polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
257-343
1.77e-18
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.
The actual alignment was detected with superfamily member cd09803:
Pssm-ID: 197361 [Multi-domain] Cd Length: 87 Bit Score: 79.70 E-value: 1.77e-18
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK ...
44-110
5.11e-16
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.
:
Pssm-ID: 431942 [Multi-domain] Cd Length: 67 Bit Score: 72.13 E-value: 5.11e-16
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin ...
392-417
1.48e-11
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction.
The actual alignment was detected with superfamily member pfam18414:
Pssm-ID: 436483 Cd Length: 26 Bit Score: 58.37 E-value: 1.48e-11
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
49-362
8.18e-09
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
The actual alignment was detected with superfamily member TIGR02169:
Pssm-ID: 481474 [Multi-domain] Cd Length: 1164 Bit Score: 57.77 E-value: 8.18e-09
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
257-343
1.77e-18
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.
Pssm-ID: 197361 [Multi-domain] Cd Length: 87 Bit Score: 79.70 E-value: 1.77e-18
Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a ...
258-343
6.29e-18
Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a leucine-zipper domain associated with the CC2 coiled-coil region of NF-kappa-B essential modulator, NEMO. It plays a regulatory role, along with the very C-terminal zinc-finger; it contains a ubiquitin-binding domain (UBD) and represents one region that contributes to NEMO oligomerization. NEMO itself is an integral part of the IkappaB kinase complex and serves as a molecular switch via which the NF-kappaB signalling pathway is regulated.
Pssm-ID: 465155 [Multi-domain] Cd Length: 100 Bit Score: 78.49 E-value: 6.29e-18
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK ...
44-110
5.11e-16
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.
Pssm-ID: 431942 [Multi-domain] Cd Length: 67 Bit Score: 72.13 E-value: 5.11e-16
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin ...
392-417
1.48e-11
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction.
Pssm-ID: 436483 Cd Length: 26 Bit Score: 58.37 E-value: 1.48e-11
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
49-362
8.18e-09
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: 57.77 E-value: 8.18e-09
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
145-286
3.29e-04
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: 42.44 E-value: 3.29e-04
MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model ...
138-322
5.25e-04
MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model describes the N-terminal 1900 amino acids of MARTX family multifunctional-autoprocessing repeats-in-toxin holotoxins, which contain both repeat regions that facilitate their entry into eukaryotic target cells, and multiple effector domains.
Pssm-ID: 467957 [Multi-domain] Cd Length: 1848 Bit Score: 42.51 E-value: 5.25e-04
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
257-343
1.77e-18
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.
Pssm-ID: 197361 [Multi-domain] Cd Length: 87 Bit Score: 79.70 E-value: 1.77e-18
Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a ...
258-343
6.29e-18
Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a leucine-zipper domain associated with the CC2 coiled-coil region of NF-kappa-B essential modulator, NEMO. It plays a regulatory role, along with the very C-terminal zinc-finger; it contains a ubiquitin-binding domain (UBD) and represents one region that contributes to NEMO oligomerization. NEMO itself is an integral part of the IkappaB kinase complex and serves as a molecular switch via which the NF-kappaB signalling pathway is regulated.
Pssm-ID: 465155 [Multi-domain] Cd Length: 100 Bit Score: 78.49 E-value: 6.29e-18
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK ...
44-110
5.11e-16
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.
Pssm-ID: 431942 [Multi-domain] Cd Length: 67 Bit Score: 72.13 E-value: 5.11e-16
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin ...
392-417
1.48e-11
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction.
Pssm-ID: 436483 Cd Length: 26 Bit Score: 58.37 E-value: 1.48e-11
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
49-362
8.18e-09
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: 57.77 E-value: 8.18e-09
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
60-320
1.27e-08
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: 57.37 E-value: 1.27e-08
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
39-321
3.53e-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: 3.53e-06
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
49-295
9.80e-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: 48.13 E-value: 9.80e-06
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
52-355
2.59e-04
exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 43.42 E-value: 2.59e-04
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
145-286
3.29e-04
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: 42.44 E-value: 3.29e-04
MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model ...
138-322
5.25e-04
MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model describes the N-terminal 1900 amino acids of MARTX family multifunctional-autoprocessing repeats-in-toxin holotoxins, which contain both repeat regions that facilitate their entry into eukaryotic target cells, and multiple effector domains.
Pssm-ID: 467957 [Multi-domain] Cd Length: 1848 Bit Score: 42.51 E-value: 5.25e-04
Cation efflux system protein CusB domain 1; The cation efflux system protein CusB from E. coli ...
152-315
1.93e-03
Cation efflux system protein CusB domain 1; The cation efflux system protein CusB from E. coli can be divided into four different domains, the first three domains of the protein are mostly beta-strands and the fourth forms an all alpha-helical domain. This entry represents the first beta-domain (domain 1) of CusB and it is formed by the N and C-terminal ends of the polypeptide (residues 89-102 and 324-385). CusB is part of the copper-transporting efflux system CusCFBA. This domain can also be found in other membrane-fusion proteins, such as HlyD, MdtN, MdtE and AaeA. HlyD is a component of the prototypical alpha-haemolysin (HlyA) bacterial type I secretion system, along with the other components HlyB and TolC. HlyD is anchored in the cytoplasmic membrane by a single transmembrane domain and has a large periplasmic domain within the carboxy-terminal 100 amino acids, HlyB and HlyD form a stable complex that binds the recombinant protein bearing a C-terminal HlyA signal sequence and ATP in the cytoplasm. HlyD, HlyB and TolC combine to form the three-component ABC transporter complex that forms a trans-membrane channel or pore through which HlyA can be transferred directly to the extracellular medium. Cutinase has been shown to be transported effectively through this pore.
Pssm-ID: 425733 [Multi-domain] Cd Length: 322 Bit Score: 40.10 E-value: 1.93e-03
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
72-365
2.12e-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: 40.44 E-value: 2.12e-03
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
56-353
3.34e-03
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 39.95 E-value: 3.34e-03
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
114-358
7.35e-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: 38.88 E-value: 7.35e-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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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,
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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.
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