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Table 1 Status of Genes Previously Reported as Affected by H37Ra-specific Mutations

From: SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis

Locus Tag Gene name Description Notes Citation
(a) Genes with all High-Confidence Variants Contradicted by our Assembly
Rv0037c Rv0037c Probable conserved integral membrane protein   
Rv0124 PE_PGRS2 PE-PGRS family protein PE_PGRS2   
Rv0189c ilvD Probable dihydroxy-acid dehydratase IlvD (dad)   [48, 58]
Rv0279c PE_PGRS4 PE-PGRS family protein PE_PGRS4  
Rv0383c Rv0383c Possible conserved secreted protein masks sequencing error in H37Rv [8]
Rv0578c PE_PGRS7 PE-PGRS family protein PE_PGRS7  
Rv0880 Rv0880 Possible MarR-family transcriptional regulatory protein   [48]
Rv0977 PE_PGRS16 PE-PGRS family protein PE_PGRS16  
Rv1068c PE_PGRS20 PE-PGRS family protein PE_PGRS20  
Rv1091 PE_PGRS22 PE-PGRS family protein PE_PGRS22   [36, 38] ∙
Rv1095 phoH2 Probable PHOH-like protein PhoH2   
Rv1196 PPE18 PPE family protein PPE18   [25, 36] ∙
Rv1386 PE15 PE family protein PE15  
Rv1450c PE_PGRS27 PE-PGRS family protein PE_PGRS27  
Rv1802 PPE30 PPE family protein PPE30 SNV instantiates CTGGAG motif
Rv1929c Rv1929c Conserved hypothetical protein   
Rv2048c pks12 Polyketide synthase Pks12   
Rv2068c blaC Class a beta-lactamase BlaC   
Rv2069 sigC RNA polymerase sigma factor, ECF subfamily, SigC   [18, 19]
Rv2098c PE_PGRS36 PE-PGRS family protein PE_PGRS36 Likely pseudogene
Rv2202c adoK Adenosine kinase Synonymous mutation  
Rv2396 PE_PGRS41 PE-PGRS family protein PE_PGRS41  
Rv2649 Rv2649 Probable transposase for IS6110   
Rv2733c Rv2733c Conserved hypothetical alanine, arginine-rich protein   
Rv2734 Rv2734 Conserved hypothetical protein   
Rv2825c Rv2825c Conserved hypothetical protein   
Rv3031 Rv3031 Conserved protein Synonymous mutation  
Rv3191c Rv3191c Probable transposase labeled intergenic in H37RaJH  
Rv3192 Rv3192 Conserved hypothetical alanine and proline-rich protein labeled intergenic in H37RaJH  
Rv3303c lpdA NAD(P)H quinone reductase LpdA tandem repeat copy number variation [48]
Rv3350c PPE56 PPE family protein  
Rv3388 PE_PGRS52 PE-PGRS family protein PE_PGRS52   [36] ∙
Rv3389c htdY Probable 3-hydroxyacyl-thioester dehydratase HtdY   
Rv3507 PE_PGRS53 PE-PGRS family protein PE_PGRS53   [37] ∙
Rv3595c PE_PGRS59 PE-PGRS family protein PE_PGRS59   [36, 38] ∙
Rv3611 Rv3611 Hypothetical arginine and proline rich protein One deletion also at ftsH -57bp  
(b) Genes with Different H37Ra-specific Variant Profiles in our Assembly
Rv1764 Rv1764 Putative transposase of insertion element IS6110 disrupted by IS6110 in our assembly  
Rv3343c PPE54 PPE family protein tandem repeat copy number variation [36] ∙
Rv3508 PE_PGRS54 PE-PGRS family protein PE_PGRS54   [3638] ∙
Rv3514 PE_PGRS57 PE-PGRS family protein PE_PGRS57   [36, 37] ∙
(c) Genes with High-Confidence Variant Profiles Fully Confirmed by our Assembly
Rv0010c Rv0010c Probable conserved membrane protein   
Rv0039c Rv0039c Possible conserved transmembrane protein   
Rv0101 nrp Probable peptide synthetase Nrp (peptide synthase)   [9, 24]
Rv0635 hadA (3R)-hydroxyacyl-ACP dehydratase subunit HadA   [33, 38]
Rv0637 hadC (3R)-hydroxyacyl-ACP dehydratase subunit HadC   [25, 33]
Rv0757 phoP Member of Two-component response complex PhoPR   [18, 23, 25, 49, 58]
Rv0878c PPE13 PPE family protein PPE13   [36, 38] ∙
Rv1005c pabB Probable para-aminobenzoate synthase component I   [48]
Rv1006 Rv1006 Unknown protein   
Rv1021 mazG NTP Pyrophosphohydrolase, MazG   [31, 32, 48, 58, 60]
Rv1755c plcD Probable phospholipase C 4 (fragment) PlcD   [8, 61]
Rv1759c wag22 PE-PGRS family protein Wag22   [36] ∙
Rv2352c PPE38 PPE family protein PPE38 exact, adjacent duplication of PPE38 [25, 40] ∙
Rv3879c espK ESX-1 secretion-associated protein EspK.   
(d) Genes with Variant Profiles Erroneously Declared as H37Ra-specific
Rv2421c† nadD Probable nicotinate-nucleotide adenylyltransferase NadD SNV instantiates CTGGAG motif [48]
Rv3053c nrdH Probable glutaredoxin electron transport component of NRDEF NrdH   [48]
  1. Studies [8, 25, 38, 49, 58] considered all of these genes. Studies [36, 59] (indicated by ∙ in the table) considered all the PE_PPE genes among the set.
  2. †: one or more variants affecting this gene reported as sequencing errors in H37Rv [8]