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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.