Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|
| MTBC0 PGAP re-annotation | RsiV family protein |
|---|
| Revised (this work) | RsiV family protein. |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YF08
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Esterase Rv3036c |
|---|
| EC (curated) |
EC 3.1.1.-
|
|---|
| Curated function | Hydrolyzes ester substrates carbon chain lengths ranging from C2 to C14. In vitro, acetate (C2), butyrate (C4) and caprylate (C6) are hydrolyzed with high efficiency. Has lower activity against laurate (C12), myristate (C14) and caproate (C8), and weak activity against palmitate (C16). |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | Protein of unknown function (DUF3298) |
|---|
| Orthologous group | 28KR0 |
|---|
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 |
0.328 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 3 missense, 0 nonsense, 0 frameshift
|
|---|
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 |
|---|
DUF3298 | PF11738.14 |
3.9e-15 | 145–220 |
Protein of unknown function (DUF3298) |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2133c hyp |
hypothetical protein |
871 |
863 |
experimental:772 database:425 |
Rv2555c alaS |
alanine--tRNA ligase |
848 |
836 |
experimental:570 database:622 |
Rv2101 helZ |
helicase HelZ |
779 |
766 |
database:613 |
Rv3529c hyp |
hypothetical protein |
778 |
766 |
experimental:454 database:583 |
Rv2267c stf3 hyp |
hypothetical protein |
778 |
766 |
experimental:454 database:583 |
Rv1691 hyp |
hypothetical protein |
778 |
766 |
experimental:454 database:583 |
Rv0719 rplF |
50S ribosomal protein L6 |
743 |
743 |
experimental:415 database:579 |
Rv0722 rpmD |
50S ribosomal protein L30 |
740 |
740 |
database:543 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha |
747 |
738 |
database:622 |
Rv3409c choD |
cholesterol oxidase |
739 |
729 |
database:573 |
Rv0492c |
GMC-type oxidoreductase |
739 |
729 |
database:573 |
Rv0697 mftG |
dehydrogenase |
739 |
729 |
database:573 |
Rv1279 |
GMC-type oxidoreductase |
739 |
729 |
database:573 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega |
720 |
719 |
database:624 |
Rv0703 rplW |
50S ribosomal protein L23 |
716 |
715 |
database:548 |
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: RsiV family protein
- Pfam (hmmscan --cut_ga): DUF3298 PF11738.14 (E=4e-15)
- (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_217552.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3298 (PF11738.14)
- 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
28KR0
- Curated reference: UniProt
I6YF08
(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 —
114 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003228|Rv3036c|TB22.2
MRYLIATAVLVAVVLVGWPAAGAPPSCAGLGGTVQAGQICHVHASGPKYMLDMTFPVDYPDQQALTDYITQNRDGFVNVAQGSPLRDQPYQMDATSEQHSSGQPPQATRSVVLKFFQDLGGAHPSTWYKAFNYNLATSQPITFDTLFVPGTTPLDSIYPIVQRELARQTGFGAAILPSTGLDPAHYQNFAITDDSLIFYFAQGELLPSFVGACQAQVPRSAIPPLAI
Spot an error? Suggest an improvement