Rv1890c Family assigned · medium auto-curated
H37Rv Rv1890c · MTBC0 - ·
203 aa · 2139076–2139687 (-) ·
RefSeq NP_216406.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains YceI (PF04264.19) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O07742
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipid/polyisoprenoid-binding YceI-like domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Belongs to the UPF0312 family |
| Orthologous group | COG2353 |
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 | 1.059 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (160) · 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 |
|---|---|---|---|---|
YceI | PF04264.19 | 1.5e-11 | 104–197 | YceI-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1889c (Rv1889c, (MTCY180.29), len: 118 aa. Conserved hypothetical protein. Part of large family of Mycobacterium tuberculosis proteins with conserv), medium confidence from genomic context alone (score 637 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) |
|---|---|---|---|---|
Rv2342 hyp |
hypothetical protein | 690 | 691 ctx | cooccurence:690 |
Rv1889c |
Rv1889c, (MTCY180.29), len: 118 aa. Conserved hypothetical protein. Part of large family of Mycobacterium tuberculosis proteins with conserv | 638 | 637 ctx | neighborhood:620 |
Rv1891 hyp |
hypothetical protein | 574 | 573 ctx | neighborhood:573 |
Rv0756c hyp |
hypothetical protein | 554 | 554 ctx | cooccurence:554 |
Rv1888c |
Rv1888c, (MTCY180.30), len: 186 aa. Possible transmembrane protein. | 553 | 553 ctx | neighborhood:551 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 546 | 546 | coexpression:534 |
Rv1945 hyp |
hypothetical protein | 540 | 541 ctx | cooccurence:467 |
Rv1892 |
membrane protein | 539 | 539 ctx | neighborhood:539 |
Rv1893 hyp |
hypothetical protein | 534 | 534 ctx | neighborhood:534 |
Rv1888A |
Rv1888A, len: 57 aa. Conserved hypothetical protein. Possibly continuation of Rv1889c, part of large family of Mycobacterium tuberculosis pr | 522 | 522 ctx | neighborhood:515 |
Rv1702c hyp |
hypothetical protein | 507 | 508 ctx | cooccurence:429 |
Rv0817c lmeA hyp |
hypothetical protein | 500 | 500 ctx | cooccurence:496 |
Rv3810 pirG |
cell surface protein | 502 | 494 | |
Rv1780 hyp |
hypothetical protein | 475 | 475 ctx | cooccurence:475 |
Rv0518 hyp |
hypothetical protein | 461 | 462 ctx | cooccurence:456 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): YceI PF04264.19 (E=1e-11)
- (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_216406.1)
- Domains: Pfam-A via hmmscan --cut_ga — YceI (PF04264.19)
- 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
COG2353 - Curated reference: UniProt O07742 (TrEMBL, unreviewed; 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 —
32 functional partner(s); context anchor
Rv1889c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1890c| MAHKTRREGRAGRSSEYSRGVSDAVWTLDASDGELVLRTGVVGRAARLGHRLTIAMTRWQALVNWSGTDPVAGELVAEVDSFEVMRGEGGVKGLSEPEKALVRANALKTLNASRFPHIRFTTEAIAQTGNGYRLTGKLHIRGKSREHVIDLHTEDLGAAWRISADTTVRQSNYGVKPYSLLMGSIRVADEVSVAFTAVRAKDD