CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily [Defense mechanisms]; CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system
The actual alignment was detected with superfamily member COG1604:
Pssm-ID: 441212 Cd Length: 239 Bit Score: 95.06 E-value: 6.06e-22
CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group ...
326-451
7.88e-11
CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group [Defense mechanisms]; CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system
The actual alignment was detected with superfamily member COG1367:
Pssm-ID: 440978 Cd Length: 272 Bit Score: 63.13 E-value: 7.88e-11
CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily [Defense mechanisms]; CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 441212 Cd Length: 239 Bit Score: 95.06 E-value: 6.06e-22
CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group ...
326-451
7.88e-11
CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group [Defense mechanisms]; CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440978 Cd Length: 272 Bit Score: 63.13 E-value: 7.88e-11
CRISPR type III-B/RAMP module RAMP protein Cmr6; CRISPR is a term for Clustered Regularly ...
107-278
1.23e-09
CRISPR type III-B/RAMP module RAMP protein Cmr6; 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. This family, represented by TM1791 of Thermotoga maritima, is designated Cmr6 [sic], for CRISPR/Cas Ramp Module protein 6. This family is both closely related to and frequently encoded next to the TM1792 family of Cas proteins described by TIGR01867. The two proteins are fused in an example from Methanopyrus kandleri.
Pssm-ID: 213662 Cd Length: 176 Bit Score: 57.80 E-value: 1.23e-09
CRISPR/Cas system-associated RAMP superfamily protein; 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 proteins
Pssm-ID: 187857 [Multi-domain] Cd Length: 177 Bit Score: 57.03 E-value: 2.54e-09
RAMP superfamily; The molecular function of these proteins is not yet known. However, they ...
79-278
2.73e-07
RAMP superfamily; The molecular function of these proteins is not yet known. However, they have been identified and called the RAMP (Repair Associated Mysterious Proteins) superfamily. The members of this family have no known function they are around 300 amino acids in length and have several conserved motifs.
Pssm-ID: 397727 [Multi-domain] Cd Length: 188 Bit Score: 51.17 E-value: 2.73e-07
CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily [Defense mechanisms]; CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 441212 Cd Length: 239 Bit Score: 95.06 E-value: 6.06e-22
CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group ...
326-451
7.88e-11
CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group [Defense mechanisms]; CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440978 Cd Length: 272 Bit Score: 63.13 E-value: 7.88e-11
CRISPR type III-B/RAMP module RAMP protein Cmr6; CRISPR is a term for Clustered Regularly ...
107-278
1.23e-09
CRISPR type III-B/RAMP module RAMP protein Cmr6; 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. This family, represented by TM1791 of Thermotoga maritima, is designated Cmr6 [sic], for CRISPR/Cas Ramp Module protein 6. This family is both closely related to and frequently encoded next to the TM1792 family of Cas proteins described by TIGR01867. The two proteins are fused in an example from Methanopyrus kandleri.
Pssm-ID: 213662 Cd Length: 176 Bit Score: 57.80 E-value: 1.23e-09
CRISPR/Cas system-associated RAMP superfamily protein; 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 proteins
Pssm-ID: 187857 [Multi-domain] Cd Length: 177 Bit Score: 57.03 E-value: 2.54e-09
CRISPR/Cas system-associated RAMP superfamily protein Cmr6; CRISPR (Clustered Regularly ...
107-278
4.01e-08
CRISPR/Cas system-associated RAMP superfamily protein Cmr6; 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; This protein is a subunit of Cmr complex
Pssm-ID: 187792 Cd Length: 210 Bit Score: 53.93 E-value: 4.01e-08
RAMP superfamily; The molecular function of these proteins is not yet known. However, they ...
79-278
2.73e-07
RAMP superfamily; The molecular function of these proteins is not yet known. However, they have been identified and called the RAMP (Repair Associated Mysterious Proteins) superfamily. The members of this family have no known function they are around 300 amino acids in length and have several conserved motifs.
Pssm-ID: 397727 [Multi-domain] Cd Length: 188 Bit Score: 51.17 E-value: 2.73e-07
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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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.
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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),
they are mapped to the query sequence and indicated through sets of triangles
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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)
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
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