chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
84-366
1.84e-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: 48.13 E-value: 1.84e-05
IQ (isoleucine-glutamine) motif containing D (IQCD); IQCD, also called dynein regulatory ...
436-467
3.68e-04
IQ (isoleucine-glutamine) motif containing D (IQCD); IQCD, also called dynein regulatory complex protein 10 (DRC10), belongs to the IQ motif-containing protein family which contains a C-terminal conserved IQ motif domain and two coiled-coil domains. The IQ motif ([ILV]QxxxRxxxx[RK]), where x stands for any amino-acid residue, interacts with calmodulin (CaM) in a calcium-independent manner and is present in proteins with a wide diversity of biological functions. The IQCD protein was found to primarily accumulate in the acrosome area of round and elongating spermatids of the testis during late stage of spermiogenesis and was then localized to the acrosome and tail regions of mature spermatozoa. The expression of IQCD follows the trajectory of acrosome development during spermatogenesis. IQCD is associated with neuroblastoma and neurodegenerative diseases, and is reported to interact with the nuclear retinoid X receptor in the presence of 9-cis-retinoic acid, thereby activating the transcriptional activity of the receptor.
:
Pssm-ID: 467745 [Multi-domain] Cd Length: 37 Bit Score: 38.29 E-value: 3.68e-04
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
84-366
1.84e-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: 48.13 E-value: 1.84e-05
IQ (isoleucine-glutamine) motif containing D (IQCD); IQCD, also called dynein regulatory ...
436-467
3.68e-04
IQ (isoleucine-glutamine) motif containing D (IQCD); IQCD, also called dynein regulatory complex protein 10 (DRC10), belongs to the IQ motif-containing protein family which contains a C-terminal conserved IQ motif domain and two coiled-coil domains. The IQ motif ([ILV]QxxxRxxxx[RK]), where x stands for any amino-acid residue, interacts with calmodulin (CaM) in a calcium-independent manner and is present in proteins with a wide diversity of biological functions. The IQCD protein was found to primarily accumulate in the acrosome area of round and elongating spermatids of the testis during late stage of spermiogenesis and was then localized to the acrosome and tail regions of mature spermatozoa. The expression of IQCD follows the trajectory of acrosome development during spermatogenesis. IQCD is associated with neuroblastoma and neurodegenerative diseases, and is reported to interact with the nuclear retinoid X receptor in the presence of 9-cis-retinoic acid, thereby activating the transcriptional activity of the receptor.
Pssm-ID: 467745 [Multi-domain] Cd Length: 37 Bit Score: 38.29 E-value: 3.68e-04
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ...
31-356
6.24e-04
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
Pssm-ID: 431111 [Multi-domain] Cd Length: 766 Bit Score: 42.89 E-value: 6.24e-04
C-terminal middle region of Androglobins (Adgbs) and related proteins; including permuted ...
330-472
5.90e-03
C-terminal middle region of Androglobins (Adgbs) and related proteins; including permuted globin domain and IQ motif; Androglobin (Adgb, also known as Calpain-7-like protein, CAPN7L) is a large multidomain protein consisting of an N-terminal peptidase C2 family calpain-like domain, an IQ calmodulin-binding motif, and an internal, circularly permuted globin domain. The canonical secondary structure of hemoglobins is an 3-over-3 alpha-helical sandwich structure, where the eight alpha-helical segments are conventionally labeled, A-H, according to their sequential order; Adgbs differ from this in having helices C-H followed by A-B. Adgbs and other phylogenetically ancient globins, such as neuroglobins and globin X, form hexacoordinated heme iron complexes. Globins contain various highly conserved residues of the heme pocket: including a Phe in the interhelical position CD1 (Phe CD1, first position in the loop between the helices C and D) that is packed against the heme, a His at the 7th position of the E-helix (His E7) that binds the heme iron distally, and a His at the 8th position of the F-helix (His F8) that binds the heme iron proximally. Unlike other hexacoordinated globins, Adgbs have an E7 Gln; their hexacoordination scheme is [Gln]-Fe-[His]. In mammals, Adgb is mainly expressed in the testes and may play an important role in spermatogenesis. Arthropod Adgbs have degenerate globin domains (DOI:10.3389/fgene.2020.00858). This model spans the permuted globin domain, the IQ motif, and a conserved region of about 200 amino acid residues located C-terminal to the globin domain; it does not include the N-terminal protease domain or the large uncharacterized C-terminal domain of approximately 500 residues.
Pssm-ID: 412094 Cd Length: 416 Bit Score: 39.46 E-value: 5.90e-03
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
84-366
1.84e-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: 48.13 E-value: 1.84e-05
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
39-363
5.39e-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: 5.39e-05
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
105-455
2.13e-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: 44.66 E-value: 2.13e-04
IQ (isoleucine-glutamine) motif containing D (IQCD); IQCD, also called dynein regulatory ...
436-467
3.68e-04
IQ (isoleucine-glutamine) motif containing D (IQCD); IQCD, also called dynein regulatory complex protein 10 (DRC10), belongs to the IQ motif-containing protein family which contains a C-terminal conserved IQ motif domain and two coiled-coil domains. The IQ motif ([ILV]QxxxRxxxx[RK]), where x stands for any amino-acid residue, interacts with calmodulin (CaM) in a calcium-independent manner and is present in proteins with a wide diversity of biological functions. The IQCD protein was found to primarily accumulate in the acrosome area of round and elongating spermatids of the testis during late stage of spermiogenesis and was then localized to the acrosome and tail regions of mature spermatozoa. The expression of IQCD follows the trajectory of acrosome development during spermatogenesis. IQCD is associated with neuroblastoma and neurodegenerative diseases, and is reported to interact with the nuclear retinoid X receptor in the presence of 9-cis-retinoic acid, thereby activating the transcriptional activity of the receptor.
Pssm-ID: 467745 [Multi-domain] Cd Length: 37 Bit Score: 38.29 E-value: 3.68e-04
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
37-372
4.86e-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: 4.86e-04
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ...
31-356
6.24e-04
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
Pssm-ID: 431111 [Multi-domain] Cd Length: 766 Bit Score: 42.89 E-value: 6.24e-04
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
102-373
7.48e-04
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: 42.70 E-value: 7.48e-04
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
24-369
9.92e-04
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: 42.36 E-value: 9.92e-04
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
31-371
1.27e-03
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: 41.93 E-value: 1.27e-03
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
31-374
5.17e-03
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: 40.00 E-value: 5.17e-03
C-terminal middle region of Androglobins (Adgbs) and related proteins; including permuted ...
330-472
5.90e-03
C-terminal middle region of Androglobins (Adgbs) and related proteins; including permuted globin domain and IQ motif; Androglobin (Adgb, also known as Calpain-7-like protein, CAPN7L) is a large multidomain protein consisting of an N-terminal peptidase C2 family calpain-like domain, an IQ calmodulin-binding motif, and an internal, circularly permuted globin domain. The canonical secondary structure of hemoglobins is an 3-over-3 alpha-helical sandwich structure, where the eight alpha-helical segments are conventionally labeled, A-H, according to their sequential order; Adgbs differ from this in having helices C-H followed by A-B. Adgbs and other phylogenetically ancient globins, such as neuroglobins and globin X, form hexacoordinated heme iron complexes. Globins contain various highly conserved residues of the heme pocket: including a Phe in the interhelical position CD1 (Phe CD1, first position in the loop between the helices C and D) that is packed against the heme, a His at the 7th position of the E-helix (His E7) that binds the heme iron distally, and a His at the 8th position of the F-helix (His F8) that binds the heme iron proximally. Unlike other hexacoordinated globins, Adgbs have an E7 Gln; their hexacoordination scheme is [Gln]-Fe-[His]. In mammals, Adgb is mainly expressed in the testes and may play an important role in spermatogenesis. Arthropod Adgbs have degenerate globin domains (DOI:10.3389/fgene.2020.00858). This model spans the permuted globin domain, the IQ motif, and a conserved region of about 200 amino acid residues located C-terminal to the globin domain; it does not include the N-terminal protease domain or the large uncharacterized C-terminal domain of approximately 500 residues.
Pssm-ID: 412094 Cd Length: 416 Bit Score: 39.46 E-value: 5.90e-03
Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like ...
110-318
9.72e-03
Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats.
Pssm-ID: 428797 [Multi-domain] Cd Length: 542 Bit Score: 39.07 E-value: 9.72e-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,
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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,
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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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