Rv2001 Resolved · high auto-curated
H37Rv Rv2001 · MTBC0 mtbc0_002128 ·
250 aa · 2270445–2271197 (+) ·
RefSeq NP_216517.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | acyl-[acyl-carrier-protein] thioesterase |
| Revised (this work) | Acyl-[acyl-carrier-protein] thioesterase. Pfam: Acyl-ACP_TE (PF01643.24), Acyl-ACP_TE_C (PF20791.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLN5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2001 |
UniProt still lists this protein as Uncharacterized protein Rv2001; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | Acyl-ACP thioesterase |
| Orthologous group | COG3884 |
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 1.102 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (148) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Acyl-ACP_TE | PF01643.24 | 2.5e-19 | 18–140 | Acyl-ACP thioesterase N-terminal domain |
Acyl-ACP_TE_C | PF20791.4 | 1.5e-09 | 163–227 | Acyl-ACP thioesterase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aftC (alpha-(1->3)-arabinofuranosyltransferase), high confidence from genomic context alone (score 714 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2000 hyp |
hypothetical protein | 972 | 973 ctx | neighborhood:867 coexpression:804 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 714 | 714 ctx | cooccurence:710 |
Rv1274 lprB |
lipoprotein LprB | 694 | 695 ctx | cooccurence:693 |
Rv3346c |
transmembrane protein | 669 | 669 ctx | cooccurence:667 |
Rv1476 |
membrane protein | 668 | 668 ctx | cooccurence:664 |
Rv1684 hyp |
hypothetical protein | 664 | 664 ctx | cooccurence:663 |
Rv0184 hyp |
hypothetical protein | 654 | 654 ctx | cooccurence:654 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 644 | 644 ctx | cooccurence:643 |
Rv3802c |
membrane protein | 639 | 639 ctx | cooccurence:639 |
Rv2739c |
transferase | 634 | 634 ctx | cooccurence:634 |
Rv1275 lprC |
lipoprotein LprC | 631 | 632 ctx | cooccurence:630 |
Rv2002 fabG3 |
3-alpha(or 20-beta)-hydroxysteroid dehydrogenase | 636 | 630 ctx | neighborhood:611 |
Rv1845c blaR |
sensor-transducer protein BlaR | 583 | 584 ctx | cooccurence:583 |
Rv1610 |
membrane protein | 581 | 581 ctx | cooccurence:581 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 571 | 571 ctx | cooccurence:571 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: acyl-[acyl-carrier-protein] thioesterase
- Pfam (hmmscan --cut_ga): Acyl-ACP_TE PF01643.24 (E=3e-19), Acyl-ACP_TE_C PF20791.4 (E=1e-09)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_216517.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-ACP_TE (PF01643.24), Acyl-ACP_TE_C (PF20791.4)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG3884 - Curated reference: UniProt P9WLN5 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
49 functional partner(s); context anchor
aftC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002128|Rv2001| MHHNRDVDLALVERPSSGYVYTTGWRLATTDIDEHQQLRLDGVARYIQEVGAEHLADAQLAEVHPHWIVLRTVIDVINPIELPSDITFHRWCAALSTRWCSMRVQLQGSAGGRIETEGFWICVNKDTLTPSRLTDDCIARFGSTTENHRLKWRPWLTGPNIDGTETPFPLRRTDIDPFEHVNNTIYWHGVHEILCQIPTLTAPYRAVLEYRSPIKSGEPLTIRYEQHDDVVRMHFVVGDDVRAAALLRRL