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Table 2 Detected head- and tail-completion proteins of Aclame

From: Automated classification of tailed bacteriophages according to their neck organization

  Detected with Psi-Blast Detected with HHsearch at 90% Detected only at 70% using a combined approach Percentage of proteins detected with the combined approach Exceptions Total protein number
Ad1 86 191 * 10 5 12 213 *
Hc1 71 158 4 2 5 167
Tc1 41 166 27 13 14 207
Ad2 17 17 0 0 0 17
Hc2 16 16 0 0 0 16
Tc2 16 16 0 0 0 16
Ad3 8 8 30 60 12 50
Hc3 17 51 0 0 0 51
Ad4 10 10 0 0 0 10
Total 282 633 71 10 43 747
  1. *Including 5 gpW-like Ad1.
  2. Head- and tail-completion proteins detected using either the profile-sequence comparison tool PSI-BLAST, the profile-profile comparison tool HHsearch with a threshold of 90% or an approach combining the HHsearch tool at a threshold of 70% with analysis of the gene contexts are detailed (percentages correspond to HHsearch confidence thresholds). Proteins counted in the “Exceptions” column correspond to proteins that were manually detected, either because their HMM profile was built from very few sequences (hindering profile-profile comparisons) but they showed consistent secondary structure prediction and genome localisation, or because they were detected by HHsearch but their genome positioning slightly deviated from the canonical positioning. The Aclame references of the detected neck proteins, as well as of the identified head and tail proteins, are displayed in Additional file 2: Table S1.