Rv3278c Family assigned · medium auto-curated
H37Rv Rv3278c · MTBC0 mtbc0_003486 ·
172 aa · 3682794–3683312 (-) ·
RefSeq NP_217795.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | PH domain-containing protein |
| Revised (this work) | PH domain-containing protein. Pfam: bPH_2 (PF03703.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96883
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial PH domain |
| Orthologous group | COG3428 |
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 | 0.082 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
bPH_2 | PF03703.21 | 7.2e-20 | 82–155 | Bacterial PH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: birA (bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase), high confidence from genomic context alone (score 823 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 822 | 823 ctx | neighborhood:822 |
Rv3281 accE5 |
bifunctional protein acetyl-/propionyl-CoAcarboxylase subunit epsilon AccE | 752 | 752 ctx | neighborhood:748 |
Rv3280 accD5 |
propionyl-CoA carboxylase subunit beta | 750 | 749 ctx | neighborhood:748 |
Rv3282 hyp |
hypothetical protein | 749 | 749 ctx | neighborhood:748 |
Rv1227c |
transmembrane protein | 633 | 585 | coexpression:561 |
Rv1234 |
transmembrane protein | 585 | 584 | coexpression:498 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 523 | 524 ctx | cooccurence:455 |
Rv3283 sseA |
thiosulfate sulfurtransferase SseA | 490 | 489 ctx | neighborhood:489 |
Rv2468c hyp |
hypothetical protein | 477 | 478 | |
Rv3284 hyp |
hypothetical protein | 475 | 475 ctx | neighborhood:474 |
Rv1638A hyp |
hypothetical protein | 474 | 475 | |
Rv0049 hyp |
hypothetical protein | 472 | 472 ctx | cooccurence:469 |
Rv1481 |
membrane protein | 449 | 450 ctx | cooccurence:432 |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 446 | 447 | coexpression:415 |
Rv3221A rshA |
anti-sigma factor RshA | 445 | 446 |
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: transmembrane protein
- MTBC0 PGAP product: PH domain-containing protein
- Pfam (hmmscan --cut_ga): bPH_2 PF03703.21 (E=7e-20)
- (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_217795.1)
- Domains: Pfam-A via hmmscan --cut_ga — bPH_2 (PF03703.21)
- 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
COG3428 - Curated reference: UniProt P96883 (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 —
18 functional partner(s); context anchor
birA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003486|Rv3278c| MSYPENVLAAGEQVVLHRHPHWNRLIWPVVVLVLLTGLAAFGSGFVNSTPWQQIAKNVIHAVIWGIWLVIVGWLTLWPFLSWLTTHFVVTNRRVMFRHGVLTRSGIDIPLARINSVEFRDRIFERIFRTGTLIIESASQDPLEFYNIPRLREVHALLYHEVFDTLGSDESPS