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Table 1. Predicted Structures and Functions of Hypothetical Proteins in Mycobacterium Tuberculosis KZN 1435 Through Comparative Genomic Approach

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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. 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  • ABSTRACT FROCK, ANDREW DAVID. Functional Genomics

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    ABSTRACT FROCK, ANDREW DAVID. Functional Genomics Analysis of the Microbial Physiology and Ecology of Hyperthermophilic Thermotoga Species. (Under the direction of Dr. Robert Kelly.) Generation of renewable fuels through biological conversion of inexpensive carbohydrate feedstocks has been the focus of intense research, which has mostly involved metabolic engineering of model mesophilic microorganisms. However, hyperthermophilic (Topt ≥ 80°C) bacteria of the genus Thermotoga exhibit several desirable traits for a potential biofuel-producing host. They ferment a variety of carbohydrates to hydrogen with high yields approaching the theoretical limit for anaerobic metabolism of 4 mol H2/mol glucose. High temperature growth facilitates biomass feedstock degradation, decreases risk of contamination, and eliminates the reactor cooling costs associated with growth of mesophiles. To further understand the glycoside hydrolase and carbohydrate transporter inventory of these bacteria, four closely-related Thermotoga species were compared. T. maritima, T. neapolitana, T. petrophila, and T. sp. strain RQ2 share approximately 75% of their genomes, yet each species exhibited distinguishing features during growth on simple and complex carbohydrates that correlated with their genotypes. T. maritima and T. neapolitana displayed similar monosaccharide utilization profiles, with a strong preference for glucose and xylose. Only T. sp. strain RQ2 has a fructose specific phosphotransferase system (PTS), and it was the only species found to utilize fructose. T. petrophila consumes glucose to a lesser extent and up-regulates a transporter normally used for xylose (XylE1F1K1) to compensate for the absence of the primary glucose transporter in these species (XylE2F2K2). In some cases, the use of mixed cultures has been proposed to combine the complementary strengths of different microbes for the development of improved bioprocesses.