NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|568935106|ref|XP_006534747|]
View 

large ribosomal subunit protein uL18 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PTZ00069 super family cl36504
60S ribosomal protein L5; Provisional
1-294 4.94e-147

60S ribosomal protein L5; Provisional


The actual alignment was detected with superfamily member PTZ00069:

Pssm-ID: 240254 [Multi-domain]  Cd Length: 300  Bit Score: 414.47  E-value: 4.94e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106   1 MGFVKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCAAYA 80
Cdd:PTZ00069   1 MAFVKVVKNKAYFKRFQVKYRRRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106  81 HELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNV-ESIDGQPGAFTCYLDAGLARTTTGNKV 159
Cdd:PTZ00069  81 HELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEADGEYYHVdEEDDEERRPFKAILDVGLARTTTGNRV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106 160 FGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPD-MEEM 238
Cdd:PTZ00069 161 FGALKGAVDGGLHIPHSPNRFPGYSKEKDSYDAEVHRDRIFGKHVAEYMKQLKEEDPDKYKKQFSKYIKAGVGPDsLEDM 240
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106 239 YKKAHAAIRENPVYEKK---PKREVKKKRWNRPKMSLAQKKDRVAQKKASFL-RAQERAA 294
Cdd:PTZ00069 241 YKKAHAAIRANPSKVKKkkkKKKKVVHKKYKTKKLTGKQRKARVKAKKAQRReRLQKKIK 300
 
Name Accession Description Interval E-value
PTZ00069 PTZ00069
60S ribosomal protein L5; Provisional
1-294 4.94e-147

60S ribosomal protein L5; Provisional


Pssm-ID: 240254 [Multi-domain]  Cd Length: 300  Bit Score: 414.47  E-value: 4.94e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106   1 MGFVKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCAAYA 80
Cdd:PTZ00069   1 MAFVKVVKNKAYFKRFQVKYRRRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106  81 HELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNV-ESIDGQPGAFTCYLDAGLARTTTGNKV 159
Cdd:PTZ00069  81 HELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEADGEYYHVdEEDDEERRPFKAILDVGLARTTTGNRV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106 160 FGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPD-MEEM 238
Cdd:PTZ00069 161 FGALKGAVDGGLHIPHSPNRFPGYSKEKDSYDAEVHRDRIFGKHVAEYMKQLKEEDPDKYKKQFSKYIKAGVGPDsLEDM 240
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106 239 YKKAHAAIRENPVYEKK---PKREVKKKRWNRPKMSLAQKKDRVAQKKASFL-RAQERAA 294
Cdd:PTZ00069 241 YKKAHAAIRANPSKVKKkkkKKKKVVHKKYKTKKLTGKQRKARVKAKKAQRReRLQKKIK 300
Ribosomal_L5e pfam17144
Ribosomal large subunit proteins 60S L5, and 50S L18; This family contains the large 60S ...
14-176 4.75e-108

Ribosomal large subunit proteins 60S L5, and 50S L18; This family contains the large 60S ribosomal L5 proteins from Eukaryota and the 50S L18 proteins from Archaea. It has been shown that the amino terminal 93 amino acids of Swiss:P09895 are necessary and sufficient to bind 5S rRNA in vitro, suggesting that the entire family has a function in rRNA binding.


Pssm-ID: 465361  Cd Length: 163  Bit Score: 310.59  E-value: 4.75e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106   14 KRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLT 93
Cdd:pfam17144   1 KRFQVKFRRRREGKTDYYARKRLITQDKNKYNTPKYRLVVRFTNKDIICQIVYAKIEGDRVLAAAYSHELPKYGIKVGLT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106   94 NYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSI 173
Cdd:pfam17144  81 NYAAAYATGLLLARRLLTKLGLDKIYEGQEEVDGEEYNVEEIDDEPRPFKAFLDVGLARTTTGARVFGAMKGAVDGGLDI 160

                  ...
gi 568935106  174 PHS 176
Cdd:pfam17144 161 PHS 163
Ribosomal_L18_L5e cd00432
Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of ...
31-171 6.28e-24

Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.


Pssm-ID: 238246  Cd Length: 103  Bit Score: 93.37  E-value: 6.28e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106  31 YARKRLVIQdknkyntPKYRMIVRVTNRDIICQIAYAriEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLllarrll 110
Cdd:cd00432    1 RRRKRLGTQ-------ERPRLVVRKSNKHIYAQIIDD--SGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGR------- 64
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568935106 111 nRFGMDKIyegqvevnggeynvesidgQPGAFTCYLDAGLARttTGNKVFGALKGAVDGGL 171
Cdd:cd00432   65 -LLAKRAL-------------------EKGIKKVVFDRGGYR--YHGRVKALAKGAREGGL 103
 
Name Accession Description Interval E-value
PTZ00069 PTZ00069
60S ribosomal protein L5; Provisional
1-294 4.94e-147

60S ribosomal protein L5; Provisional


Pssm-ID: 240254 [Multi-domain]  Cd Length: 300  Bit Score: 414.47  E-value: 4.94e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106   1 MGFVKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCAAYA 80
Cdd:PTZ00069   1 MAFVKVVKNKAYFKRFQVKYRRRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106  81 HELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNV-ESIDGQPGAFTCYLDAGLARTTTGNKV 159
Cdd:PTZ00069  81 HELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEADGEYYHVdEEDDEERRPFKAILDVGLARTTTGNRV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106 160 FGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPD-MEEM 238
Cdd:PTZ00069 161 FGALKGAVDGGLHIPHSPNRFPGYSKEKDSYDAEVHRDRIFGKHVAEYMKQLKEEDPDKYKKQFSKYIKAGVGPDsLEDM 240
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106 239 YKKAHAAIRENPVYEKK---PKREVKKKRWNRPKMSLAQKKDRVAQKKASFL-RAQERAA 294
Cdd:PTZ00069 241 YKKAHAAIRANPSKVKKkkkKKKKVVHKKYKTKKLTGKQRKARVKAKKAQRReRLQKKIK 300
Ribosomal_L5e pfam17144
Ribosomal large subunit proteins 60S L5, and 50S L18; This family contains the large 60S ...
14-176 4.75e-108

Ribosomal large subunit proteins 60S L5, and 50S L18; This family contains the large 60S ribosomal L5 proteins from Eukaryota and the 50S L18 proteins from Archaea. It has been shown that the amino terminal 93 amino acids of Swiss:P09895 are necessary and sufficient to bind 5S rRNA in vitro, suggesting that the entire family has a function in rRNA binding.


Pssm-ID: 465361  Cd Length: 163  Bit Score: 310.59  E-value: 4.75e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106   14 KRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLT 93
Cdd:pfam17144   1 KRFQVKFRRRREGKTDYYARKRLITQDKNKYNTPKYRLVVRFTNKDIICQIVYAKIEGDRVLAAAYSHELPKYGIKVGLT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106   94 NYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSI 173
Cdd:pfam17144  81 NYAAAYATGLLLARRLLTKLGLDKIYEGQEEVDGEEYNVEEIDDEPRPFKAFLDVGLARTTTGARVFGAMKGAVDGGLDI 160

                  ...
gi 568935106  174 PHS 176
Cdd:pfam17144 161 PHS 163
rpl18p PRK08569
50S ribosomal protein L18P; Reviewed
15-248 4.37e-37

50S ribosomal protein L18P; Reviewed


Pssm-ID: 236294 [Multi-domain]  Cd Length: 193  Bit Score: 130.44  E-value: 4.37e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106  15 RYQVRFRRRREGKTDYYARKRLVIQDKNkyntpkyRMIVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTN 94
Cdd:PRK08569   6 RYKVPFRRRREGKTDYRKRLKLLLSGKP-------RLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGDTGN 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106  95 YAAAYCTGlllarrllNRFGMDKIYEGQVEvnggeynvesidgqpgaftCYLDAGLARTTTGNKVFGALKGAVDGGLSIP 174
Cdd:PRK08569  79 TPAAYLTG--------LLAGKKALKAGVEE-------------------AVLDIGLHRPTKGSRVFAALKGAIDAGLEIP 131
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568935106 175 HSTKRFPgydSESKefnaevhrkhIMGQNVADYMRYLmeeDEDAYKKQFSQYIKNNVTP-DMEEMYKKAHAAIRE 248
Cdd:PRK08569 132 HGEEVLP---DEDR----------IRGEHIAEYAESL---KEENYKKQFSKYLERGLDPeDLPEHFEEVKEKILE 190
Ribosomal_L18_L5e cd00432
Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of ...
31-171 6.28e-24

Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.


Pssm-ID: 238246  Cd Length: 103  Bit Score: 93.37  E-value: 6.28e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935106  31 YARKRLVIQdknkyntPKYRMIVRVTNRDIICQIAYAriEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLllarrll 110
Cdd:cd00432    1 RRRKRLGTQ-------ERPRLVVRKSNKHIYAQIIDD--SGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGR------- 64
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568935106 111 nRFGMDKIyegqvevnggeynvesidgQPGAFTCYLDAGLARttTGNKVFGALKGAVDGGL 171
Cdd:cd00432   65 -LLAKRAL-------------------EKGIKKVVFDRGGYR--YHGRVKALAKGAREGGL 103
Ribosomal_L18_c pfam14204
Ribosomal L18 C-terminal region; This domain is the C-terminal end of ribosomal L18/L5 ...
235-288 2.86e-16

Ribosomal L18 C-terminal region; This domain is the C-terminal end of ribosomal L18/L5 proteins.


Pssm-ID: 464103 [Multi-domain]  Cd Length: 55  Bit Score: 71.43  E-value: 2.86e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568935106  235 MEEMYKKAHAAIRENPVYEKKP-KREVKKKRWNRPKMSLAQKKDRVAQKKASFLR 288
Cdd:pfam14204   1 IEEMYKKAHAAIREDPSKKKKEkKKPAESKKYKKKKLTLAQRKARVAQKKAALLA 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH