Rv1419 Resolved · high auto-curated
H37Rv Rv1419 · MTBC0 mtbc0_001519 ·
157 aa · 1602849–1603322 (+) ·
RefSeq NP_215935.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | lectin |
| Revised (this work) | Lectin. Pfam: Ricin_B_lectin (PF00652.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLX9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1419 |
UniProt still lists this protein as Uncharacterized protein Rv1419; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Ricin-type beta-trefoil |
| Orthologous group | 2AUAB |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 0.783 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.95% of strains (1375) · 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 |
|---|---|---|---|---|
Ricin_B_lectin | PF00652.29 | 7.3e-19 | 37–153 | Ricin-type beta-trefoil lectin domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uvrC (excinuclease ABC subunit UvrC), medium confidence from genomic context alone (score 616 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) |
|---|---|---|---|---|
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 615 | 616 ctx | neighborhood:607 |
Rv1421 rapZ hyp |
hypothetical protein | 607 | 608 ctx | neighborhood:607 |
Rv1423 whiA |
transcriptional regulator WhiA | 597 | 598 ctx | neighborhood:594 |
Rv1422 cuvA hyp |
hypothetical protein | 596 | 597 ctx | neighborhood:594 |
Rv1418 lprH |
lipoprotein LprH | 486 | 487 ctx | neighborhood:485 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 446 | 446 ctx | neighborhood:417 |
Rv1417 |
membrane protein | 432 | 432 ctx | neighborhood:417 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 423 | 423 ctx | neighborhood:417 |
Rv1251c hyp |
hypothetical protein | 422 | 423 | coexpression:423 |
Rv0440 groEL2 |
molecular chaperone GroEL | 439 | 391 | |
Rv3417c groEL1 |
chaperonin GroEL | 412 | 390 | |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 560 | 353 | |
Rv1677 dsbF |
lipoprotein DsbF | 412 | 106 | |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 804 | 50 | textmining:803 |
Rv1252c lprE |
lipoprotein LprE | 406 | 50 | textmining:401 |
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: lectin
- Pfam (hmmscan --cut_ga): Ricin_B_lectin PF00652.29 (E=7e-19)
- (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_215935.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ricin_B_lectin (PF00652.29)
- 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
2AUAB - Curated reference: UniProt P9WLX9 (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 —
21 functional partner(s); context anchor
uvrC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001519|Rv1419| MGELRLVGGVLRVLVVVGAVFDVAVLNAGAASADGPVQLKSRLGDVCLDAPSGSWFSPLVINPCNGTDFQRWNLTDDRQVESVAFPGECVNIGNALWARLQPCVNWISQHWTVQPDGLVKSDLDACLTVLGGPDPGTWVSTRWCDPNAPDQQWDSVP