44.89  E-value: 5.02e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 6321942     109 RRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVtrNMEDYVTWVDNSK 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 2.24e-22

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: 86.06  E-value: 2.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942      4 KLKHHEQKLLKKVDFLEWKQDQGHRDTQVMrtyhiQNREDYHKYNRICGDIRRLANKLSLLPPTDPFRRKHEQL--LLDK 81
Cdd:pfam00163   1 RYKGPEQKLLRRVGFKLWKKGRCHRELKVA-----QNRREYPKYPGQHGKIRKLSEYLLQLREKQKVRRKYGLLekQLRK 75

                          90       100
                  ....*....|....*....|....*..
gi 6321942     82 LYAMGvlttkSKISDLeNKVTVSAICR 108
Cdd:pfam00163  76 LYDMG-----LKLKGV-TGENLLQLLE 96
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 21-167 2.46e-17

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: 74.77  E-value: 2.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942     21 WKQDQGHRDTQVMRTYHIQNREDYHKYNRICGDIRRLANKLSLLPptDPFRRKHEQLLLDKLYAMGVL-TTKSKISDLEN 99
Cdd:TIGR01018  18 WIKERLDRELKLMGKYGLRNKKEVWKAETTLRKYRRAARELLTLD--DEQRLFEGNQLLRRLVRLGILdEENAKLDDVLG 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6321942    100 kVTVSAICRRRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNMEDYVTWVDNSKIK 167
Cdd:TIGR01018  96 -LTVEDFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSYIVRLEEEKKIDFALSSPFG 162
rps4p PRK04051
30S ribosomal protein S4P; Validated
 28-177 3.63e-17

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 74.91  E-value: 3.63e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942    28 RDTQVMRTYHIQNREDYHKYNRICGDIRRLANKLSLLPPTDpfRRKHEQLLLDKLYAMGVLTTKSKISDLENkVTVSAIC 107
Cdd:PRK04051  25 EERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEE--RAKEEEQLLGKLKRYGILKENATLDDVLS-LTVEDIL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942   108 RRRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNMEDYVTWVDNSKIKKTLLRYRNQI 177
Cdd:PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLADELHPERAEA 171
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 28-164 3.42e-11

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 58.94  E-value: 3.42e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942    28 RDTQVMRTYHIQNREDYHKYNRICGDIRRLANKLSLLPPTDPFRRKHEQLLLDKLYAMGVLTTKSKISDLENKVTVSAIC 107
Cdd:PTZ00155  26 AELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDEDERKLDYVLGLTVEKLL 105

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 6321942   108 RRRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNMEDYVTWVDNS 164
Cdd:PTZ00155 106 ERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTS 162
PLN00189 PLN00189
40S ribosomal protein S9; Provisional
 54-164 1.09e-10

40S ribosomal protein S9; Provisional


Pssm-ID: 177783 [Multi-domain]  Cd Length: 194  Bit Score: 57.84  E-value: 1.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321942    54 IRRLANKLSLLPPTDPFRRKHEQLLLDKLYAMGVLTTKSKISDLENKVTVSAICRRRLPVIMHRLKMAETIQDAVKFIEQ 133
Cdd:PLN00189  54 IRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQ 133

                         90       100       110
                 ....*....|....*....|....*....|.
gi 6321942   134 GHVRVGPNLINDPAYLVTRNMEDYVTWVDNS 164
Cdd:PLN00189 134 RHIRVGKQIVNVPSFMVRVDSQKHIDFSLTS 164
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 109-155 8.56e-09

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: 49.41  E-value: 8.56e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 6321942    109 RRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNME 155
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDE 47
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 109-170 3.48e-07

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: 45.70  E-value: 3.48e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6321942  109 RRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVTRNmeDYVTWVDNSKIKKTL 170
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPG--DVIEVDGKSIEEDIV 60
S4 smart00363
S4 RNA-binding domain;
109-165 5.02e-07

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 44.89  E-value: 5.02e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 6321942     109 RRLPVIMHRLKMAETIQDAVKFIEQGHVRVGPNLINDPAYLVtrNMEDYVTWVDNSK 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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