NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1864380612|ref|YP_009885839|]
View 

receptor binding tail protein [Lactococcus phage CHPC964]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RBP-H super family cl23908
Head domain of virus receptor-binding proteins (RBP); Virus receptor-binding proteins (RBPs) ...
 1-153 3.76e-80

Head domain of virus receptor-binding proteins (RBP); Virus receptor-binding proteins (RBPs) are found in lactococcal bacteriophages, as well as in adenoviruses and reoviruses, which invade mammalian cells. Lactococcus lactis is widely used in dairy fermentations and infection of L. lactis by phages greatly impairs the fermentation process. Adenovirus typically infects respiratory tracts with symptoms ranging from the common cold to pneumonia. Onset of viral infections begin with the recognition of host cells through the receptor-binding protein complex located at the distal part of the virion. The RBP has three domains: the N- terminal shoulders domain, the interlaced neck domain, and the C-terminal head domain. Phages recognize their host through an interaction between the RBP head (RBP-H) domain and saccharidic receptors at the host cell surface. Adenovirus recognizes the membrane cofactor protein, CD46, as a cellular receptor.


The actual alignment was detected with superfamily member pfam08931:

Pssm-ID: 305065  Cd Length: 262  Bit Score: 242.83  E-value: 3.76e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864380612   1 MTIKNFTFFSPNSTEFPVGSNNDAKLYMMLSGMDYTTFRRTDWSSPVNTALNVQYVNTSFIVAGRYFELINETVALKADS 80
Cdd:pfam08931   1 MTIKNFTFFSPNGTEFPVGSNNDGKLYMMLTGMDYGTIRRKDWTSPLNTALNVQYTNTSIIAGGRYFELLNETVALKGNS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1864380612  81 LNYIHINIDLTKTTAPVSLSCETADNSNTIDLNNASGVYKRVVDIITTNGLGVMNRVTPTQKTTVGDLTSNSL 153
Cdd:pfam08931  81 VNYIHANIDLTQTANPVSLSAETSNNSNNVDINNGSGVLKVCFDIVTTSGTGVISTKPIVQTSYLDSISINDV 153
 
Name Accession Description Interval E-value
Caudo_bapla_RBP pfam08931
Receptor-binding protein of phage tail base-plate Siphoviridae, head; Caudo_bapla_RBP is a ...
 1-153 3.76e-80

Receptor-binding protein of phage tail base-plate Siphoviridae, head; Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein species, shoulders, neck, and head, that form the phage tail base-plate. In the overall structure this head domain exists as six trimers, and is necessary for specific recognition of the receptors at the host cell surface. Siphoviridae are the P2-like Caudovirales of Lactococcus. This family now includes DUF1914. Family Baseplate, pfam16774, is the ORF15 or shoulder component of the base-plate complex.


Pssm-ID: 286074  Cd Length: 262  Bit Score: 242.83  E-value: 3.76e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864380612   1 MTIKNFTFFSPNSTEFPVGSNNDAKLYMMLSGMDYTTFRRTDWSSPVNTALNVQYVNTSFIVAGRYFELINETVALKADS 80
Cdd:pfam08931   1 MTIKNFTFFSPNGTEFPVGSNNDGKLYMMLTGMDYGTIRRKDWTSPLNTALNVQYTNTSIIAGGRYFELLNETVALKGNS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1864380612  81 LNYIHINIDLTKTTAPVSLSCETADNSNTIDLNNASGVYKRVVDIITTNGLGVMNRVTPTQKTTVGDLTSNSL 153
Cdd:pfam08931  81 VNYIHANIDLTQTANPVSLSAETSNNSNNVDINNGSGVLKVCFDIVTTSGTGVISTKPIVQTSYLDSISINDV 153
 
Name Accession Description Interval E-value
Caudo_bapla_RBP pfam08931
Receptor-binding protein of phage tail base-plate Siphoviridae, head; Caudo_bapla_RBP is a ...
 1-153 3.76e-80

Receptor-binding protein of phage tail base-plate Siphoviridae, head; Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein species, shoulders, neck, and head, that form the phage tail base-plate. In the overall structure this head domain exists as six trimers, and is necessary for specific recognition of the receptors at the host cell surface. Siphoviridae are the P2-like Caudovirales of Lactococcus. This family now includes DUF1914. Family Baseplate, pfam16774, is the ORF15 or shoulder component of the base-plate complex.


Pssm-ID: 286074  Cd Length: 262  Bit Score: 242.83  E-value: 3.76e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864380612   1 MTIKNFTFFSPNSTEFPVGSNNDAKLYMMLSGMDYTTFRRTDWSSPVNTALNVQYVNTSFIVAGRYFELINETVALKADS 80
Cdd:pfam08931   1 MTIKNFTFFSPNGTEFPVGSNNDGKLYMMLTGMDYGTIRRKDWTSPLNTALNVQYTNTSIIAGGRYFELLNETVALKGNS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1864380612  81 LNYIHINIDLTKTTAPVSLSCETADNSNTIDLNNASGVYKRVVDIITTNGLGVMNRVTPTQKTTVGDLTSNSL 153
Cdd:pfam08931  81 VNYIHANIDLTQTANPVSLSAETSNNSNNVDINNGSGVLKVCFDIVTTSGTGVISTKPIVQTSYLDSISINDV 153
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH