Genes
1086 genes matched.
| Gene | MTBC0 | Legacy (H37Rv) | MTBC0 PGAP / revised | Pfam | Verdict |
|---|---|---|---|---|---|
| Rv3189 Rv3189 |
mtbc0_003386 |
hypothetical protein | RES family NAD+ phosphorylase. Pfam: RES (PF08808.18). | RES |
Family assigned |
| Rv3190A Rv3190A |
- |
hypothetical protein | Tentatively a small DNA-binding module of the ribbon-helix-helix / HTH type: several converging HHpred hits (~72-75%) to ParB C-terminal, the CcdA post-segregation antitoxin, a plasmid ribbon-helix-helix DNA-binding protein and ECF sigma factors. LOW confidence (no hit >95%; the top LOV-domain hit at 91% is a short 18-column match, likely spurious). Flanked by an IS30-family transposase (Rv3191c), so possibly an IS-associated DNA-binding peptide; NOT asserted as a toxin-antitoxin antitoxin (no adjacent toxin). A lead to validate. | Family assigned | |
| Rv3190c Rv3190c |
mtbc0_003387 |
hypothetical protein | Conserved hypothetical protein; no recognised domain. Function unknown. | Still unknown | |
| Rv3192 Rv3192 |
- |
hypothetical protein | Contains Bac_luciferase (PF00296.27) domain(s); putative function inferred from the domain architecture. | Bac_luciferase |
Family assigned |
| Rv3194c Rv3194c |
mtbc0_003395 |
hypothetical protein | PDZ domain-containing protein. Pfam: PDZ_2 (PF13180.13), Lon_C (PF05362.20). | PDZ_2 Lon_C |
Family assigned |
| Rv3195 Rv3195 |
mtbc0_003396 |
hypothetical protein | Zinc-dependent metalloprotease. Pfam: Zincin_2 (PF10103.16). | Zincin_2 |
Resolved |
| Rv3196 Rv3196 |
- |
hypothetical protein | Probable ThiF/MoeB/E1-family adenylyltransferase of undetermined substrate; NOT a YcaO heterocyclase. RefSeq leaves it 'hypothetical protein'. A strong Foldseek hit to the cyanobactin heterocyclase TruD (4bs9, query-normalised TM-score 0.72) is a normalised-TM-score artefact: the alignment covers only the N-terminal scaffold (TruD residues 3-321), stops before the YcaO catalytic domain, and the target-normalised TM-score is 0.33 (~38% coverage); none of the YcaO catalytic residues lies in the aligned region. HHpred re-routes it (>=99.9%) to standalone adenylyltransferases (MccB, PaaA) and the ThiF/MoeB/E1-like adenylation superfamily, within which the CxxC pair (C208/C211) matches the MoeB-type zinc motif. A RiPP role is independently improbable (no precursor-peptide cassette, maturation protease, or TfuA in H37Rv). A worked example of the normalised-TM-score trap. | Family assigned | |
| Rv3196A Rv3196A |
- |
hypothetical protein | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 4jq5-assembly2_H Crystal structure of the human Nup49CCS2+3* coiled-co (prob 0.66, TM 0.87). | Still unknown | |
| Rv3202a Rv3202a |
- |
hypothetical protein | Belongs to a conserved Mycobacterium-specific protein family (Pfam PF29473, the 'Rv3202A family', HHpred 99.6%). This is a self-named family (built from Rv3202A and its homologues) with NO known function, so the assignment confirms it is a genuine conserved family (not a spurious ORF) but the molecular function remains unknown (DUF-like). | Family assigned | |
| Rv3205c Rv3205c |
- |
hypothetical protein | Protein-kinase-like (APH/ePK) fold whose active site is NOT retained. RefSeq leaves it 'hypothetical protein'. The AlphaFold model superposes on an aminoglycoside 3',5"-phosphotransferase (PDB 1l8t = M-CSA entry 640, EC 2.7.1.95), but the M-CSA active-site check shows the 4 catalytic residues are all ALIGNED yet SUBSTITUTED (0/4 conserved) -> same fold, active site not retained. A worked negative control: the kinase fold is present but the gene is NOT an active aminoglycoside phosphotransferase. | Family assigned | |
| Rv3207c Rv3207c |
- |
hypothetical protein | Zinc-dependent metalloprotease (eggNOG COG5479, cell-envelope COG category M; DUF3152). RefSeq leaves it 'hypothetical protein'. Metallopeptidase fold; substrate undetermined. | DUF3152 |
Family assigned |
| TB9.4 Rv3208A |
- |
hypothetical protein | Structurally characterized DUF3107 protein (Pfam) of unknown biochemical function. RefSeq leaves it 'hypothetical protein'. A crystal structure of the hexadecameric form of this family was solved (PDB 7rur; Foldseek prob 1.0, E 3e-11, TM 0.95). STRING context links it to the cytochrome bcc subunit qcrC (Rv2194). Family/structure assigned; molecular function unfixed. | DUF3107 |
Family assigned |
| Rv3209 Rv3209 |
mtbc0_003415 |
hypothetical protein | MmpS family transport accessory protein. Pfam: Mycobact_memb (PF05423.19). | Mycobact_memb |
Family assigned |
| Rv3210c Rv3210c |
mtbc0_003416 |
hypothetical protein | Ferritin-like fold-containing protein. Pfam: Ferritin_fold-like (PF13794.13). | Ferritin_fold-like |
Family assigned |
| Rv3212 Rv3212 |
mtbc0_003418 |
hypothetical protein | Beta-propeller protein of the BamB/quinoprotein-like family (eggNOG COG1520). A WD40/PQQ-type beta-propeller scaffold; specific partner/role in M. tuberculosis undetermined. | Family assigned | |
| Rv3218 Rv3218 |
mtbc0_003424 |
hypothetical protein | Diacylglycerol kinase family lipid kinase. Pfam: DAGK_cat (PF00781.30). | DAGK_cat |
Family assigned |
| Rv3222c Rv3222c |
mtbc0_003429 |
hypothetical protein | Essential (Tn-seq ES) and HIGHLY VULNERABLE (CRISPRi vulnerability index -15.5, the most vulnerable of the atlas hypotheticals) conserved protein (strong purifying selection) encoded WITHIN the sigH stress-response operon: it overlaps (-4 bp on both sides) the alternative sigma factor SigH (Rv3223c) and its cognate anti-sigma factor RshA (Rv3221A), is transcriptionally activated by SigH, and its top STRING partner is RshA (score 979). This places it as a candidate essential component of the SigH-RshA oxidative/heat-stress regulatory module (a co-regulated factor or a modulator of the sigma / anti-sigma switch). Its molecular function is not established; the low-complexity, poorly-ordered sequence (183 aa, G/A/V-rich, pLDDT 40, no Pfam or Foldseek hit) limits structural inference. NOT previously characterised in the literature (WebSearch + tbmonitor negative) - a novel, essential, highly vulnerable, uncharacterised drug-target candidate. HHpred profile-profile gives NO confident hit (best is DUF7993 / Pfam PF25956 at only 9.5% probability, E-value 1300 = noise), consistent with the low-complexity, poorly-ordered sequence; the SigH-RshA contextual hypothesis remains the sole functional handle. | Family assigned | |
| Rv3224A Rv3224A |
|
Conserved hypothetical protein | Belongs to the prolyl-tRNA editing family. YbaK EbsC subfamily | Family assigned | |
| Rv3224B Rv3224B |
|
Conserved hypothetical protein | Belongs to the prolyl-tRNA editing family. YbaK EbsC subfamily | Family assigned | |
| Rv3226c Rv3226c |
mtbc0_003435 |
hypothetical protein | SOS response-associated peptidase. Pfam: SRAP (PF02586.20). | SRAP |
Resolved |
| rsgA Rv3228 |
mtbc0_003437 |
hypothetical protein | Ribosome small subunit-dependent GTPase A. Pfam: RsgA_GTPase (PF03193.23), MMR_HSR1 (PF01926.30). | RsgA_GTPase MMR_HSR1 |
Family assigned |
| Rv3231c Rv3231c |
mtbc0_003440 |
hypothetical protein | Conserved cytoplasmic protein co-transcribed with ppk2 (polyphosphate kinase 2, Rv3232c) as a two-gene operon, under strong purifying selection and required for in-vivo fitness. The genomic context (operon with ppk2) points to a candidate role associated with polyphosphate metabolism, a persistence- and stress-linked pathway; the specific molecular function is not established. | DUF6912 |
Family assigned |
| Rv3235 Rv3235 |
- |
hypothetical protein | Conserved hypothetical protein; DUF domain(s) DUF6459. Function unknown. Foldseek best (non-significant) hit: 8j07-assembly1_k1 96nm repeat of human respiratory doublet microtubule (prob 0.01, TM 0.10). | DUF6459 |
Still unknown |
| Rv3237c Rv3237c |
mtbc0_003445 |
hypothetical protein | Cation:proton antiporter regulatory subunit. Pfam: KhtT_N (PF25991.1), TrkA_C (PF02080.27). | KhtT_N TrkA_C |
Family assigned |
| raiA Rv3241c |
mtbc0_003449 |
hypothetical protein | Ribosome-associated translation inhibitor RaiA. Pfam: Ribosomal_S30AE (PF02482.26), Ribosom_S30AE_C (PF16321.11). | Ribosomal_S30AE Ribosom_S30AE_C |
Resolved |
| Rv3242c Rv3242c |
mtbc0_003450 |
hypothetical protein | ComF family protein. | Family assigned | |
| Rv3243c Rv3243c |
mtbc0_003451 |
hypothetical protein | LmeA family phospholipid-binding protein. | Family assigned | |
| Rv3254 Rv3254 |
mtbc0_003462 |
hypothetical protein | Oxidoreductase. | Resolved | |
| Rv3256c Rv3256c |
mtbc0_003464 |
hypothetical protein | TobH protein. | Resolved | |
| Rv3258c Rv3258c |
- |
hypothetical protein | Conserved hypothetical protein; DUF domain(s) DUF3499. Function unknown. Foldseek best (non-significant) hit: 6wwa-assembly2_Y Crystal structure of human SHLD2-SHLD3-REV7 complex (prob 0.02, TM 0.13). | DUF3499 |
Still unknown |
| Rv3259 Rv3259 |
mtbc0_003467 |
hypothetical protein | Metallopeptidase family protein. Pfam: Zincin_1 (PF06262.18). | Zincin_1 |
Family assigned |
| lcp1 Rv3267 |
mtbc0_003475 |
hypothetical protein | Phosphotransferase Lcp1. Pfam: LytR_cpsA_psr (PF03816.20), LytR_C (PF13399.12). | LytR_cpsA_psr LytR_C |
Resolved |
| Rv3268 Rv3268 |
- |
hypothetical protein | TIGR03089-family protein, uncharacterised. NOTE: the acetyl-CoA-synthetase fold is shared, but the genuine Mtb acetyl-CoA synthetase is Rv3667 (acsA), a different gene. | Family assigned | |
| Rv3269 Rv3269 |
mtbc0_003477 |
hypothetical protein | DUF1490 family protein. | DUF1490 |
Family assigned |
| Rv3272 Rv3272 |
mtbc0_003480 |
hypothetical protein | CoA transferase. Pfam: CoA_transf_3 (PF02515.23). | CoA_transf_3 |
Resolved |
| Rv3282 Rv3282 |
mtbc0_003490 |
hypothetical protein | Nucleoside triphosphate pyrophosphatase. Pfam: Maf (PF02545.20). | Maf |
Resolved |
| Rv3284 Rv3284 |
mtbc0_003492 |
hypothetical protein | SufE family protein. Pfam: SufE (PF02657.21). | SufE |
Family assigned |
| usfY Rv3288c |
- |
hypothetical protein | UsfY, an open reading frame of the sigF gene cluster, located immediately upstream of usfX-sigF (the stress/stationary-phase sigma factor and its anti-sigma factor). UsfY has no significant homologues and may not be co-transcribed with usfX-sigF; molecular function unknown but its genomic context ties it to the SigF stress-response locus. | Family assigned | |
| Rv3292 Rv3292 |
mtbc0_003500 |
hypothetical protein | VOC family protein. Pfam: HGLS (PF07063.20). | HGLS |
Family assigned |
| Rv3294c Rv3294c |
- |
hypothetical protein | Predicted AAA+-superfamily ATPase (eggNOG COG1373, COG category J). AAA+ ATPase fold at orthology level; role undetermined. | DUF4143 |
Family assigned |
| Rv3300c Rv3300c |
mtbc0_003508 |
hypothetical protein | RluA family pseudouridine synthase. Pfam: PseudoU_synth_2 (PF00849.28). | PseudoU_synth_2 |
Family assigned |
| Rv3304 Rv3304 |
mtbc0_003512 |
hypothetical protein | Gamma-glutamylcyclotransferase. Pfam: GGACT (PF06094.18), AIG2_2 (PF13772.12). | GGACT AIG2_2 |
Resolved |
| Rv3311 Rv3311 |
mtbc0_003519 |
hypothetical protein | Primosomal protein. | Family assigned | |
| Rv3312b Rv3312b |
- |
hypothetical protein | Conserved hypothetical protein; no recognised domain. Function unknown. | Still unknown | |
| Rv3312c Rv3312c |
mtbc0_003520 |
hypothetical protein | Alpha/beta hydrolase. Pfam: Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14). | Abhydrolase_1 Abhydrolase_6 |
Family assigned |
| prp1 Rv3333c |
mtbc0_003546 |
hypothetical protein | PDZ-interacting protease regulator Ppr1. | DUF732 |
Resolved |
| Rv3337 Rv3337 |
|
Conserved hypothetical protein | Putative esterase: the AlphaFold model matches solved carboxylesterases (TM 0.85 to a Bacillus stearothermophilus carboxylesterase, TM 0.82 to esterase D of Lactobacillus rhamnosus). The previous wording was the raw eggNOG/GO term 'hydrolase activity, acting on ester bonds'. Fold-level only — no Pfam domain, no verified catalytic triad, no publication. | Family assigned | |
| Rv3338 Rv3338 |
|
Conserved hypothetical protein | Catalyzes the hydrolysis of epoxide-containing substrates (PubMed:36777032). In vitro, catalyzes the hydrolysis of the synthetic compounds PHOME and styrene oxide (PubMed:36777032). Plays an essential role in subverting phagosomal acidification (PubMed:36777032). Plays a major role in the survival of M.tuberculosis (Mtb) during in vitro acidic stress and protects Mtb in response to phagosomal acidification inside macrophages (PubMed:36777032). Also supports Mtb growth under the nutrient-deprived condition at pH 7.0 (PubMed:36777032) | Abhydrolase_6 |
Family assigned |
| Rv3351c Rv3351c |
- |
hypothetical protein | Contains BBE (PF08031.18) domain(s); putative function inferred from the domain architecture. | BBE |
Family assigned |
| Rv3353c Rv3353c |
mtbc0_003568 |
hypothetical protein | Oxidoreductase. | Resolved |