phage portal protein belonging to the SPP1-like portal protein family forms the portal vertex of the capsid; the portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection
Phage portal protein, SPP1 Gp6-like; This bacteriophage protein forms a gateway that enables ...
6-441
3.97e-122
Phage portal protein, SPP1 Gp6-like; This bacteriophage protein forms a gateway that enables DNA passage during packaging and ejection of the phage genome. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, the portal protein, Gp6, participates in the procapsid assembly reaction. In the mature SPP1 virion, Gp6 exists as a dodecamer, while recombinant SPP1 Gp6 has been shown to form 13-subunit assemblies. This protein is common to Siphoviridae (phages with long non-contractile tails) and Myoviridae (phages with contractile tails). It is also found in a number of bacterial species. This family also includes the old Pfam family Phage_min_cap (PF:PF05126). RC Paper describing PDB structure 2jes
:
Pssm-ID: 398687 Cd Length: 416 Bit Score: 362.42 E-value: 3.97e-122
Phage portal protein, SPP1 Gp6-like; This bacteriophage protein forms a gateway that enables ...
6-441
3.97e-122
Phage portal protein, SPP1 Gp6-like; This bacteriophage protein forms a gateway that enables DNA passage during packaging and ejection of the phage genome. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, the portal protein, Gp6, participates in the procapsid assembly reaction. In the mature SPP1 virion, Gp6 exists as a dodecamer, while recombinant SPP1 Gp6 has been shown to form 13-subunit assemblies. This protein is common to Siphoviridae (phages with long non-contractile tails) and Myoviridae (phages with contractile tails). It is also found in a number of bacterial species. This family also includes the old Pfam family Phage_min_cap (PF:PF05126). RC Paper describing PDB structure 2jes
Pssm-ID: 398687 Cd Length: 416 Bit Score: 362.42 E-value: 3.97e-122
phage portal protein, SPP1 family; This model represents one of several distantly related ...
3-424
7.09e-94
phage portal protein, SPP1 family; This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa. [Mobile and extrachromosomal element functions, Prophage functions]
Pssm-ID: 273678 Cd Length: 412 Bit Score: 290.21 E-value: 7.09e-94
Phage portal protein, SPP1 Gp6-like; This bacteriophage protein forms a gateway that enables ...
6-441
3.97e-122
Phage portal protein, SPP1 Gp6-like; This bacteriophage protein forms a gateway that enables DNA passage during packaging and ejection of the phage genome. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, the portal protein, Gp6, participates in the procapsid assembly reaction. In the mature SPP1 virion, Gp6 exists as a dodecamer, while recombinant SPP1 Gp6 has been shown to form 13-subunit assemblies. This protein is common to Siphoviridae (phages with long non-contractile tails) and Myoviridae (phages with contractile tails). It is also found in a number of bacterial species. This family also includes the old Pfam family Phage_min_cap (PF:PF05126). RC Paper describing PDB structure 2jes
Pssm-ID: 398687 Cd Length: 416 Bit Score: 362.42 E-value: 3.97e-122
phage portal protein, SPP1 family; This model represents one of several distantly related ...
3-424
7.09e-94
phage portal protein, SPP1 family; This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa. [Mobile and extrachromosomal element functions, Prophage functions]
Pssm-ID: 273678 Cd Length: 412 Bit Score: 290.21 E-value: 7.09e-94
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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The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
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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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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
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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