Table 2 Models and methods used in the targetTB pipeline

(A) Systems Analysis

   (i) Network

Single node deletions

   (ii) FBA

a) Mtb iNJ 661

FBA

b) GSMN-TB

FBA

c) MAP

FBA

   (iii) TraSH

Summary ((i) or (ii) or (iii))

(A_X)

(B) Sequence Analysis

(B_X)

3,989 Mtb vs. 33,453 human sequence comparisons

(A&B) Systems & Sequence Passed

(A_X∪ B_X)

(C) Structural Assessment (PMScore < 0:8) [942 from A&B only considered]

(C_X)

3,500 sites of Mtb (767 proteins) vs 70,149 sites of Human pocketome (15,830 proteins) = 245,521,500 pairwise comparisons

(D) A & B & C

(A_X∪ B_X∪ C_X∪ C')

(E) Expression

   (i) Gao-expression

   (ii) Rachman-expression

   (iii) Boshoff-expression

   Summary ((i) or (ii) or (iii))

(E_X)

   Summary (for (D))

(F) Non-similarity to Anti-targets

(F_X)

306 vs. 3,989 sequence comparisons

   Non-similarity to Anti-targets (for (D))

(G) Non-similarity to gut flora

296,017 vs. 3,989 sequence comparisons

   Non-similarity to gut flora (for (D))

(H) D & E & F &; G

(I) Expression during Persistence

   (i) Muttucumaru-expression

   (ii) Boshoff-expression

   (iii) Betts-expression

   (iv) Voskuil-expression

   (v) Hampshire-expression

   Summary ((i) or (ii) or (iii) or (iv) or (v))

   Summary (for (H))

(J) Broad-spectrum Targets [present in > 100/228 pathogenic genomes]

2,295,901 vs. 3,989 sequence comparisons (phylo-Genetic profiling against 707 genomes)

(K) Targets unique to Mycobacteria