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Table 1 Predicted local holes and Chokepoints (shown in bold) in M. tb using the ‘Hole finding protocol’

From: Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study

Predicted hole/missing enzymes Known neighbors in M. tb from EE graph Protein ID
3.1.3.37 (Sedoheptulose-bisphosphatase/carbon metabolism) 4.1.2.13 (Fructose-bisphosphate aldolase) Rv0363c
2.2.1.1 (Transketolase) Rv1449c
2.2.1.2 (Transaldolase) Rv1448c
2.7.1.11 (6-phosphofructokinase) Rv3010c
2.1.1.152 (Precorrin-6A synthase/porphyrin and chlorophyll metabolism) 1.3.1.54 (Precorrin-6A reductase) Rv2070c
2.5.1.6 (Methionine adenosyltransferase) Rv1392
2.1.1.133 (Precorrin-4 C (11)-methyltransferase) Rv2071c
2.3.2.10 (UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase/ Peptidoglycan biosynthesis) 6.1.1.14 (Glycine–tRNA ligase) Rv0041
6.1.1.7 Alanine–tRNA ligase Rv2555c
6.3.2.10 (MurF synthetase) Rv2157c
6.3.1.2 (Glutamine synthetase) Rv2222c
1.14.13.83 (Precorrin-3B synthase/porphyrin and chlorophyll metabolism) 2.1.1.131 (Precorrin-3B C(17)-methyltransferase) Rv2066
2.1.1.130 (Precorrin-2C (20)-methyltransferase) Rv2066
1.3.3.3 (Coprogen oxidase/porphyrin and chlorophyll metabolism) 1.3.3.4 (Protoporphyrinogen oxidase) Rv2677c
4.1.1.37 (Uroporphyrinogen decarboxylase) Rv2678c
3.6.1.40 (Guanosine-5-triphosphate, 3diphosphate diphosphatase/purine metabolism) 3.1.7.2 (Guanosine-3,5-bis(diphosphate) 3-diphosphatase) Rv2583c
2.7.6.5 (GTP diphosphokinase) Rv2583c
3.6.2.2 (Phosphoadenylylsulfatase/sulphur metabolism) 3.1.3.7 (3′(2′),5′-biphosphate nucleotidase) Rv2131c
2.7.1.25 (Adenylyl-sulfate kinase) Rv1286
4.1.1.21(Phosphoribosylaminoimidazole carboxylase/purine metabolism) 6.3.4.18 (5-(carboxyamino)imidazole ribonucleotide synthase) Rv3276c
5.4.99.18 (5-(carboxyamino)imidazole ribonucleotide mutase Rv3275c
5.4.99.61(Precorrin isomerase/porphyrin and chlorophyll metabolism) 6.3.5.9 (Hydrogenobyrinic acid a,c-diamide synthase) Rv2847c
2.1.1.132 (Precorrin-6 methyltransferase) Rv2072c
6.2.1.28 (DHCA-CoA ligase) 1.2.1.3 (Aldehyde dehydrogenase (NAD(+)) Rv0458
2.3.1.16 (Acyl CoA C-acyltransferase)  
6.3.3.1 (Phosphoribosylformylglycinamidine cyclo-ligase/purine metabolism) 6.3.4.18 (5-(carboxyamino)imidazole ribonucleotide synthase) Rv3276c
6.3.5.3 (Phosphoribosylformylglycinamidine synthase) Rv0803
  1. The table lists the local holes and chokepoints in the first column, along with the known neighbors in M. tb in the second column and the protein ID for the known neighbors in the third column