Table 1. Predicted Structures and functions of hypothetical proteins in Mycobacterium tuberculosis KZN 1435 through comparative genomic approach EGG Gene ID CDD-Blast Interproscan Pfam COGs PS2 structure mtb:TBMG_00004 NO NO Bacterial chaperone NO NO lipoprotein (PulS_OutS) mtb:TBMG_00007 DNA polymerase III NO NO NO 2pziA- 14- 38- 0.003 subunits gamma and tau; Validated mtb:TBMG_00008 NO NO RUN domain; VirB8 NO NO protein mtb:TBMG_00012 NO NO NO NO 2f23A-14 -38- 0.002 mtb:TBMG_00019 FHA [cd00060], Forkhead- FHA domain FHA-domain- 2ff4A-23 -101-6e-23 Forkhead associated associated (FHA) containing domain (FHA); found domain; proteins in eukaryotic and SMAD/FHA prokaryotic proteins. domain mtb:TBMG_00020 FHA [cd00060], Forkhead- FHA domain NO 1y0fB-14- 45-3e-05 Forkhead associated associated (FHA) domain (FHA); found domain; Annexin; in eukaryotic and SMAD/FHA prokaryotic proteins. domain mtb:TBMG_00025 Biofilm regulator BssS; NO Roadblock/LC7 NO NO BssS (also known as domain ; NOSIC YliH) regulates (NUC001) domain Escherichia coli K-12 biofilm formation through quorum sensing. BssS is also involved in motility regulation as it represses motility 7 fold by decreasing transcription of the flagella and motility loci. mtb:TBMG_00026 Biofilm regulator BssS; NO NO NO 1qvrA- 24- 42-2e-04 BssS (also known as YliH) regulates Escherichia coli K-12 biofilm formation through quorum sensing. mtb:TBMG_00027 Proteins of 100 ESX-1 secretion- Plant invertase/pectin NO NO residues with WXG; associated protein methylesterase ESAT-6 is a small EspC inhibitor ; KIF-1 protein appears to be of binding protein C fundamental terminal ; FlgN importance in virulence protein and protective immunity in Mycobacterium tuberculosis. mtb:TBMG_00035 DinB superfamily; The tRNA wybutosine- Mycothiol NO 2nsfA-14-132-9e-32 DinB family are an synthesis; maleylpyruvate uncharacterised family Mycothiol- isomerase N-terminal of potential enzymes; dependent domain ; Wyosine Wyosine base maleylpyruvate base formation formation; Some isomerase, metal- proteins in this family binding domain appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. ; TIGR03084 family protein; This family, like Pfam family pfam07398, belongs to the larger set of probable enzymes modeled by TIGRFAMs family TIGR03083. mtb:TBMG_00036 H+ Antiporter protein; Major facilitator Major Facilitator Permeases of the 2cfqA-12-48-7e-06 superfamily; Superfamily major facilitator general substrate superfamily transporter mtb:TBMG_00038 NO NO PRA1 family protein NO NO mtb:TBMG_00039 Probable lipoprotein Lipoprotein LpqT, Probable lipoprotein NO NO LpqN; This family is predicted LpqN conserved in Mycobacteriaceae and is likely to be a lipoprotein. mtb:TBMG_00046 Helix -turn-helix Transcription Transcriptional Predicted 1yg2A-21-116-2e-27 domains; A large regulator PadR N- regulator PadR-like transcriptional family of mostly alpha- terminal; Winged family regulators helical protein domains helix-turn-helix with a characteristic transcription fold repressor DNA- binding mtb:TBMG_00048 NO NO LITAF-like zinc NO NO ribbon domain mtb:TBMG_00050 NO; This is a putative Uncharacterised NO NO 2a65A-14-30-0.008 transmembrane protein conserved protein from bacteria UCP010361, membrane mtb:TBMG_00051 Type 1 glutamine ThiJ/PfpI Putative Putative 3bhnA-20-165-7e-42 amidotransferase amidotransferase intracellular (GATase1)-like domain protease/amidas found in a subgroup of e proteins similar to PfpI from Pyrococcus furiosus; mtb:TBMG_00059 Macro domain, Appr-1-p Macro domain Uncharacterized 2dx6A-22-138-1e-33 Poa1p_like family. The processing ACR related to macro domain is a the C-terminal high-affinity ADP- domain of ribose binding module; histone macroH2A1 mtb:TBMG_00074 Superfamily of metallo- Amidohydrolase 1; Amidohydrolase Imidazolonepro 2qs8A-27-303-3e-83 dependent hydrolases Metal-dependent family pionase and (also called hydrolase, related amidohydrolase composite domain amidohydrolases superfamily); Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism] mtb:TBMG_00079 NO NO Nucleotidyl NO 2ewrA-10-50-3e-07 transferase of unknown function (DUF1814) ; Homoserine dehydrogenase, NAD binding domain mtb:TBMG_00080 NO NO NO NO 1n3gA-8-48-2e-06 mtb:TBMG_00081 Pyridoxine 5'- FMN-binding split Pyridoxamine 5'- NO 3cp3A-29-118-5e-28 phosphate (PNP) barrel-related; phosphate oxidase oxidase-like proteins; Pyridoxamine 5'- The PNPOx-like phosphate oxidase- superfamily is related composed of pyridoxine 5'- phosphate (PNP) oxidases and other flavin mononucleotide (FMN) binding proteins, which catalyze FMN- mediated redox reactions. mtb:TBMG_00089 Ligand -binding Polyketide Polyketide cyclase / NO 1xuvA-13-62-1e-10 SRPBCC domain of an cyclase/dehydrase; dehydrase and lipid uncharacterized START-like transport subfamily of proteins; domain mtb:TBMG_00091 Predicted membrane NO Predicted membrane Uncharacterized NO protein (DUF2127) protein (DUF2127) membrane protein mtb:TBMG_00094 Anti -sigma-K factor NO Putative zinc-finger NO 2q1zB-23-37-0.007 rskA mtb:TBMG_00095 HNH nucleases; HNH HNH nuclease HNH endonuclease NO 2qgpB-17-36-0.010 endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. mtb:TBMG_00096 NO NO MIF4G domain NO NO mtb:TBMG_00099 FcoT -like thioesterase Long-chain fatty FcoT-like thioesterase NO 2pfcA-97-282-3e-77 domain acyl-CoA domain thioesterase, Rv0098-like mtb:TBMG_00101 Phosphopantetheine Phosphopantetheine Phosphopantetheine NO 1n8lA-28-35-0.003 attachment site; A 4'- -binding; Acyl attachment site phosphopantetheine carrier protein-like prosthetic group is attached through a serine. mtb:TBMG_00105 effector domain of the Cyclic nucleotide- Cyclic nucleotide- cAMP-binding no CAP family of binding domain; binding domain domains - transcription factors RmlC-like jelly roll Catabolite gene fold; NAD(P)- activator and binding domain; regulatory Cyclic nucleotide- subunit of binding-like cAMP- dependent protein kinases mtb:TBMG_00107 Cobalamin synthesis Cobalamin (vitamin CobW/HypB/UreG, Putative 1nijA-15-187-2e-48 protein cobW C- B12) biosynthesis nucleotide-binding GTPases (G3E terminal domain; CobW-like; C- domain ; Cobalamin family) Putative GTPases (G3E terminal synthesis protein family) cobW C-terminal domain mtb:TBMG_00111 Rhomboid family; This Peptidase S54, Rhomboid family Uncharacterized 3b44A-20-109-7e-25 family contains integral rhomboid domain membrane membrane proteins that protein are related to (homolog of Drosophila rhomboid Drosophila protein. rhomboid) mtb:TBMG_00117 L,D -transpeptidase L,D-transpeptidase L,D-transpeptidase Uncharacterized 1zatA-19-129-8e-31 catalytic domain catalytic domain catalytic domain BCR mtb:TBMG_00124 NO CopG-like DNA- Ribbon-helix-helix NO 1e4fT-30-35-0.004 binding protein, copG family mtb:TBMG_00128 Uncharacterized Aminoglycoside Phosphotransferase Uncharacterized no protein, probably phosphotransferase enzyme family protein, involved in trehalose probably biosynthesis involved in [Carbohydrate transport trehalose and metabolism] biosynthesis mtb:TBMG_00131 NodN (nodulation MaoC-like MaoC like domain Predicted acyl 2c2iA-100-182-3e-47 factor N) contains a dehydratase dehydratase single hot dog fold similar to those of the peroxisomal Hydratase- Dehydrogenase- Epimerase (HDE) protein, and the fatty acid synthase beta subunit. mtb:TBMG_00139 Nuclear transport factor NO SnoaL-like domain NO 1nwwB-16-60-3e-10 2 (NTF2-like) superfamily mtb:TBMG_00141 NO NO NO Uncharacterized 3djmB-32-149-3e-37 BCR mtb:TBMG_00143 endonuclease III; DNA glycosylase NO 3- 1mpgA-16-152-1e-37 includes endonuclease Methyladenine III (DNA-(apurinic or DNA apyrimidinic site) glycosylase lyase), alkylbase DNA glycosidases (Alka- family) and other DNA glycosidases; 3- methyladenine DNA glycosylase/8- oxoguanine DNA glycosylase [DNA replication, recombination, and repair] mtb:TBMG_00146 NO Leucine carboxyl Leucine carboxyl NO 2uyoA-47 -45-5e-06 methyltransferase methyltransferase mtb:TBMG_00147 Leucine carboxyl Leucine carboxyl Leucine carboxyl O- 2uyoA-72-214-3e-56 methyltransferase methyltransferase; methyltransferase Methyltransferas S-adenosyl-L- e involved in methionine- polyketide dependent biosynthesis methyltransferase, putative mtb:TBMG_00151 NO NO NO NO 2b5uA-22-35-0.004 mtb:TBMG_00164 4 -hydroxybenzoyl-CoA Thioesterase Thioesterase Predicted 2o5uA 43 138 9e-34 thioesterase (4HBT). superfamily superfamily thioesteras mtb:TBMG_00165 Ligand -binding Streptomyces Polyketide cyclase / NO 2d4rA-18-95-7e-21 SRPBCC domain of an cyclase/dehydrase; dehydrase and lipid uncharacterized START-like transport subfamily of proteins domain mtb:TBMG_00168 NO NO Permease ABC-type NO toluene export system, permease component mtb:TBMG_00176 NO NO Staphylococcus NO NO haemolytic protein mtb:TBMG_00177 RDD family; This RDD RDD family NO NO family of proteins contain three highly conserved amino acids: one arginine and two aspartates mtb:TBMG_00181 YhgE/Pip N-terminal NO NO Predicted 3cniA-14-49-2e-06 domain; ABC-2 type membrane transporter protein mtb:TBMG_00182 Cupin domain; Pirin- Pirin, N-terminal; Pirin Pirin-related 1tq5A-35-256-3e-69 related protein Cupin, RmlC-type; protein RmlC-like jelly roll fold mtb:TBMG_00189 SPW repeat; A short SPW repeat SPW repeat ; Poly- NO NO repeat found in a small beta-hydroxybutyrate family of membrane- polymerase N terminal bound proteins. This repeat contains a conserved SPW motif in the first of two transmembrane helices. mtb:TBMG_00191 Transcriptional