Rv1085c Family assigned · medium auto-curated
H37Rv Rv1085c · MTBC0 mtbc0_001165 ·
242 aa · 1218025–1218753 (-) ·
RefSeq NP_215601.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hemolysin-like protein |
|---|---|
| MTBC0 PGAP re-annotation | hemolysin III family protein |
| Revised (this work) | Hemolysin III family protein. Pfam: HlyIII (PF03006.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFN7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | UPF0073 membrane protein Rv1085c |
UniProt still lists this protein as UPF0073 membrane protein Rv1085c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | hlyI |
| eggNOG description | protein, hemolysin III |
| Orthologous group | COG1272 |
| KEGG orthology |
K11068
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
HlyIII | PF03006.27 | 9.4e-52 | 31–234 | Haemolysin-III related |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1086 ((2Z,6E)-farnesyl diphosphate synthase), medium confidence from genomic context alone (score 596 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 595 | 596 ctx | neighborhood:596 |
Rv3696c glpK |
glycerol kinase | 605 | 554 | database:546 |
Rv1770 hyp |
hypothetical protein | 532 | 532 | database:532 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 532 | 532 | database:532 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 476 | 477 | database:475 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 476 | 477 | database:475 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 476 | 477 | database:475 |
Rv0435c |
ATPase | 476 | 477 | database:475 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 446 | 426 | |
Rv1329c dinG |
ATP-dependent helicase DinG | 414 | 415 | database:404 |
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 413 | 414 | |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 413 | 414 | |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 413 | 414 | |
Rv1817 |
flavoprotein | 413 | 414 | |
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 413 | 414 |
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: hemolysin-like protein
- MTBC0 PGAP product: hemolysin III family protein
- Pfam (hmmscan --cut_ga): HlyIII PF03006.27 (E=9e-52)
- (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_215601.1)
- Domains: Pfam-A via hmmscan --cut_ga — HlyIII (PF03006.27)
- 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
COG1272 - Curated reference: UniProt P9WFN7 (SwissProt, reviewed; Inferred from homology)
- 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 —
28 functional partner(s); context anchor
Rv1086 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001165|Rv1085c| MSGQADTATTAEARTPAHAAHHLVEGVARVLTKPRFRGWIHVYSAGTAVLAGASLVAVSWAVGSAKAGLTTLAYTAATITMFTVSATYHRVNWKSATARNWMKRADHSMIFVFIAGSYTPFALLALPAHDGRVVLSIVWGGAIAGILLKMCWPAAPRSVGVPLYLLLGWVAVWYTATILHNAGVTALVLLFVGGALYSIGGILYAVRWPDPWPTTFGYHEFFHACTAVAAICHYIAMWFVVF