HEC/Ndc80p family; Members of this family are components of the mitotic spindle. It has been ...
73-221
2.41e-62
HEC/Ndc80p family; Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle.
:
Pssm-ID: 461058 Cd Length: 159 Bit Score: 203.67 E-value: 2.41e-62
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
259-398
5.21e-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: 46.59 E-value: 5.21e-05
HEC/Ndc80p family; Members of this family are components of the mitotic spindle. It has been ...
73-221
2.41e-62
HEC/Ndc80p family; Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle.
Pssm-ID: 461058 Cd Length: 159 Bit Score: 203.67 E-value: 2.41e-62
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
260-586
6.40e-08
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.
Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 55.80 E-value: 6.40e-08
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
259-398
5.21e-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: 46.59 E-value: 5.21e-05
Intraflagellar transport complex B, subunit 20; IFT20 is subunit 20 of the intraflagellar ...
268-358
8.58e-04
Intraflagellar transport complex B, subunit 20; IFT20 is subunit 20 of the intraflagellar transport complex B. The intraflagellar transport complex assembles and maintains eukaryotic cilia and flagella. IFT20 is localized to the Golgi complex and is anchored there by the Golgi polypeptide, GMAP210, whereas all other subunits except IFT172 localize to cilia and the peri-basal body or centrosomal region at the base of cilia. IFT20 accompanies Golgi-derived vesicles to the point of exocytosis near the basal bodies where the other IFT polypeptides are present, and where the intact IFT particle is assembled in association with the inner surface of the cell membrane. Passage of the IFT complex then follows, through the flagellar pore recognition site at the transition region, into the ciliary compartment. There also appears to be a role of intraflagellar transport (IFT) polypeptides in the formation of the immune synapse in non ciliated cells. The flagellum, in addition to being a sensory and motile organelle, is also a secretory organelle. A number of IFT components are expressed in haematopoietic cells, which have no cilia, indicating an unexpected role of IFT proteins in immune synapse-assembly and intracellular membrane trafficking in T lymphocytes; this suggests that the immune synapse could represent the functional homolog of the primary cilium in these cells.
Pssm-ID: 464383 [Multi-domain] Cd Length: 109 Bit Score: 39.10 E-value: 8.58e-04
HEC/Ndc80p family; Members of this family are components of the mitotic spindle. It has been ...
73-221
2.41e-62
HEC/Ndc80p family; Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle.
Pssm-ID: 461058 Cd Length: 159 Bit Score: 203.67 E-value: 2.41e-62
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
260-586
6.40e-08
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.
Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 55.80 E-value: 6.40e-08
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
333-623
2.82e-07
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: 53.92 E-value: 2.82e-07
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
265-548
1.51e-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: 51.60 E-value: 1.51e-06
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
259-557
6.21e-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: 49.67 E-value: 6.21e-06
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
327-608
8.03e-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: 49.28 E-value: 8.03e-06
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
264-574
3.90e-05
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.
Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 46.94 E-value: 3.90e-05
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
259-398
5.21e-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: 46.59 E-value: 5.21e-05
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
259-453
8.56e-04
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.
Pssm-ID: 463796 [Multi-domain] Cd Length: 712 Bit Score: 42.36 E-value: 8.56e-04
Intraflagellar transport complex B, subunit 20; IFT20 is subunit 20 of the intraflagellar ...
268-358
8.58e-04
Intraflagellar transport complex B, subunit 20; IFT20 is subunit 20 of the intraflagellar transport complex B. The intraflagellar transport complex assembles and maintains eukaryotic cilia and flagella. IFT20 is localized to the Golgi complex and is anchored there by the Golgi polypeptide, GMAP210, whereas all other subunits except IFT172 localize to cilia and the peri-basal body or centrosomal region at the base of cilia. IFT20 accompanies Golgi-derived vesicles to the point of exocytosis near the basal bodies where the other IFT polypeptides are present, and where the intact IFT particle is assembled in association with the inner surface of the cell membrane. Passage of the IFT complex then follows, through the flagellar pore recognition site at the transition region, into the ciliary compartment. There also appears to be a role of intraflagellar transport (IFT) polypeptides in the formation of the immune synapse in non ciliated cells. The flagellum, in addition to being a sensory and motile organelle, is also a secretory organelle. A number of IFT components are expressed in haematopoietic cells, which have no cilia, indicating an unexpected role of IFT proteins in immune synapse-assembly and intracellular membrane trafficking in T lymphocytes; this suggests that the immune synapse could represent the functional homolog of the primary cilium in these cells.
Pssm-ID: 464383 [Multi-domain] Cd Length: 109 Bit Score: 39.10 E-value: 8.58e-04
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
284-571
1.81e-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: 41.58 E-value: 1.81e-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.
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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
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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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