Rv2862c Still unknown · low auto-curated
H37Rv Rv2862c · MTBC0 mtbc0_003043 ·
194 aa · 3194725–3195309 (-) ·
RefSeq NP_217378.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1707 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF1707. Function unknown. Foldseek best (non-significant) hit: 7yh8-assembly2_C Crystal structure of a heterochiral protein complex (prob 0.69, TM 0.74). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y1W7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DUF1707 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF1707) |
| Orthologous group | COG4758 |
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 | 1.493 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF1707 | PF08044.17 | 6.3e-17 | 11–63 | DUF1707 SHOCT-like domain |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 91.9 (very high). 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 |
|---|---|---|---|---|
7yh8-assembly2_C |
0.69 | 0.74 | 3.0e+00 | 7yh8-assembly2_C Crystal structure of a heterochiral protein complex |
9ir4-assembly1_C |
0.63 | 0.65 | 2.6e+00 | 9ir4-assembly1_C Cryo-EM structure of Nipah virus L-P (H1165Y) polymerase complex |
9ir3-assembly1_C |
0.54 | 0.78 | 5.2e+00 | 9ir3-assembly1_C Cryo-EM structure of Nipah virus L-P polymerase complex |
4kjm-assembly1_A |
0.47 | 0.80 | 6.2e+00 | 4kjm-assembly1_A Crystal structure of the Staphylococcus aureus protein (NP_646141.1, domain 3912-4037) similar to streptococcal adhesins emb and ebhA/ebhB |
4kjm-assembly1_B |
0.25 | 0.63 | 5.0e+00 | 4kjm-assembly1_B Crystal structure of the Staphylococcus aureus protein (NP_646141.1, domain 3912-4037) similar to streptococcal adhesins emb and ebhA/ebhB |
7puk-assembly2_C |
0.21 | 0.64 | 6.5e+00 | 7puk-assembly2_C Crystal structure of Endoglycosidase E GH18 domain from Enterococcus faecalis in complex with Man5 product |
7oyd-assembly1_R |
0.15 | 0.59 | 8.6e+00 | 7oyd-assembly1_R Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b |
7bqn-assembly1_A |
0.11 | 0.57 | 9.1e+00 | 7bqn-assembly1_A Solution NMR structure of fold-C Rei; de novo designed protein with an asymmetric all-alpha topology |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mapB (methionine aminopeptidase), medium confidence from genomic context alone (score 689 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) |
|---|---|---|---|---|
Rv2861c mapB |
methionine aminopeptidase | 689 | 689 ctx | neighborhood:687 |
Rv0320 hyp |
hypothetical protein | 686 | 687 ctx | cooccurence:673 |
Rv2712c hyp |
hypothetical protein | 617 | 618 ctx | cooccurence:617 |
Rv1728c hyp |
hypothetical protein | 584 | 584 ctx | cooccurence:584 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 582 | 583 | coexpression:426 |
Rv2863 vapC23 |
ribonuclease VapC23 | 543 | 543 ctx | neighborhood:543 |
Rv2862A vapB23 |
antitoxin VapB23 | 543 | 543 ctx | neighborhood:543 |
Rv3660c ssd hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:539 |
Rv2980 hyp |
hypothetical protein | 507 | 507 ctx | cooccurence:507 |
Rv0845 narS |
sensor histidine kinase NarS | 520 | 500 | coexpression:483 |
Rv3132c devS |
two component sensor histidine kinase DevS | 519 | 499 | coexpression:482 |
Rv2027c dosT |
two component sensor histidine kinase DosT | 519 | 499 | coexpression:482 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 482 | 482 ctx | cooccurence:482 |
Rv3753c hyp |
hypothetical protein | 476 | 477 ctx | cooccurence:475 |
Rv2721c hyp |
hypothetical protein | 472 | 456 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
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: DUF1707 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF1707 PF08044.17 (E=6e-17)
- Foldseek best: 7yh8-assembly2_C Crystal structure of a heterochiral protein complex (prob 0.69, E=3e+00, TM=0.74)
- (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_217378.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1707 (PF08044.17)
- 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
COG4758 - Curated reference: UniProt I6Y1W7 (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 91.9, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
25 functional partner(s); context anchor
mapB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003043|Rv2862c| MTETGGDMVALRVSDADRNGTMRRLHNAVALGLINIDEFEQRSSRVSFARTRSELDGLVGDLPRPGAIVTSAADRVELRGWAGSLKRHGEWIVPTRLALVRRLGSIELDLVKARFAGPVVVIELDMMFGSLEVRLPNGASASIDDVEVYVGSASDRRKDAPAEGTPHVVLTGRMVCGSVVIKGPRRALLRRHRG