Rv3360 Family assigned · medium auto-curated
H37Rv Rv3360 · MTBC0 mtbc0_003575 ·
122 aa · 3799359–3799727 (+) ·
RefSeq NP_217877.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | FHA domain-containing protein |
| Revised (this work) | FHA domain-containing protein. Pfam: FHA (PF00498.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50389
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | FHA domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | Inner membrane component of T3SS, cytoplasmic domain |
| Orthologous group | COG1716 |
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) pseudogene candidate
| pN/pS | 0.343 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 6.00% of strains (8707) · 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 |
|---|---|---|---|---|
FHA | PF00498.32 | 6.5e-13 | 26–89 | FHA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3359 (oxidoreductase), medium confidence from genomic context alone (score 509 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) |
|---|---|---|---|---|
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 985 | 984 | experimental:984 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 937 | 732 | experimental:711 textmining:775 |
Rv1364c |
sigma factor regulatory protein | 687 | 686 | coexpression:646 |
Rv1277 hyp |
hypothetical protein | 641 | 628 | database:579 |
Rv1278 hyp |
hypothetical protein | 641 | 628 | database:579 |
Rv3451 cut3 |
cutinase | 595 | 596 | database:530 |
Rv3724A cut5a |
Rv3724A, (MTV025.072), len: 80 aa. Probable cut5a,truncated cutinase precursor, similar to N-terminal end of others e.g. Q9KK87 serine ester | 595 | 596 | database:530 |
Rv3483c hyp |
hypothetical protein | 595 | 595 | database:530 |
Rv3724B cut5b |
Rv3724B, (MTV025.072), len: 187 aa. Probable cut5b,truncated cutinase, similar to C-terminal end of others e.g. Q9XB09|RVD2-RV1758 protein ( | 593 | 594 | database:530 |
Rv2301 cut2 |
cutinase | 593 | 594 | database:530 |
Rv1758 cut1 |
cutinase | 593 | 594 | database:530 |
Rv0434 hyp |
hypothetical protein | 587 | 562 | database:560 |
Rv1334 mec |
[CysO | 546 | 532 | database:518 |
Rv3359 |
oxidoreductase | 509 | 509 ctx | neighborhood:506 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 489 | 457 | experimental:420 |
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: FHA domain-containing protein
- Pfam (hmmscan --cut_ga): FHA PF00498.32 (E=6e-13)
- (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_217877.1)
- Domains: Pfam-A via hmmscan --cut_ga — FHA (PF00498.32)
- 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
COG1716 - Curated reference: UniProt O50389 (TrEMBL, unreviewed; Predicted)
- 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 —
44 functional partner(s); context anchor
Rv3359 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003575|Rv3360| MSRPHPPVLTVRSDRSQQCFAAGRDVVVGSDLRADMRVAHPLIARAHLLLRFDRGNWIAIDNDSQSGMFVDGQRVSEVDIYDGLTINIGKPTGPWITFEVGHHQGIIGRLSRTPSSRPGSPI