CCDC93, coiled-coil domain; This is a coiled-coil domain found in CCDC93. Human CCDC93 is part ...
1-73
2.11e-17
CCDC93, coiled-coil domain; This is a coiled-coil domain found in CCDC93. Human CCDC93 is part of the COMMD/CCDC22/CCDC93 (CCC) complex that interacts with the multisubunit WASH complex, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. The CCC complex controls Notch activation by modulating its intracellular trafficking.
The actual alignment was detected with superfamily member pfam09762:
Pssm-ID: 462886 Cd Length: 173 Bit Score: 79.64 E-value: 2.11e-17
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
78-407
4.47e-05
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]
The actual alignment was detected with superfamily member TIGR02168:
Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 46.20 E-value: 4.47e-05
CCDC93, coiled-coil domain; This is a coiled-coil domain found in CCDC93. Human CCDC93 is part ...
1-73
2.11e-17
CCDC93, coiled-coil domain; This is a coiled-coil domain found in CCDC93. Human CCDC93 is part of the COMMD/CCDC22/CCDC93 (CCC) complex that interacts with the multisubunit WASH complex, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. The CCC complex controls Notch activation by modulating its intracellular trafficking.
Pssm-ID: 462886 Cd Length: 173 Bit Score: 79.64 E-value: 2.11e-17
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
78-407
4.47e-05
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: 46.20 E-value: 4.47e-05
CCDC93, coiled-coil domain; This is a coiled-coil domain found in CCDC93. Human CCDC93 is part ...
1-73
2.11e-17
CCDC93, coiled-coil domain; This is a coiled-coil domain found in CCDC93. Human CCDC93 is part of the COMMD/CCDC22/CCDC93 (CCC) complex that interacts with the multisubunit WASH complex, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. The CCC complex controls Notch activation by modulating its intracellular trafficking.
Pssm-ID: 462886 Cd Length: 173 Bit Score: 79.64 E-value: 2.11e-17
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
78-407
4.47e-05
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: 46.20 E-value: 4.47e-05
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
98-385
2.07e-04
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: 44.28 E-value: 2.07e-04
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
190-467
3.50e-04
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: 43.51 E-value: 3.50e-04
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
159-492
3.57e-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: 40.05 E-value: 3.57e-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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of your query sequence and the protein sequences used to curate the domain model,
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The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
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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
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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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