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Conserved domains on  [gi|341830993|gb|AEK93887|]
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30S ribosomal protein S4, partial [Synechococcus sp. A15-30]

Protein Classification

30S ribosomal protein S4( domain architecture ID 11480735)

30S ribosomal protein S4 binds directly to 16S rRNA and plays an important role in translational accuracy

Gene Ontology:  GO:0003735|GO:0006412|GO:0019843

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpsD PRK05327
30S ribosomal protein S4; Validated
 2-179 7.26e-100

30S ribosomal protein S4; Validated


:

Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 286.23  E-value: 7.26e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   2 DLTGLTRKAAKRSYPPGQHGQARRKR--SEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENRLDN 79
Cdd:PRK05327  18 DLFKSGKRCLKRKYPPGQHGQRRRKPklSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDN 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993  80 VCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAKLSA 159
Cdd:PRK05327  98 VVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEG 177

                        170       180
                 ....*....|....*....|
gi 341830993 160 KVTGRCEREWVALEINELLV 179
Cdd:PRK05327 178 TFKRLPEREEIPVPINEQLI 197
 
Name Accession Description Interval E-value
rpsD PRK05327
30S ribosomal protein S4; Validated
 2-179 7.26e-100

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 286.23  E-value: 7.26e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   2 DLTGLTRKAAKRSYPPGQHGQARRKR--SEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENRLDN 79
Cdd:PRK05327  18 DLFKSGKRCLKRKYPPGQHGQRRRKPklSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDN 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993  80 VCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAKLSA 159
Cdd:PRK05327  98 VVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEG 177

                        170       180
                 ....*....|....*....|
gi 341830993 160 KVTGRCEREWVALEINELLV 179
Cdd:PRK05327 178 TFKRLPEREEIPVPINEQLI 197
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 2-179 3.47e-92

Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4 or related protein is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440288 [Multi-domain]  Cd Length: 204  Bit Score: 266.94  E-value: 3.47e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   2 DLTGLTRKA---AKRSYPPGQHGQARRKRSEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENRLD 78
Cdd:COG0522   18 KLFLKGERKcalERRPYPPGQHGQRRKKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLD 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993  79 NVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAKLS 158
Cdd:COG0522   98 NVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLS 177

                        170       180
                 ....*....|....*....|.
gi 341830993 159 AKVTGRCEREWVALEINELLV 179
Cdd:COG0522  178 GTVVRLPEREEIPVPINEQLI 198
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 2-179 1.35e-86

ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 200066 [Multi-domain]  Cd Length: 200  Bit Score: 252.61  E-value: 1.35e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993    2 DLTGLTRKA-AKRSYPPGQHGQARRKRSEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENRLDNV 80
Cdd:TIGR01017  16 NLFGKSRKLlLKRKYPPGQHGQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   81 CFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAKLSAK 160
Cdd:TIGR01017  96 VYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGK 175

                         170
                  ....*....|....*....
gi 341830993  161 VTGRCEREWVALEINELLV 179
Cdd:TIGR01017 176 VLRVPERSQLPLPINESLV 194
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 12-74 4.17e-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: 85.29  E-value: 4.17e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 341830993   12 KRSYP--PGQHGQaRRKRSEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLE 74
Cdd:pfam00163  33 RREYPkyPGQHGK-IRKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 76-137 7.48e-18

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: 73.44  E-value: 7.48e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 341830993  76 RLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGN 137
Cdd:cd00165    2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
S4 smart00363
S4 RNA-binding domain;
76-128 2.58e-13

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 61.45  E-value: 2.58e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 341830993    76 RLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERK 128
Cdd:smart00363   2 RLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKE 54
 
Name Accession Description Interval E-value
rpsD PRK05327
30S ribosomal protein S4; Validated
 2-179 7.26e-100

30S ribosomal protein S4; Validated


Pssm-ID: 235411 [Multi-domain]  Cd Length: 203  Bit Score: 286.23  E-value: 7.26e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   2 DLTGLTRKAAKRSYPPGQHGQARRKR--SEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENRLDN 79
Cdd:PRK05327  18 DLFKSGKRCLKRKYPPGQHGQRRRKPklSDYGLQLREKQKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDN 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993  80 VCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAKLSA 159
Cdd:PRK05327  98 VVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEG 177

                        170       180
                 ....*....|....*....|
gi 341830993 160 KVTGRCEREWVALEINELLV 179
Cdd:PRK05327 178 TFKRLPEREEIPVPINEQLI 197
rps4 CHL00113
ribosomal protein S4; Reviewed
 1-179 1.55e-94

ribosomal protein S4; Reviewed


Pssm-ID: 177038 [Multi-domain]  Cd Length: 201  Bit Score: 272.86  E-value: 1.55e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   1 GDLTGLTRKaakrsYPPGQHGQAR----RKRSEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENR 76
Cdd:CHL00113  16 GALPGLTSK-----TPRPGSDLRNqsrsGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993  77 LDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAK 156
Cdd:CHL00113  91 LDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQ 170

                        170       180
                 ....*....|....*....|...
gi 341830993 157 LSAKVTGRCEREWVALEINELLV 179
Cdd:CHL00113 171 YKGLVNQIIDRKWVGLKINELLV 193
RpsD COG0522
Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; ...
 2-179 3.47e-92

Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein S4 or related protein is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440288 [Multi-domain]  Cd Length: 204  Bit Score: 266.94  E-value: 3.47e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   2 DLTGLTRKA---AKRSYPPGQHGQARRKRSEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENRLD 78
Cdd:COG0522   18 KLFLKGERKcalERRPYPPGQHGQRRKKLSDYGLQLREKQKLRRIYGVLEKQFRRYFEEAARRKGNTGENLLQLLERRLD 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993  79 NVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAKLS 158
Cdd:COG0522   98 NVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALESAEQRGVPEWLEVDAEKLS 177

                        170       180
                 ....*....|....*....|.
gi 341830993 159 AKVTGRCEREWVALEINELLV 179
Cdd:COG0522  178 GTVVRLPEREEIPVPINEQLI 198
rpsD_bact TIGR01017
ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and ...
 2-179 1.35e-86

ribosomal protein S4, bacterial/organelle type; This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 200066 [Multi-domain]  Cd Length: 200  Bit Score: 252.61  E-value: 1.35e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993    2 DLTGLTRKA-AKRSYPPGQHGQARRKRSEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLENRLDNV 80
Cdd:TIGR01017  16 NLFGKSRKLlLKRKYPPGQHGQRRKKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341830993   81 CFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGNLEFPGLANVPTHLELDKAKLSAK 160
Cdd:TIGR01017  96 VYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGK 175

                         170
                  ....*....|....*....
gi 341830993  161 VTGRCEREWVALEINELLV 179
Cdd:TIGR01017 176 VLRVPERSQLPLPINESLV 194
Ribosomal_S4 pfam00163
Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 ...
 12-74 4.17e-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: 85.29  E-value: 4.17e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 341830993   12 KRSYP--PGQHGQaRRKRSEYAIRLEEKQKLRFNYGVSERQLVRYVKKARAQEGSTGTNLLKLLE 74
Cdd:pfam00163  33 RREYPkyPGQHGK-IRKLSEYLLQLREKQKVRRKYGLLEKQLRKLYDMGLKLKGVTGENLLQLLE 96
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 76-137 7.48e-18

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: 73.44  E-value: 7.48e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 341830993  76 RLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERKCSKQLAEGN 137
Cdd:cd00165    2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 76-122 1.58e-15

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: 66.75  E-value: 1.58e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341830993   76 RLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVV 122
Cdd:pfam01479   2 RLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
76-128 2.58e-13

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 61.45  E-value: 2.58e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 341830993    76 RLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASYQCKPGDVVAIRERK 128
Cdd:smart00363   2 RLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKE 54
rps4p PRK04051
30S ribosomal protein S4P; Validated
 72-114 1.38e-08

30S ribosomal protein S4P; Validated


Pssm-ID: 179730 [Multi-domain]  Cd Length: 177  Bit Score: 51.79  E-value: 1.38e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 341830993  72 LLENRLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASY 114
Cdd:PRK04051 100 ILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142
uS4_arch TIGR01018
ribosomal protein uS4, eukaryotic/archaeal type; This model finds eukaryotic ribosomal protein ...
 71-114 3.23e-07

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: 47.80  E-value: 3.23e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 341830993   71 KLLENRLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASY 114
Cdd:TIGR01018 100 DFLERRLQTQVYKKGLARTIHQARQLIVHGHIAVNGRVVTSPSY 143
PTZ00155 PTZ00155
40S ribosomal protein S9; Provisional
 71-114 5.41e-04

40S ribosomal protein S9; Provisional


Pssm-ID: 185484 [Multi-domain]  Cd Length: 181  Bit Score: 38.91  E-value: 5.41e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 341830993  71 KLLENRLDNVCFRLGFGPTVPGARQLVNHGHVTVNGRVTDIASY 114
Cdd:PTZ00155 103 KLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146
HslR COG1188
Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal ...
 93-125 1.95e-03

Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440801  Cd Length: 120  Bit Score: 36.35  E-value: 1.95e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 341830993  93 ARQLVNHGHVTVNGRVTDiASYQCKPGDVVAIR 125
Cdd:COG1188   23 AAEACDGGRVRVNGQRAK-PSREVKVGDVLTIR 54
 
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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