NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|28416940|ref|NP_057122|]
View 

ribosome maturation protein SBDS [Homo sapiens]

Protein Classification

ribosome maturation protein SBDS( domain architecture ID 1006011)

ribosome maturation protein SBDS is required for the assembly of mature ribosomes and ribosome biogenesis

Gene Symbol:  SBDS
Gene Ontology:  GO:0003723|GO:0042256

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PTZ00448 super family cl29187
hypothetical protein; Provisional
 1-223 1.08e-74

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PTZ00448:

Pssm-ID: 185627 [Multi-domain]  Cd Length: 373  Bit Score: 231.46  E-value: 1.08e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940    1 MSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQ 80
Cdd:PTZ00448   1 MSLFQPSNQIKLTNVAVVRYKSHGKRFEVACYKNKILNWRSGVEWDLDEVLQIRTIFANVSKGQLANSDDLNTVFGTNSI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940   81 TEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQ 160
Cdd:PTZ00448  81 DNICKTILSKGEIQVSETERSYMLDKQFTDICHMLNRMTVNPKNNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDI 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28416940  161 LKEKM--KIERAHMRLRFILP-VNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDEL 223
Cdd:PTZ00448 161 LKKRIpdQIERAKMMLKLSVDiVNKQNITKKLNEFNVFPISSEEKHNTYSITFLCEPRYYREIDQL 226
 
Name Accession Description Interval E-value
PTZ00448 PTZ00448
hypothetical protein; Provisional
 1-223 1.08e-74

hypothetical protein; Provisional


Pssm-ID: 185627 [Multi-domain]  Cd Length: 373  Bit Score: 231.46  E-value: 1.08e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940    1 MSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQ 80
Cdd:PTZ00448   1 MSLFQPSNQIKLTNVAVVRYKSHGKRFEVACYKNKILNWRSGVEWDLDEVLQIRTIFANVSKGQLANSDDLNTVFGTNSI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940   81 TEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQ 160
Cdd:PTZ00448  81 DNICKTILSKGEIQVSETERSYMLDKQFTDICHMLNRMTVNPKNNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDI 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28416940  161 LKEKM--KIERAHMRLRFILP-VNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDEL 223
Cdd:PTZ00448 161 LKKRIpdQIERAKMMLKLSVDiVNKQNITKKLNEFNVFPISSEEKHNTYSITFLCEPRYYREIDQL 226
RNA_SBDS TIGR00291
rRNA metabolism protein, SBDS family; This protein family, possibly universal in both archaea ...
 9-230 8.07e-48

rRNA metabolism protein, SBDS family; This protein family, possibly universal in both archaea and eukaryotes, appears to be involved in (ribosomal) RNA metabolism. Mutations in the human ortholog are associated with Shwachman-Bodian-Diamond syndrome. [Protein synthesis, Other]


Pssm-ID: 129392 [Multi-domain]  Cd Length: 231  Bit Score: 158.07  E-value: 8.07e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940     9 QIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQIL 88
Cdd:TIGR00291   1 MVSLENAVIARLKKHGERFEVLVDPYLAADLREGIEVDFEDVLAIEEVFRDASKGEKASEEDLRKIFGTTDVDEVAEKII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940    89 TKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIE 168
Cdd:TIGR00291  81 LKGEIQLTAEQRREMLEKKRNQIINIISRNTINPQTKKPHPPTRIEKALEEAKVHIDIFKSVEEQVLEIVKALKQIIPIK 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28416940   169 RAHMRLRF-ILPVNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDELIKKETKG 230
Cdd:TIGR00291 161 FEKMKVAIkIPPERAGEAIEAISNFGAVTPEEWQEDGSWICVGEIPSGNYRDLMTLLDKKTKG 223
SBDS pfam01172
Shwachman-Bodian-Diamond syndrome (SBDS) protein; This family is highly conserved in species ...
 17-98 5.36e-36

Shwachman-Bodian-Diamond syndrome (SBDS) protein; This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterized by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism. In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition.


Pssm-ID: 460097 [Multi-domain]  Cd Length: 82  Bit Score: 122.53  E-value: 5.36e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940    17 VVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVS 96
Cdd:pfam01172   1 KVRYKGGGKRFEIAVDPNKVKKWRKGKSIPLDEVLQSFKVFTNVSKGDRASKEDLEKEFGTTDEDEIIKKILEKGELQLT 80


                  ..
gi 28416940    97 DK 98
Cdd:pfam01172  81 EE 82
 
Name Accession Description Interval E-value
PTZ00448 PTZ00448
hypothetical protein; Provisional
 1-223 1.08e-74

hypothetical protein; Provisional


Pssm-ID: 185627 [Multi-domain]  Cd Length: 373  Bit Score: 231.46  E-value: 1.08e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940    1 MSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQ 80
Cdd:PTZ00448   1 MSLFQPSNQIKLTNVAVVRYKSHGKRFEVACYKNKILNWRSGVEWDLDEVLQIRTIFANVSKGQLANSDDLNTVFGTNSI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940   81 TEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQ 160
Cdd:PTZ00448  81 DNICKTILSKGEIQVSETERSYMLDKQFTDICHMLNRMTVNPKNNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDI 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28416940  161 LKEKM--KIERAHMRLRFILP-VNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDEL 223
Cdd:PTZ00448 161 LKKRIpdQIERAKMMLKLSVDiVNKQNITKKLNEFNVFPISSEEKHNTYSITFLCEPRYYREIDQL 226
RNA_SBDS TIGR00291
rRNA metabolism protein, SBDS family; This protein family, possibly universal in both archaea ...
 9-230 8.07e-48

rRNA metabolism protein, SBDS family; This protein family, possibly universal in both archaea and eukaryotes, appears to be involved in (ribosomal) RNA metabolism. Mutations in the human ortholog are associated with Shwachman-Bodian-Diamond syndrome. [Protein synthesis, Other]


Pssm-ID: 129392 [Multi-domain]  Cd Length: 231  Bit Score: 158.07  E-value: 8.07e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940     9 QIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQIL 88
Cdd:TIGR00291   1 MVSLENAVIARLKKHGERFEVLVDPYLAADLREGIEVDFEDVLAIEEVFRDASKGEKASEEDLRKIFGTTDVDEVAEKII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940    89 TKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIE 168
Cdd:TIGR00291  81 LKGEIQLTAEQRREMLEKKRNQIINIISRNTINPQTKKPHPPTRIEKALEEAKVHIDIFKSVEEQVLEIVKALKQIIPIK 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28416940   169 RAHMRLRF-ILPVNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDELIKKETKG 230
Cdd:TIGR00291 161 FEKMKVAIkIPPERAGEAIEAISNFGAVTPEEWQEDGSWICVGEIPSGNYRDLMTLLDKKTKG 223
SBDS pfam01172
Shwachman-Bodian-Diamond syndrome (SBDS) protein; This family is highly conserved in species ...
 17-98 5.36e-36

Shwachman-Bodian-Diamond syndrome (SBDS) protein; This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterized by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism. In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition.


Pssm-ID: 460097 [Multi-domain]  Cd Length: 82  Bit Score: 122.53  E-value: 5.36e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28416940    17 VVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVS 96
Cdd:pfam01172   1 KVRYKGGGKRFEIAVDPNKVKKWRKGKSIPLDEVLQSFKVFTNVSKGDRASKEDLEKEFGTTDEDEIIKKILEKGELQLT 80


                  ..
gi 28416940    97 DK 98
Cdd:pfam01172  81 EE 82
SBDS_domain_II pfam09377
SBDS protein, domain II; Members containing this domain are highly conserved in species ...
 109-170 1.66e-31

SBDS protein, domain II; Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants, including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. SBDS protein is composed of three domains. The N-terminal (pfam01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II) represented in this entry consists of a three-helical bundle and the C-terminal domain that has a ferredoxin-like fold.


Pssm-ID: 462778  Cd Length: 62  Bit Score: 110.60  E-value: 1.66e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28416940   109 RDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIERA 170
Cdd:pfam09377   1 KEIITIIARKCVNPQTKRPYPPTMIEKALEEAKFSVDPNKSAKEQALEAIKALRQIIPIKRA 62
SBDS_C pfam20268
SBDS protein, C-terminal domain; Members containing this domain are highly conserved in ...
 172-238 4.47e-13

SBDS protein, C-terminal domain; Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants, including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. The SBDS protein is composed of three domains. The N-terminal (pfam01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II, pfam09377) consists of a three-helical bundle and this C-terminal domain which has a ferredoxin-like fold.


Pssm-ID: 466418  Cd Length: 67  Bit Score: 62.62  E-value: 4.47e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28416940   172 MRLRFILPVNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDELIKKETKGKGSLEVLN 238
Cdd:pfam20268   1 MRLAVKIPAKYAGKAYGKLKKLGVIEKEEWQSGSWEAVVEIPPGLYRELIDLLNKETKGEGEVEVLS 67
 
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