usfY Family assigned · low
H37Rv Rv3288c · MTBC0 - ·
137 aa · 3669586–3669999 (-) ·
RefSeq NP_217805.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | UsfY, an open reading frame of the sigF gene cluster, located immediately upstream of usfX-sigF (the stress/stationary-phase sigma factor and its anti-sigma factor). UsfY has no significant homologues and may not be co-transcribed with usfX-sigF; molecular function unknown but its genomic context ties it to the SigF stress-response locus. |
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 |
L7N685
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein USFY |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | usfY |
|---|---|
| Orthologous group | 2B4VS |
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 | 0.356 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 82.0 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
6s7o-assembly1_F |
0.25 | 0.42 | 2.3e+00 | 6s7o-assembly1_F Cryo-EM structure of human oligosaccharyltransferase complex OST-A |
7o3x-assembly1_E |
0.14 | 0.46 | 7.8e+00 | 7o3x-assembly1_E Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3289c (transmembrane protein), high confidence from genomic context alone (score 968 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) |
|---|---|---|---|---|
Rv3289c |
transmembrane protein | 967 | 968 ctx | neighborhood:817 coexpression:831 |
Rv3290c lat |
L-lysine-epsilon aminotransferase | 945 | 946 ctx | neighborhood:657 coexpression:848 |
Rv3287c rsbW |
anti-sigma factor RsbW | 858 | 853 ctx | neighborhood:463 coexpression:738 |
Rv3286c sigF |
RNA polymerase sigma factor SigF | 805 | 805 ctx | neighborhood:701 |
Rv3291c lrpA |
transcriptional regulator LrpA | 551 | 551 ctx | neighborhood:534 |
Rv3292 hyp |
hypothetical protein | 437 | 437 ctx | neighborhood:406 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 416 | 416 | |
Rv0188 |
transmembrane protein | 639 | 76 | textmining:626 |
Rv2558 hyp |
hypothetical protein | 808 | 70 | textmining:803 |
Rv2557 hyp |
hypothetical protein | 542 | 65 | textmining:531 |
Rv2660c hyp |
hypothetical protein | 664 | 53 | textmining:660 |
Rv1954c hyp |
hypothetical protein | 633 | 49 | textmining:630 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 438 | 49 | textmining:434 |
Rv0723 rplO |
50S ribosomal protein L15 | 729 | 46 | textmining:729 |
Rv3661 hyp |
hypothetical protein | 549 | 46 | textmining:547 |
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
- Member of the sigF gene cluster (upstream of usfX-sigF); named usfY (DeMaio 1997, PMID 9666957)
- Curated from the literature crible (project 'Still unknown gene function', 2026-06-09)
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_217805.1)
- 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
2B4VS - Curated reference: UniProt L7N685 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 82.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
19 functional partner(s); context anchor
Rv3289c - Primary literature: DeMaio J, Zhang Y, Ko C, Bishai WR (1997). Mycobacterium tuberculosis sigF is part of a gene cluster with similarities to the Bacillus subtilis sigF and sigB operons Tuber Lung Dis 78(1):3-12. doi:10.1016/s0962-8479(97)90010-1 PMID:9666957
Ancestral MTBC0 protein sequence
>H37Rv|Rv3288c|usfY MGQIPPQPVRRVLPLMVVPGNGQKWRNRTETEEAMGDTYRDPVDHLRTTRPLAGESLIDVVHWPGYLLIVAGVVGGVGALAAFGTGHHAEGMTFGVVAIVVTVVGLAWLAFEHRRIRKIADRWYTEHPEVRRQRLAG