S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
8-84
3.15e-07
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
The actual alignment was detected with superfamily member cd00315:
Pssm-ID: 473071 [Multi-domain] Cd Length: 275 Bit Score: 53.01 E-value: 3.15e-07
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
77-119
7.23e-06
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
The actual alignment was detected with superfamily member pfam13403:
Pssm-ID: 451395 [Multi-domain] Cd Length: 147 Bit Score: 46.85 E-value: 7.23e-06
DNA adenine methylase (dam); All proteins in this family for which functions are known are ...
829-1085
2.07e-78
DNA adenine methylase (dam); All proteins in this family for which functions are known are DNA-adenine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The DNA adenine methylase (dam) of E. coli and related species is instrumental in distinguishing the newly synthesized strand during DNA replication for methylation-directed mismatch repair. This family includes several phage methylases and a number of different restriction enzyme chromosomal site-specific modification systems. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273146 Cd Length: 267 Bit Score: 258.07 E-value: 2.07e-78
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
419-803
5.47e-17
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. 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: 273211 [Multi-domain] Cd Length: 315 Bit Score: 83.14 E-value: 5.47e-17
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
419-803
1.94e-15
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Pssm-ID: 238192 [Multi-domain] Cd Length: 275 Bit Score: 77.66 E-value: 1.94e-15
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
8-84
3.15e-07
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Pssm-ID: 238192 [Multi-domain] Cd Length: 275 Bit Score: 53.01 E-value: 3.15e-07
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. ...
386-419
2.79e-06
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Pssm-ID: 197641 Cd Length: 46 Bit Score: 45.24 E-value: 2.79e-06
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
8-84
2.31e-04
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. 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: 273211 [Multi-domain] Cd Length: 315 Bit Score: 44.62 E-value: 2.31e-04
intein C-terminal splicing region; This model represents the well-conserved C-terminal region ...
398-417
2.39e-04
intein C-terminal splicing region; This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity.
Pssm-ID: 213622 [Multi-domain] Cd Length: 21 Bit Score: 38.94 E-value: 2.39e-04
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
385-418
9.50e-04
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Pssm-ID: 238035 [Multi-domain] Cd Length: 136 Bit Score: 40.72 E-value: 9.50e-04
DNA adenine methylase (dam); All proteins in this family for which functions are known are ...
829-1085
2.07e-78
DNA adenine methylase (dam); All proteins in this family for which functions are known are DNA-adenine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The DNA adenine methylase (dam) of E. coli and related species is instrumental in distinguishing the newly synthesized strand during DNA replication for methylation-directed mismatch repair. This family includes several phage methylases and a number of different restriction enzyme chromosomal site-specific modification systems. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273146 Cd Length: 267 Bit Score: 258.07 E-value: 2.07e-78
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
419-803
5.47e-17
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. 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: 273211 [Multi-domain] Cd Length: 315 Bit Score: 83.14 E-value: 5.47e-17
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
419-803
1.94e-15
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Pssm-ID: 238192 [Multi-domain] Cd Length: 275 Bit Score: 77.66 E-value: 1.94e-15
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
8-84
3.15e-07
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Pssm-ID: 238192 [Multi-domain] Cd Length: 275 Bit Score: 53.01 E-value: 3.15e-07
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. ...
386-419
2.79e-06
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Pssm-ID: 197641 Cd Length: 46 Bit Score: 45.24 E-value: 2.79e-06
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
8-84
2.31e-04
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. 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: 273211 [Multi-domain] Cd Length: 315 Bit Score: 44.62 E-value: 2.31e-04
intein C-terminal splicing region; This model represents the well-conserved C-terminal region ...
398-417
2.39e-04
intein C-terminal splicing region; This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity.
Pssm-ID: 213622 [Multi-domain] Cd Length: 21 Bit Score: 38.94 E-value: 2.39e-04
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
385-418
9.50e-04
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Pssm-ID: 238035 [Multi-domain] Cd Length: 136 Bit Score: 40.72 E-value: 9.50e-04
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification
Pssm-ID: 440505 [Multi-domain] Cd Length: 183 Bit Score: 39.68 E-value: 3.90e-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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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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Others (non-specific hits) and
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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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advanced search options)
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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