The best aligned T4-related phage genes for the neighbor genes of ϕpp2 and KVP40 HEs using the neighbor-direct method. The approach is described in the text and Additional file2. The same color arrows represents the homologous genes. The cyan arrows indicate the HE genes for ϕpp2 and KVP40. (A) Neighbors of ϕpp2 PEG79: 78 for RegA translational repressor of early genes, 80 for phage hypothetical protein, and 81 for DNA polymerase. (B) Neighbors of ϕpp2 PEG119: 118 for GTP cyclohydrolase I from Bdellovibrio bacteriovorus HD100, Vibrio angustum S14, and Cytophaga hutchinsonii ATCC 33406; 120 for phage hypothetical protein. (C) Neighbors of ϕpp2 PEG274: 273 & 275 for Nrd, ribonucleotide reductase Ia; 276 for NrdC thioredoxin. (D) Neighbors of KVP40.146: 143 for rIIA protector; 144 for rIIB protector.