VIRFAM: Downloads


Tables and Supplementary materials available for the head-neck-tail module analysis


Tables and Supplementary materials available for the recombinases analysis



head-neck-tail module database
Table of all head-neck-tail components This page corresponds to the sup table 1 of the paper with details for every component of the head-neck-tail module
Genetic contexts (zipfile) Representations of the genetic contexts for every types



recombinase database
Table of all recombinases This page corresponds to the sup table 3 of the paper with links towards the recombinases sequences and profiles
models
RedB_model.pdb This file contains the 3D coordinates of the Redβ model. The Redβ undecamers have been generated using the H. sapiens Rad52 Nterminal domain as template (PDB:1h2i) and the sequence is taken from the phage 933W (NP_049474).
Sak_model.pdb This file contains the 3D coordinates of the Sak model. The Sak undecamers have been generated using the H. sapiens Rad52 Nterminal domain as template (PDB:1h2i) and the sequence is taken from the phage ul36 (NP_663647).
ERF_model.pdb This file contains the 3D coordinates of the ERF model. The ERF undecamers have been generated using the H. sapiens Rad52 Nterminal domain as template (PDB:1h2i) and the sequence is taken from the phage D3 (NP_061548).
Sak4_model.pdb This file contains the 3D coordinates of the Sak4 model. It has been generated using the T. kodakarensis RadB structure as template (PDB:2cvh) and the sequence is taken from the phage φ31 (AAC48871).
Gp2.5_model.pdb This file contains the 3D coordinates of the Gp2.5 model. It has been generated using the Gp2.5 structure from the phage T7 as template (PDB:2je5) and the sequence is taken from the phage φ12 (NP_803317).
templates
1H2I.pdb This file contains the 3D coordinates of the Homo sapiens Rad52 Nterminal domain that has been used for the Redβ, Sak and ERF models generation.
2CVH.pdb This file contains the 3D coordinates of the Thermococcus kodakarensis RadB recombinase that has been used for the Sak4 model generation.
1JE5.pdb This file contains the 3D coordinates of the Gp2.5 protein from the T7 phage that has been used for the Gp2.5 model generation.
alignments
Rad52_like.fasta This file contains a multiple sequence alignment of Rad52-like proteins such as Rad52 Nterminal domain from H. sapiens, Redβ from phage 933W (NP_049474), Sak from phage ul36 (NP_663647) and ERF from phage D3 (NP_061548).
RecA_Rad51_like.fasta This file contains a multiple sequence alignment of Rad51-like proteins such as Sak4 from phage φ31 and other members of the RecA/RadA/Rad51 superfamily such as RecA from E. coli (B7N6S9), RadA (Q9V233) and RadB (Q9V2F6) from P. abyssi, Rad51 (Q06609), Rad51B(O15315), Rad51C (O43502), Rad51D (O75771), XRCC2 (O43543) and XRCC3 (O43542) from H. sapiens.
Gp2.5_like.fasta This file contains a pairwise sequence alignment of Gp2.5-like protein of phage φ12 and the template Gp2.5 from phage T7.
HMM profiles
Rec_profiles_Rad52-like.hhmThis file contains the HMM profiles for each Rad52-like recombinases we have identified. This file groups HMM profiles of Redβ, Sak and ERF recombinases.
Rec_profiles_Sak4.hhmThis file contains the HMM profiles for each Sak4 recombinases we have identified.
Rec_profiles_gp2.5.hhmThis file contains the HMM profiles for each Gp2.5-like recombinases we have identified.
Rec_profiles_UvsX.hhmThis file contains the HMM profiles for each UvsX/RecA recombinases we have identified.
Rec_profiles.hhmThis file contains the HMM profiles for each recombinases we have identified. This file groups together, Rad52-like, Sak4, Gp2.5-like and UvsX/RecA recombinases.