Rv0610c Still unknown · low auto-curated
H37Rv Rv0610c · MTBC0 mtbc0_000642 ·
385 aa · 708304–709461 (-) ·
RefSeq NP_215124.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 2z0r-assembly7_B Crystal structure of hypothetical protein TTHA0547 (prob 1.00, TM 0.70). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y481
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains) pseudogene candidate
| pN/pS | 1.563 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 12 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 17.55% of strains (25481) · 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).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 65.9 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
2z0r-assembly7_B |
1.00 | 0.70 | 6.0e-03 sig | 2z0r-assembly7_B Crystal structure of hypothetical protein TTHA0547 |
4ev1-assembly1_A |
0.51 | 0.21 | 3.1e-03 sig | 4ev1-assembly1_A Anabaena Tic22 (protein transport) |
4e6z-assembly1_A |
0.21 | 0.24 | 7.6e-02 | 4e6z-assembly1_A Tic22 from Plasmodium falciparum |
8xqx-assembly1_Q |
0.12 | 0.20 | 1.3e-01 | 8xqx-assembly1_Q Cryo-EM structure of the Ycf2-FtsHi motor complex from Chlamydomonas reinhardtii in apo state |
8xks-assembly1_I |
0.10 | 0.18 | 1.2e-01 | 8xks-assembly1_I The cryo-EM structure of Orf2971-FtsHi motor complex |
7nzm-assembly1_E |
0.02 | 0.26 | 7.1e+00 | 7nzm-assembly1_E Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I) |
8any-assembly1_Y |
0.01 | 0.17 | 3.8e+00 | 8any-assembly1_Y Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA |
7z1l-assembly1_O |
0.01 | 0.22 | 7.5e+00 | 7z1l-assembly1_O Structure of yeast RNA Polymerase III Pre-Termination Complex (PTC) |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0611c hyp |
hypothetical protein | 667 | 667 ctx | neighborhood:662 |
Rv0612 hyp |
hypothetical protein | 470 | 470 ctx | neighborhood:467 |
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: hypothetical protein
- Foldseek best: 2z0r-assembly7_B Crystal structure of hypothetical protein TTHA0547 (prob 1.00, E=6e-03, TM=0.70)
- (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_215124.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt I6Y481 (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 65.9, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 2 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000642|Rv0610c| MDDELRGLLARYARGELSADDARRAILRYPKWRVAEIDGELETVALDDGTPMLIAESSASDGREYSGLELVRDIAPLVGGLSFDPDEPWGSAFRPGALPELQSWARTVELEDAVAKPGPGQRDLLYEGPWWVAVSPGTGRPAVHRADGLDVITIMTAPDAAATFRRTERHRGLDVVRLGPALWGDLAKRSDFDGVRLNPLRPLAQLWPPHVPAMLVAGCDPRPNAEPLPARTVAEIHLWLDQHGARQEKRELSNRATPVGEVTVARAWWNYDRREIAFTRVAPASDTEGLGSVPSRILCAGKLRQSIQSKLAGLPRLTWRADAWHRQRAALAVGWALELEKLVCGERVPFAALRTPEGAHLWHLEPQAFTARAIRKLRDRAASFR