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Conserved domains on  [gi|1588048325|gb|QBK75251|]
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30S ribosomal protein S13 [Myroides odoratimimus]

Protein Classification

30S ribosomal protein S13( domain architecture ID 10012263)

30S ribosomal protein S13 is a structural element of the small subunit of ribosome that is located at the top of the head of the 30S subunit; it contacts several helices of the 16S rRNA

Gene Ontology:  GO:0019843|GO:0000028|GO:0003735
PubMed:  24524803

Graphical summary

 Zoom to residue level

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List of domain hits

Name Accession Description Interval E-value
rpsM PRK05179
30S ribosomal protein S13; Validated
1-121 2.20e-76

30S ribosomal protein S13; Validated


:

Pssm-ID: 235358  Cd Length: 122  Bit Score: 221.49  E-value: 2.20e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKR 79
Cdd:PRK05179    1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKnYKVEGDLRREVSMNIKR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1588048325  80 LMDIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRKTVANKKK 121
Cdd:PRK05179   81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKKK 122
 
Name Accession Description Interval E-value
rpsM PRK05179
30S ribosomal protein S13; Validated
1-121 2.20e-76

30S ribosomal protein S13; Validated


Pssm-ID: 235358  Cd Length: 122  Bit Score: 221.49  E-value: 2.20e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKR 79
Cdd:PRK05179    1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKnYKVEGDLRREVSMNIKR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1588048325  80 LMDIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRKTVANKKK 121
Cdd:PRK05179   81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKKK 122
RpsM COG0099
Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S13 ...
1-124 1.31e-69

Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S13 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 439869  Cd Length: 125  Bit Score: 204.53  E-value: 1.31e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVG-QFTIEGELRSEISLNIKR 79
Cdd:COG0099     1 MARIAGVDLPGNKRVEIALTYIYGIGRTTARKILEKAGIDPDKRVGDLTDEEIAKIREVIEnNHLVEGDLRREVRMDIKR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1588048325  80 LMDIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRKTVANKKKATK 124
Cdd:COG0099    81 LKDIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKTVGVKKKKKK 125
uS13_bact TIGR03631
ribosomal protein uS13, bacterial form; This model describes bacterial ribosomal protein S13, ...
3-114 2.47e-61

ribosomal protein uS13, bacterial form; This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 274688  Cd Length: 113  Bit Score: 183.08  E-value: 2.47e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   3 RIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKRLM 81
Cdd:TIGR03631   1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAkYKVEGDLRREVTLNIKRLM 80
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1588048325  82 DIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRK 114
Cdd:TIGR03631  81 DIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113
Ribosomal_S13 pfam00416
Ribosomal protein S13/S18; This family includes ribosomal protein S13 from prokaryotes and S18 ...
3-108 2.12e-36

Ribosomal protein S13/S18; This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.


Pssm-ID: 425669  Cd Length: 107  Bit Score: 120.11  E-value: 2.12e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   3 RIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKRLM 81
Cdd:pfam00416   1 RILGTDIDGDKKVEIALTYIKGIGRRRANIILKKAGIDRDKRAGELTEEEIDRLRDIVANsHVVEGDLRREVRADIERLK 80
                          90       100
                  ....*....|....*....|....*..
gi 1588048325  82 DIGCYRGIRHRAGLPLRGQRTKNNSRT 108
Cdd:pfam00416  81 EIRCYRGLRHRRGLPVRGQRTKTNGRT 107
 
Name Accession Description Interval E-value
rpsM PRK05179
30S ribosomal protein S13; Validated
1-121 2.20e-76

30S ribosomal protein S13; Validated


Pssm-ID: 235358  Cd Length: 122  Bit Score: 221.49  E-value: 2.20e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKR 79
Cdd:PRK05179    1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKnYKVEGDLRREVSMNIKR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1588048325  80 LMDIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRKTVANKKK 121
Cdd:PRK05179   81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKKK 122
RpsM COG0099
Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S13 ...
1-124 1.31e-69

Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S13 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 439869  Cd Length: 125  Bit Score: 204.53  E-value: 1.31e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVG-QFTIEGELRSEISLNIKR 79
Cdd:COG0099     1 MARIAGVDLPGNKRVEIALTYIYGIGRTTARKILEKAGIDPDKRVGDLTDEEIAKIREVIEnNHLVEGDLRREVRMDIKR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1588048325  80 LMDIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRKTVANKKKATK 124
Cdd:COG0099    81 LKDIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKTVGVKKKKKK 125
uS13_bact TIGR03631
ribosomal protein uS13, bacterial form; This model describes bacterial ribosomal protein S13, ...
3-114 2.47e-61

ribosomal protein uS13, bacterial form; This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 274688  Cd Length: 113  Bit Score: 183.08  E-value: 2.47e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   3 RIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKRLM 81
Cdd:TIGR03631   1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAkYKVEGDLRREVTLNIKRLM 80
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1588048325  82 DIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRK 114
Cdd:TIGR03631  81 DIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113
rps13 CHL00137
ribosomal protein S13; Validated
1-121 7.79e-52

ribosomal protein S13; Validated


Pssm-ID: 177059  Cd Length: 122  Bit Score: 159.42  E-value: 7.79e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKR 79
Cdd:CHL00137    1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEEnYQVEGDLRRFESLNIKR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1588048325  80 LMDIGCYRGIRHRAGLPLRGQRTKNNSRTRKGKRKTVANKKK 121
Cdd:CHL00137   81 LMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGKKK 122
Ribosomal_S13 pfam00416
Ribosomal protein S13/S18; This family includes ribosomal protein S13 from prokaryotes and S18 ...
3-108 2.12e-36

Ribosomal protein S13/S18; This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.


Pssm-ID: 425669  Cd Length: 107  Bit Score: 120.11  E-value: 2.12e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   3 RIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQ-FTIEGELRSEISLNIKRLM 81
Cdd:pfam00416   1 RILGTDIDGDKKVEIALTYIKGIGRRRANIILKKAGIDRDKRAGELTEEEIDRLRDIVANsHVVEGDLRREVRADIERLK 80
                          90       100
                  ....*....|....*....|....*..
gi 1588048325  82 DIGCYRGIRHRAGLPLRGQRTKNNSRT 108
Cdd:pfam00416  81 EIRCYRGLRHRRGLPVRGQRTKTNGRT 107
uS13_arch TIGR03629
ribosomal protein uS13, archaeal form; This model describes exclusively the archaeal ribosomal ...
1-108 2.55e-20

ribosomal protein uS13, archaeal form; This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 213839  Cd Length: 144  Bit Score: 80.01  E-value: 2.55e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQFT---------------- 64
Cdd:TIGR03629   5 IVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEygipswllnrrkdyet 84
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1588048325  65 ------IEGELRSEISLNIKRLMDIGCYRGIRHRAGLPLRGQRTKNNSRT 108
Cdd:TIGR03629  85 gedlhlIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRR 134
rps13p PRK04053
30S ribosomal protein S13P; Reviewed
3-108 3.40e-20

30S ribosomal protein S13P; Reviewed


Pssm-ID: 235215  Cd Length: 149  Bit Score: 79.87  E-value: 3.40e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   3 RIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQFTIEG--------------- 67
Cdd:PRK04053   11 RIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGipswmlnrrkdyetg 90
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1588048325  68 ----ELRSEISL----NIKRLMDIGCYRGIRHRAGLPLRGQRTKNNSRT 108
Cdd:PRK04053   91 edlhLIGSDLILtvreDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRT 139
PTZ00134 PTZ00134
40S ribosomal protein S18; Provisional
1-120 9.35e-07

40S ribosomal protein S18; Provisional


Pssm-ID: 185469  Cd Length: 154  Bit Score: 45.02  E-value: 9.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1588048325   1 MARIAGVDIPKHKRGIIALTYIFGIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVG---QFTI------------ 65
Cdd:PTZ00134   14 ILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIAnplQFKIpdwflnrqrdpk 93
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1588048325  66 EG--------ELRSEISLNIKRLMDIGCYRGIRHRAGLPLRGQRTKnnSRTRKGKRKTVANKK 120
Cdd:PTZ00134   94 DGknshltsnMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTK--TTGRRGRTVGVSRKK 154
PRK04184 PRK04184
DNA topoisomerase VI subunit B; Validated
19-65 1.82e-03

DNA topoisomerase VI subunit B; Validated


Pssm-ID: 235246 [Multi-domain]  Cd Length: 535  Bit Score: 36.79  E-value: 1.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1588048325  19 LTYIF-GIGSSRAKEILERAKVDENKKVQDWNDDEIGAIREAVGQFTI 65
Cdd:PRK04184  262 LVEEFsRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKYKF 309
 
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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