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Conserved domains on  [gi|1980524063|ref|YP_009988338|]
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ribosomal protein L16 (mitochondrion) [Gelidiella flabella]

Protein Classification

uL16 family ribosomal protein( domain architecture ID 664)

uL16 family ribosomal protein such as human 60S ribosomal protein L10, bacteria 50S ribosomal protein L16, chloroplast 50S ribosomal protein L16, and mitochondrial 39S ribosomal protein L16

Gene Ontology:  GO:0006412|GO:0003735|GO:0019843
PubMed:  24524803

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ribosomal_L16_L10e super family cl00353
Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, ...
 22-111 1.27e-08

Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.


The actual alignment was detected with superfamily member cd01433:

Pssm-ID: 469737  Cd Length: 112  Bit Score: 49.41  E-value: 1.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063  22 LNYGTLGVKATSSGRLIDKKWELLQKALHKKIKLICGanrcKVWSPIEFNNTLTKLSLESRMGKGKGSIYANSKFIREGE 101
Cdd:cd01433     5 LFFGEYGLVALEPGRITAEQLEAARIAINRYLKKKGG----KLWIRVFPDHPVTKKPLETRMGKGKGKPEGWVARVKPGQ 80

                          90
                  ....*....|
gi 1980524063 102 IIIEFSGIPK 111
Cdd:cd01433    81 ILFEVRGVPE 90
 
Name Accession Description Interval E-value
Ribosomal_L16_L10e cd01433
Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, ...
 22-111 1.27e-08

Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.


Pssm-ID: 238714  Cd Length: 112  Bit Score: 49.41  E-value: 1.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063  22 LNYGTLGVKATSSGRLIDKKWELLQKALHKKIKLICGanrcKVWSPIEFNNTLTKLSLESRMGKGKGSIYANSKFIREGE 101
Cdd:cd01433     5 LFFGEYGLVALEPGRITAEQLEAARIAINRYLKKKGG----KLWIRVFPDHPVTKKPLETRMGKGKGKPEGWVARVKPGQ 80

                          90
                  ....*....|
gi 1980524063 102 IIIEFSGIPK 111
Cdd:cd01433    81 ILFEVRGVPE 90
rplP_bact TIGR01164
ribosomal protein L16, bacterial/organelle; This model describes bacterial and organellar ...
 5-110 1.94e-08

ribosomal protein L16, bacterial/organelle; This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10 [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273476  Cd Length: 125  Bit Score: 49.29  E-value: 1.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063   5 KKTHNKEVIRGR-----KKFQFLNYGTLGVKATSSGRLIDKKWELLQKALHKKIKlicgaNRCKVWSPIEFNNTLTKLSL 79
Cdd:TIGR01164   3 KRTKYRKQQRGRvkgkaKRGNTVAFGEYGLQALEPGWITARQIEAARVAMTRYVK-----RGGKLWIRIFPDKPYTKKPL 77

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1980524063  80 ESRMGKGKGSIYANSKFIREGEIIIEFSGIP 110
Cdd:TIGR01164  78 ETRMGKGKGNPEYWVAVVKPGKILFEIAGVP 108
Ribosomal_L16 pfam00252
Ribosomal protein L16p/L10e;
10-108 2.62e-07

Ribosomal protein L16p/L10e;


Pssm-ID: 459733  Cd Length: 132  Bit Score: 46.27  E-value: 2.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063  10 KEVIRGR-KKFQFLNYGTLGVKATSSGRLIDKKWELLQKALHKKIKLICGAnrcKVWSPIEFNNTLTKLSLESRMGKGKG 88
Cdd:pfam00252  11 KRYIRGVpTKGTTLDFGDYGLVALEGGQITARQLEAARIAINRYLKKTRGG---KLWIRVFPDKPVTKKPGEDRMGKGKG 87

                          90       100
                  ....*....|....*....|
gi 1980524063  89 SIYANSKFIREGEIIIEFSG 108
Cdd:pfam00252  88 KPEGWVARVKPGRILFEIKG 107
RplP COG0197
Ribosomal protein L16/L10AE [Translation, ribosomal structure and biogenesis]; Ribosomal ...
 1-110 2.23e-03

Ribosomal protein L16/L10AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein L16/L10AE is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 439967  Cd Length: 136  Bit Score: 35.78  E-value: 2.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063   1 MQIRKKTHNKEVIRGR-----KKFQFLNYGTLGVKATSSGRLIDKKWELLQKALHKKIKlicgaNRCKVWSPIEFNNTLT 75
Cdd:COG0197     1 MLMPKRVKYRKQQRGRikgvaKRGNKFAFGNYGLKALEPGQITSRQIEAARIAITRYLK-----RGGKVWIRIFPDKPLT 75

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1980524063  76 KLSLESRMGKGKGSI---YANskfIREGEIIIEFSGIP 110
Cdd:COG0197    76 KKPAETRMGAGKGKPegwVAV---VKPGRILFEIAGVS 110
 
Name Accession Description Interval E-value
Ribosomal_L16_L10e cd01433
Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, ...
 22-111 1.27e-08

Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.


Pssm-ID: 238714  Cd Length: 112  Bit Score: 49.41  E-value: 1.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063  22 LNYGTLGVKATSSGRLIDKKWELLQKALHKKIKLICGanrcKVWSPIEFNNTLTKLSLESRMGKGKGSIYANSKFIREGE 101
Cdd:cd01433     5 LFFGEYGLVALEPGRITAEQLEAARIAINRYLKKKGG----KLWIRVFPDHPVTKKPLETRMGKGKGKPEGWVARVKPGQ 80

                          90
                  ....*....|
gi 1980524063 102 IIIEFSGIPK 111
Cdd:cd01433    81 ILFEVRGVPE 90
rplP_bact TIGR01164
ribosomal protein L16, bacterial/organelle; This model describes bacterial and organellar ...
 5-110 1.94e-08

ribosomal protein L16, bacterial/organelle; This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10 [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273476  Cd Length: 125  Bit Score: 49.29  E-value: 1.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063   5 KKTHNKEVIRGR-----KKFQFLNYGTLGVKATSSGRLIDKKWELLQKALHKKIKlicgaNRCKVWSPIEFNNTLTKLSL 79
Cdd:TIGR01164   3 KRTKYRKQQRGRvkgkaKRGNTVAFGEYGLQALEPGWITARQIEAARVAMTRYVK-----RGGKLWIRIFPDKPYTKKPL 77

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1980524063  80 ESRMGKGKGSIYANSKFIREGEIIIEFSGIP 110
Cdd:TIGR01164  78 ETRMGKGKGNPEYWVAVVKPGKILFEIAGVP 108
Ribosomal_L16 pfam00252
Ribosomal protein L16p/L10e;
10-108 2.62e-07

Ribosomal protein L16p/L10e;


Pssm-ID: 459733  Cd Length: 132  Bit Score: 46.27  E-value: 2.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063  10 KEVIRGR-KKFQFLNYGTLGVKATSSGRLIDKKWELLQKALHKKIKLICGAnrcKVWSPIEFNNTLTKLSLESRMGKGKG 88
Cdd:pfam00252  11 KRYIRGVpTKGTTLDFGDYGLVALEGGQITARQLEAARIAINRYLKKTRGG---KLWIRVFPDKPVTKKPGEDRMGKGKG 87

                          90       100
                  ....*....|....*....|
gi 1980524063  89 SIYANSKFIREGEIIIEFSG 108
Cdd:pfam00252  88 KPEGWVARVKPGRILFEIKG 107
RplP COG0197
Ribosomal protein L16/L10AE [Translation, ribosomal structure and biogenesis]; Ribosomal ...
 1-110 2.23e-03

Ribosomal protein L16/L10AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein L16/L10AE is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 439967  Cd Length: 136  Bit Score: 35.78  E-value: 2.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1980524063   1 MQIRKKTHNKEVIRGR-----KKFQFLNYGTLGVKATSSGRLIDKKWELLQKALHKKIKlicgaNRCKVWSPIEFNNTLT 75
Cdd:COG0197     1 MLMPKRVKYRKQQRGRikgvaKRGNKFAFGNYGLKALEPGQITSRQIEAARIAITRYLK-----RGGKVWIRIFPDKPLT 75

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1980524063  76 KLSLESRMGKGKGSI---YANskfIREGEIIIEFSGIP 110
Cdd:COG0197    76 KKPAETRMGAGKGKPegwVAV---VKPGRILFEIAGVS 110
 
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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