TSG101 and ALIX binding domain of CEP55; This domain family is found in eukaryotes, and is ...
17-50
5.95e-08
TSG101 and ALIX binding domain of CEP55; This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR.
:
Pssm-ID: 463486 [Multi-domain] Cd Length: 34 Bit Score: 47.87 E-value: 5.95e-08
TSG101 and ALIX binding domain of CEP55; This domain family is found in eukaryotes, and is ...
17-50
5.95e-08
TSG101 and ALIX binding domain of CEP55; This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR.
Pssm-ID: 463486 [Multi-domain] Cd Length: 34 Bit Score: 47.87 E-value: 5.95e-08
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
11-240
8.55e-06
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]
Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 47.36 E-value: 8.55e-06
Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and ...
85-202
1.64e-05
Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and similar proteins; This model includes Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, both parts of two-component alpha-helical pore-forming toxins (alpha-PFTs). The xaxAB genes encoding the XaxAB toxin have also been also identified in various plant and human pathogens. XaxAB triggers necrosis and apoptosis in both insect hemocytes and mammalian cells. Structure studies show that component A binds to component B's back, forming a subunit; twelve to fifteen of these subunits then conjoin as the pore-forming toxin. Component A stabilizes each subunit on the membrane and activates component B, which then punctures the membrane by swinging out its lower end. Similarly, Yersinia enterocolitica YaxA, encoded by the yaxAB gene, forms a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Although both subunits bear membrane-active moieties, only YaxA is capable of binding to membranes by itself and YaxB is subsequently recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices; pore formation then progresses by further oligomerization of YaxA-YaxB dimers. YaxAB has been found to be strongly upregulated by the Yersinia master regulator RovA, a transcriptional activator of Yersinia outer membrane protein invasion which is involved in bacterial attachment and invasion across the intestinal epithelium.
Pssm-ID: 439155 [Multi-domain] Cd Length: 306 Bit Score: 45.66 E-value: 1.64e-05
Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are ...
89-199
6.95e-04
Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.
Pssm-ID: 462986 [Multi-domain] Cd Length: 347 Bit Score: 40.90 E-value: 6.95e-04
TSG101 and ALIX binding domain of CEP55; This domain family is found in eukaryotes, and is ...
17-50
5.95e-08
TSG101 and ALIX binding domain of CEP55; This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR.
Pssm-ID: 463486 [Multi-domain] Cd Length: 34 Bit Score: 47.87 E-value: 5.95e-08
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
11-240
8.55e-06
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]
Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 47.36 E-value: 8.55e-06
Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and ...
85-202
1.64e-05
Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and similar proteins; This model includes Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, both parts of two-component alpha-helical pore-forming toxins (alpha-PFTs). The xaxAB genes encoding the XaxAB toxin have also been also identified in various plant and human pathogens. XaxAB triggers necrosis and apoptosis in both insect hemocytes and mammalian cells. Structure studies show that component A binds to component B's back, forming a subunit; twelve to fifteen of these subunits then conjoin as the pore-forming toxin. Component A stabilizes each subunit on the membrane and activates component B, which then punctures the membrane by swinging out its lower end. Similarly, Yersinia enterocolitica YaxA, encoded by the yaxAB gene, forms a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Although both subunits bear membrane-active moieties, only YaxA is capable of binding to membranes by itself and YaxB is subsequently recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices; pore formation then progresses by further oligomerization of YaxA-YaxB dimers. YaxAB has been found to be strongly upregulated by the Yersinia master regulator RovA, a transcriptional activator of Yersinia outer membrane protein invasion which is involved in bacterial attachment and invasion across the intestinal epithelium.
Pssm-ID: 439155 [Multi-domain] Cd Length: 306 Bit Score: 45.66 E-value: 1.64e-05
Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are ...
89-199
6.95e-04
Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.
Pssm-ID: 462986 [Multi-domain] Cd Length: 347 Bit Score: 40.90 E-value: 6.95e-04
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
98-193
2.42e-03
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.
Pssm-ID: 462900 [Multi-domain] Cd Length: 305 Bit Score: 38.97 E-value: 2.42e-03
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
54-244
4.53e-03
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]
Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 38.90 E-value: 4.53e-03
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
35-241
6.72e-03
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]
Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 38.11 E-value: 6.72e-03
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
82-240
9.04e-03
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]
Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 37.74 E-value: 9.04e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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Domains are color coded according to superfamilies
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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