NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2570698075|gb|WMK03965|]
View 

maturation protein SBDS-like, partial [Colotis evagore]

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
 2-124 1.39e-37

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PTZ00448:

Pssm-ID: 185627 [Multi-domain]  Cd Length: 373  Bit Score: 130.54  E-value: 1.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570698075   2 EKDIDEVLQTHTVFTNVSKGQVAKKEDLVKVFGKDDLTEICKEILEKGELQVSDKERHSQIDALFKDIATTVADKCVNPE 81
Cdd:PTZ00448   44 EWDLDEVLQIRTIFANVSKGQLANSDDLNTVFGTNSIDNICKTILSKGEIQVSETERSYMLDKQFTDICHMLNRMTVNPK 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2570698075  82 TKRPYPVSIIEKAMKDIHFSVNVNKSAKQQALEVIQLIKKEIP 124
Cdd:PTZ00448  124 NNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDILKKRIP 166
 
Name Accession Description Interval E-value
PTZ00448 PTZ00448
hypothetical protein; Provisional
 2-124 1.39e-37

hypothetical protein; Provisional


Pssm-ID: 185627 [Multi-domain]  Cd Length: 373  Bit Score: 130.54  E-value: 1.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570698075   2 EKDIDEVLQTHTVFTNVSKGQVAKKEDLVKVFGKDDLTEICKEILEKGELQVSDKERHSQIDALFKDIATTVADKCVNPE 81
Cdd:PTZ00448   44 EWDLDEVLQIRTIFANVSKGQLANSDDLNTVFGTNSIDNICKTILSKGEIQVSETERSYMLDKQFTDICHMLNRMTVNPK 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2570698075  82 TKRPYPVSIIEKAMKDIHFSVNVNKSAKQQALEVIQLIKKEIP 124
Cdd:PTZ00448  124 NNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDILKKRIP 166
RNA_SBDS TIGR00291
rRNA metabolism protein, SBDS family; This protein family, possibly universal in both archaea ...
 2-125 2.40e-34

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: 118.78  E-value: 2.40e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570698075   2 EKDIDEVLQTHTVFTNVSKGQVAKKEDLVKVFGKDDLTEICKEILEKGELQVSDKERHSQIDALFKDIATTVADKCVNPE 81
Cdd:TIGR00291  36 EVDFEDVLAIEEVFRDASKGEKASEEDLRKIFGTTDVDEVAEKIILKGEIQLTAEQRREMLEKKRNQIINIISRNTINPQ 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2570698075  82 TKRPYPVSIIEKAMKDIHFSVNVNKSAKQQALEVIQLIKKEIPL 125
Cdd:TIGR00291 116 TKKPHPPTRIEKALEEAKVHIDIFKSVEEQVLEIVKALKQIIPI 159
SBDS_domain_II pfam09377
SBDS protein, domain II; Members containing this domain are highly conserved in species ...
 67-126 4.11e-29

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: 100.20  E-value: 4.11e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570698075  67 KDIATTVADKCVNPETKRPYPVSIIEKAMKDIHFSVNVNKSAKQQALEVIQLIKKEIPLE 126
Cdd:pfam09377   1 KEIITIIARKCVNPQTKRPYPPTMIEKALEEAKFSVDPNKSAKEQALEAIKALRQIIPIK 60
 
Name Accession Description Interval E-value
PTZ00448 PTZ00448
hypothetical protein; Provisional
 2-124 1.39e-37

hypothetical protein; Provisional


Pssm-ID: 185627 [Multi-domain]  Cd Length: 373  Bit Score: 130.54  E-value: 1.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570698075   2 EKDIDEVLQTHTVFTNVSKGQVAKKEDLVKVFGKDDLTEICKEILEKGELQVSDKERHSQIDALFKDIATTVADKCVNPE 81
Cdd:PTZ00448   44 EWDLDEVLQIRTIFANVSKGQLANSDDLNTVFGTNSIDNICKTILSKGEIQVSETERSYMLDKQFTDICHMLNRMTVNPK 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2570698075  82 TKRPYPVSIIEKAMKDIHFSVNVNKSAKQQALEVIQLIKKEIP 124
Cdd:PTZ00448  124 NNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDILKKRIP 166
RNA_SBDS TIGR00291
rRNA metabolism protein, SBDS family; This protein family, possibly universal in both archaea ...
 2-125 2.40e-34

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: 118.78  E-value: 2.40e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570698075   2 EKDIDEVLQTHTVFTNVSKGQVAKKEDLVKVFGKDDLTEICKEILEKGELQVSDKERHSQIDALFKDIATTVADKCVNPE 81
Cdd:TIGR00291  36 EVDFEDVLAIEEVFRDASKGEKASEEDLRKIFGTTDVDEVAEKIILKGEIQLTAEQRREMLEKKRNQIINIISRNTINPQ 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2570698075  82 TKRPYPVSIIEKAMKDIHFSVNVNKSAKQQALEVIQLIKKEIPL 125
Cdd:TIGR00291 116 TKKPHPPTRIEKALEEAKVHIDIFKSVEEQVLEIVKALKQIIPI 159
SBDS_domain_II pfam09377
SBDS protein, domain II; Members containing this domain are highly conserved in species ...
 67-126 4.11e-29

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: 100.20  E-value: 4.11e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570698075  67 KDIATTVADKCVNPETKRPYPVSIIEKAMKDIHFSVNVNKSAKQQALEVIQLIKKEIPLE 126
Cdd:pfam09377   1 KEIITIIARKCVNPQTKRPYPPTMIEKALEEAKFSVDPNKSAKEQALEAIKALRQIIPIK 60
SBDS pfam01172
Shwachman-Bodian-Diamond syndrome (SBDS) protein; This family is highly conserved in species ...
 1-56 9.55e-21

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: 79.39  E-value: 9.55e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2570698075   1 REKDIDEVLQTHTVFTNVSKGQVAKKEDLVKVFGKDDLTEICKEILEKGELQVSDK 56
Cdd:pfam01172  27 KSIPLDEVLQSFKVFTNVSKGDRASKEDLEKEFGTTDEDEIIKKILEKGELQLTEE 82
 
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