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Conserved domains on  [gi|15232275|ref|NP_189422|]
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ribosomal protein L12-B [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ribosomal_L7_L12 super family cl46846
Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit ...
 65-193 3.99e-36

Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises L7/L12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that L7/L12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors. In eukaryotes, the proteins that perform the equivalent function to L7/L12 are called P1 and P2, which do not share sequence similarity with L7/L12. However, a bacterial L7/L12 homolog is found in some eukaryotes, in mitochondria and chloroplasts. In archaea, the protein equivalent to L7/L12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to L7/L12.


The actual alignment was detected with superfamily member CHL00083:

Pssm-ID: 481186 [Multi-domain]  Cd Length: 131  Bit Score: 122.77  E-value: 3.99e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232275   65 KKIKKIGSEISSLTLEESRILVDYVQDKFGVSILFSAPAAAALPPPLDNGGATASVERQTTFDVVINDVPRGNRIAVITA 144
Cdd:CHL00083   3 TKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMSAPAAAAAQAAEEVEEKTEFDVILEEVPADKRIAVLKV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 15232275  145 IRAMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSIV 193
Cdd:CHL00083  83 VRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131
 
Name Accession Description Interval E-value
rpl12 CHL00083
ribosomal protein L12
 65-193 3.99e-36

ribosomal protein L12


Pssm-ID: 214358 [Multi-domain]  Cd Length: 131  Bit Score: 122.77  E-value: 3.99e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232275   65 KKIKKIGSEISSLTLEESRILVDYVQDKFGVSILFSAPAAAALPPPLDNGGATASVERQTTFDVVINDVPRGNRIAVITA 144
Cdd:CHL00083   3 TKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMSAPAAAAAQAAEEVEEKTEFDVILEEVPADKRIAVLKV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 15232275  145 IRAMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSIV 193
Cdd:CHL00083  83 VRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131
RplL COG0222
Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 66-192 1.79e-31

Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]; Ribosomal protein L7/L12 is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 439992  Cd Length: 125  Bit Score: 110.59  E-value: 1.79e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232275  66 KIKKIGSEISSLTLEESRILVDYVQDKFGVSilfsaPAAAALPPPLDNGGATASVERQTTFDVVINDVPrGNRIAVITAI 145
Cdd:COG0222   4 TKEEIIEAIKELTVLELSELVKALEEKFGVS-----AAAPVAVAAAAAAAAAAAAEEKTEFDVILKSAG-DKKIAVIKVV 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 15232275 146 RAMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSI 192
Cdd:COG0222  78 REITGLGLKEAKDLVEGAPKPVKEGVSKEEAEEIKKKLEEAGAKVEL 124
L12 TIGR00855
ribosomal protein L7/L12; Ribosomal proteins L7 and L12 are synonymous except for ...
 67-192 2.24e-23

ribosomal protein L7/L12; Ribosomal proteins L7 and L12 are synonymous except for post-translational modification of the N-terminal amino acid. THis model resembles pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273301 [Multi-domain]  Cd Length: 123  Bit Score: 89.82  E-value: 2.24e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232275    67 IKKIGSEISSLTLEESRILVDYVQDKFGVSilfsaPAAAALPPPLDNGGATASVERQTTFDVVInDVPRGNRIAVITAIR 146
Cdd:TIGR00855   3 KEQIIEALKSMTVLELSELVKALEEKFGVS-----AAAPVAAGAAGAAAGAAAAEEKTEFDVIL-KGAGDNKIAVIKVVR 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 15232275   147 AMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSI 192
Cdd:TIGR00855  77 EITGLGLKEAKDLVEGAPKALKEGVSKEEAEELKKKLEEAGAKVEV 122
Ribosomal_L12 pfam00542
Ribosomal protein L7/L12 C-terminal domain;
126-192 2.51e-22

Ribosomal protein L7/L12 C-terminal domain;


Pssm-ID: 425742  Cd Length: 67  Bit Score: 85.21  E-value: 2.51e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232275   126 FDVVINDVPrGNRIAVITAIRAMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSI 192
Cdd:pfam00542   1 FDVILTSAG-ANKIAVIKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGATVEL 66
 
Name Accession Description Interval E-value
rpl12 CHL00083
ribosomal protein L12
 65-193 3.99e-36

ribosomal protein L12


Pssm-ID: 214358 [Multi-domain]  Cd Length: 131  Bit Score: 122.77  E-value: 3.99e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232275   65 KKIKKIGSEISSLTLEESRILVDYVQDKFGVSILFSAPAAAALPPPLDNGGATASVERQTTFDVVINDVPRGNRIAVITA 144
Cdd:CHL00083   3 TKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMSAPAAAAAQAAEEVEEKTEFDVILEEVPADKRIAVLKV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 15232275  145 IRAMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSIV 193
Cdd:CHL00083  83 VRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131
RplL COG0222
Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 66-192 1.79e-31

Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]; Ribosomal protein L7/L12 is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 439992  Cd Length: 125  Bit Score: 110.59  E-value: 1.79e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232275  66 KIKKIGSEISSLTLEESRILVDYVQDKFGVSilfsaPAAAALPPPLDNGGATASVERQTTFDVVINDVPrGNRIAVITAI 145
Cdd:COG0222   4 TKEEIIEAIKELTVLELSELVKALEEKFGVS-----AAAPVAVAAAAAAAAAAAAEEKTEFDVILKSAG-DKKIAVIKVV 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 15232275 146 RAMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSI 192
Cdd:COG0222  78 REITGLGLKEAKDLVEGAPKPVKEGVSKEEAEEIKKKLEEAGAKVEL 124
L12 TIGR00855
ribosomal protein L7/L12; Ribosomal proteins L7 and L12 are synonymous except for ...
 67-192 2.24e-23

ribosomal protein L7/L12; Ribosomal proteins L7 and L12 are synonymous except for post-translational modification of the N-terminal amino acid. THis model resembles pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273301 [Multi-domain]  Cd Length: 123  Bit Score: 89.82  E-value: 2.24e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232275    67 IKKIGSEISSLTLEESRILVDYVQDKFGVSilfsaPAAAALPPPLDNGGATASVERQTTFDVVInDVPRGNRIAVITAIR 146
Cdd:TIGR00855   3 KEQIIEALKSMTVLELSELVKALEEKFGVS-----AAAPVAAGAAGAAAGAAAAEEKTEFDVIL-KGAGDNKIAVIKVVR 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 15232275   147 AMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSI 192
Cdd:TIGR00855  77 EITGLGLKEAKDLVEGAPKALKEGVSKEEAEELKKKLEEAGAKVEV 122
Ribosomal_L12 pfam00542
Ribosomal protein L7/L12 C-terminal domain;
126-192 2.51e-22

Ribosomal protein L7/L12 C-terminal domain;


Pssm-ID: 425742  Cd Length: 67  Bit Score: 85.21  E-value: 2.51e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232275   126 FDVVINDVPrGNRIAVITAIRAMTSLSLSESKELIEGFPKKFKEGVTKDEAEEDKTQLEEAGAKVSI 192
Cdd:pfam00542   1 FDVILTSAG-ANKIAVIKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGATVEL 66
Ribosomal_L12_N pfam16320
Ribosomal protein L7/L12 dimerization domain; This is the N-terminal dimerization domain of ...
 66-96 3.65e-04

Ribosomal protein L7/L12 dimerization domain; This is the N-terminal dimerization domain of ribosomal protein L7/L12.


Pssm-ID: 465091  Cd Length: 48  Bit Score: 37.00  E-value: 3.65e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15232275    66 KIKKIGSEISSLTLEESRILVDYVQDKFGVS 96
Cdd:pfam16320   1 TIEEIIEAIKELTLLELSELVKALEEKFGVS 31
 
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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