CRISPR type III-A/MTUBE-associated RAMP protein Csm4; CRISPR is a term for Clustered Regularly ...
5-296
3.73e-107
CRISPR type III-A/MTUBE-associated RAMP protein Csm4; CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4.
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Pssm-ID: 273866 Cd Length: 297 Bit Score: 313.60 E-value: 3.73e-107
CRISPR type III-A/MTUBE-associated RAMP protein Csm4; CRISPR is a term for Clustered Regularly ...
5-296
3.73e-107
CRISPR type III-A/MTUBE-associated RAMP protein Csm4; CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4.
Pssm-ID: 273866 Cd Length: 297 Bit Score: 313.60 E-value: 3.73e-107
CRISPR/Cas system-associated RAMP superfamily protein Csm4; CRISPR (Clustered Regularly ...
5-296
3.47e-105
CRISPR/Cas system-associated RAMP superfamily protein Csm4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein
Pssm-ID: 187794 Cd Length: 301 Bit Score: 308.61 E-value: 3.47e-105
CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group ...
1-298
8.05e-85
CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group [Defense mechanisms]; CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 441175 Cd Length: 313 Bit Score: 257.22 E-value: 8.05e-85
CRISPR Csm4 C-terminal domain; Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show, Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2).
Pssm-ID: 465582 Cd Length: 91 Bit Score: 118.84 E-value: 8.41e-34
CRISPR type III-A/MTUBE-associated RAMP protein Csm4; CRISPR is a term for Clustered Regularly ...
5-296
3.73e-107
CRISPR type III-A/MTUBE-associated RAMP protein Csm4; CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4.
Pssm-ID: 273866 Cd Length: 297 Bit Score: 313.60 E-value: 3.73e-107
CRISPR/Cas system-associated RAMP superfamily protein Csm4; CRISPR (Clustered Regularly ...
5-296
3.47e-105
CRISPR/Cas system-associated RAMP superfamily protein Csm4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein
Pssm-ID: 187794 Cd Length: 301 Bit Score: 308.61 E-value: 3.47e-105
CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group ...
1-298
8.05e-85
CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group [Defense mechanisms]; CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 441175 Cd Length: 313 Bit Score: 257.22 E-value: 8.05e-85
CRISPR Csm4 C-terminal domain; Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show, Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2).
Pssm-ID: 465582 Cd Length: 91 Bit Score: 118.84 E-value: 8.41e-34
CRISPR-associated protein (Cas_Cmr3); CRISPR is a term for Clustered Regularly Interspaced ...
59-267
3.06e-03
CRISPR-associated protein (Cas_Cmr3); CRISPR is a term for Clustered Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This highly divergent family, found in at least ten different archaeal and bacterial species, is represented by TM1793 from Thermotoga maritima.
Pssm-ID: 430761 Cd Length: 366 Bit Score: 38.95 E-value: 3.06e-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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
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
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
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)
mapped to the query sequence.
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
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
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
(CDART).
Modify your query to search against a different database and/or use advanced search options
