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Table 1 Examples of control proteins used to develop the scoring scheme, and a summary of the outputs from each of ReVac’s components

From: ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates

General Information

No

ReVac Score

Score Breakdown

Organism

Gram Stain

Type

  

 1

14.853

15.253–0.400

Bordetella pertussis

Antigen

  

 2

13.709

13.709–0.000

Non-typable Hemophilus influenzae

Antigen

  

 3

9.049

9.049–0.000

Moraxella catarrhallis

Antigen

  

 4

8.192

8.192–0.000

Streptococcus agalactiae A909

+

Antigen

  

 5

6.791

6.791–0.000

Streptococcus pneumoniae

+

Antigen

  

 6

6.32

6.520–0.200

Neisseria meningitidis LNP21362

Antigen

  

 7

5.768

7.768–2.000

Streptococcus pneumoniae

+

Non Antigen

  

 8

2.475

5.542–3.066

Clostridium perfringens str. 13

+

Non Antigen

  

Surface Exposure Predictions

No.

PSORTB Localization

LipoProtein

Transmembrane Helices

Signal Peptide

SPAAN adhesin ratio

HMM mapping to surface exposed database

Annotation/GO Terms

 1

OuterMembrane

SignalPeptidase I

None

MNMSLSRIVKAAPLRRTTLAMALGALGAAPAAHA

None

Positive

outer membrane autotransporter barrel|GO:0009405,GO:0015474,GO:0045203,GO:0046819

 2

OuterMembrane

SignalPeptidase II

None

MNKFVKSLLVAGSVAALAACSSSNNDA

None

Positive

peptidoglycan-associated lipoprotein|GO:0009279

 3

None

SignalPeptidase II

None

MQFSKSIPLFFLFSIPFLA

None

Positive

Bacterial extracellular solute-binding protein

 4

Cellwall

SignalPeptidase I

1

None

0.782535

Positive

hypothetical protein

 5

Extracellular

Intracellular

None

None

None

None

Thiol-activated cytolysin family protein|GO:0015485,GO:0009405

 6

Periplasmic

SignalPeptidase II

None

MFKRSVIAMACIFALSACG

None

None

Transferrin binding family protein|GO:0016020

 7

None

Intracellular

None

None

None

None

Capsular polysaccharide synthesis family protein

 8

None

Intracellular

None

None

None

None

shikimate dehydrogenase ec::1.1.1.25|GO:0004764,GO:0009423

Antigenicity Predictionsa

No.

Antigenicity

B cell epitopes

MHC I binding

MHC II binding

MHC binding + Antigen Processing

Immunogenicity within MHC complex

Alignment to curated epitopes

 1

45.05%

15.16%

94.07%

100.00%

61.10%

13.08%

26.92%

 2

30.72%

5.23%

96.73%

94.12%

79.08%

17.65%

99.35%

 3

44.02%

16.03%

94.57%

100.00%

69.57%

23.91%

None

 4

50.40%

38.97%

83.10%

90.46%

43.34%

1.79%

None

 5

43.74%

13.80%

95.33%

98.94%

73.04%

12.10%

22.08%

 6

30.33%

15.16%

81.56%

86.68%

46.93%

1.84%

None

 7

48.94%

4.61%

96.81%

100%

81.91%

30.85%

None

 8

34.32%

7.75%

96.31%

98.89%

77.49%

16.61%

None

Adverse Features

No.

Autoimmunity with humans

Repeat regions genes & copy number

Repeat regions proteins & copy number

    

 1

None

None

|APAGGAVPGG 2||PQP 3|

    

 2

None

None

None

    

 3

None

None

None

    

 4

None

None

None

    

 5

None

None

None

    

 6

None

None

|ARFRRS 2|

    

 7

None

None

None

    

 8

3.32%

None

None

    
  1. aPercents are relative to the length of the amino acid sequence