Rv3896c Resolved · medium auto-curated
H37Rv Rv3896c · MTBC0 mtbc0_004130 ·
302 aa · 4406189–4407097 (-) ·
RefSeq NP_218413.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | transglycosylase |
| Revised (this work) | Transglycosylase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05448
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Transglycosylase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | SLT domain |
| Orthologous group | COG3953 |
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) pseudogene candidate
| pN/pS | 0.287 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 15 synonymous, 12 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 11.78% of strains (17106) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccC2 (ESX-2 type VII secretion system protein EccC), high confidence from genomic context alone (score 818 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) |
|---|---|---|---|---|
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 818 | 818 ctx | neighborhood:776 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 812 | 812 ctx | neighborhood:774 |
Rv2633c hyp |
hypothetical protein | 757 | 757 ctx | cooccurence:756 |
Rv1978 hyp |
hypothetical protein | 698 | 699 ctx | cooccurence:698 |
Rv1733c |
transmembrane protein | 695 | 696 ctx | cooccurence:694 |
Rv3786c hyp |
hypothetical protein | 699 | 688 ctx | cooccurence:641 |
Rv0804 hyp |
hypothetical protein | 671 | 671 ctx | cooccurence:671 |
Rv3413c rsdA |
anti-sigma-D factor RsdA | 657 | 658 ctx | cooccurence:656 |
Rv3604c |
transmembrane protein | 643 | 643 ctx | cooccurence:641 |
Rv3484 cpsA hyp |
hypothetical protein | 610 | 610 ctx | cooccurence:609 |
Rv1057 hyp |
hypothetical protein | 585 | 586 ctx | cooccurence:584 |
Rv1435c hyp |
hypothetical protein | 571 | 571 ctx | cooccurence:570 |
Rv1158c hyp |
hypothetical protein | 552 | 552 ctx | cooccurence:552 |
Rv2812 |
transposase | 552 | 552 ctx | cooccurence:551 |
Rv0210 hyp |
hypothetical protein | 551 | 552 ctx | cooccurence:545 |
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: transglycosylase
- (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_218413.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG3953 - Curated reference: UniProt O05448 (TrEMBL, unreviewed; Predicted)
- 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 —
42 functional partner(s); context anchor
eccC2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004130|Rv3896c| MSTWHRIGTEGEPLTDPLTTQAIAALSRGHGLFAGGVSGADIDAPQIQQYANAISWVANAVPTAAAYRWRGAARALRRLANTDEALAQIMAAAQIDHAHARTATRALLEAAKTDAMALTDTPLGRREAMARMAARLRAQHRHIARCRSRARLLGLRLRRLRYLRTAAARRPQVTTPGGRAQVLAAIQKALDIKGVHDPAARARWTRGMDLVARRESNYNANAINHWDSNAARGTPSRGVWQFIAPTFAAYHEPGTSTNIHDLVAQACAFINYARGHYGVAADASNLADLIQQADPRRSPRGY