Rv3662c Resolved · medium auto-curated
H37Rv Rv3662c · MTBC0 mtbc0_003880 ·
256 aa · 4125095–4125865 (-) ·
RefSeq NP_218179.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | oxidoreductase |
| Revised (this work) | Oxidoreductase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YCP7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Fido domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Filamentation induced by cAMP protein fic |
| Orthologous group | COG3177 |
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 | 0.799 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 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).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dppD (dipeptide ABC transporter ATP-binding protein DppD), high confidence from genomic context alone (score 883 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) |
|---|---|---|---|---|
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 928 | 883 ctx | neighborhood:881 textmining:412 |
Rv3664c dppC |
dipeptide ABC transporter permease DppC | 917 | 882 ctx | neighborhood:881 |
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 886 | 808 ctx | neighborhood:807 textmining:433 |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 864 | 808 ctx | neighborhood:807 |
Rv0487 hyp |
hypothetical protein | 743 | 743 ctx | cooccurence:741 |
Rv3202c adnA |
ATP-dependent DNA helicase | 723 | 724 ctx | cooccurence:702 |
Rv0877 hyp |
hypothetical protein | 635 | 636 ctx | cooccurence:631 |
Rv3256c hyp |
hypothetical protein | 623 | 623 ctx | cooccurence:606 |
Rv1417 |
membrane protein | 586 | 586 ctx | cooccurence:579 |
Rv3679 |
anion transporter ATPase | 585 | 585 ctx | cooccurence:582 |
Rv0822c hyp |
hypothetical protein | 568 | 569 ctx | cooccurence:566 |
Rv2170 |
GCN5-like N-acetyltransferase | 568 | 569 ctx | cooccurence:563 |
Rv2709 |
transmembrane protein | 559 | 560 ctx | cooccurence:557 |
Rv1171 hyp |
hypothetical protein | 550 | 550 ctx | cooccurence:537 |
Rv1638A hyp |
hypothetical protein | 550 | 550 ctx | cooccurence:545 |
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: oxidoreductase
- (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_218179.1)
- 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
COG3177 - Curated reference: UniProt I6YCP7 (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 —
52 functional partner(s); context anchor
dppD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003880|Rv3662c| MTVDPLAPLMELPGVAAASDRVRDALSRVHRHRANLRGWPVAAAEASLRAARASSVLDGGPARLHDAGAPTSGKPALSDPVFAGALRVGQALEGGAGPVVGVWRRAPLQALARLHMLAAADQVDDDRLGRPRSDADVGPRLELLADVVTHPTLASAPVVAAVAHGELLTLRPFGCADGVVARAVSRLVTIATGLDPHGLGVPEVIWMRQPAEYHDAARRFAGGTPDGVAGWLLLCCGAMLDGAREALSIAESLSPG