Rv1376 Family assigned · medium auto-curated
H37Rv Rv1376 · MTBC0 mtbc0_001477 ·
497 aa · 1558492–1559985 (+) ·
RefSeq NP_215892.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TfuA-like protein |
| Revised (this work) | TfuA-like protein. Pfam: TfuA (PF07812.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71804
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | TfuA-like core domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | TfuA-like protein |
| Orthologous group | COG3482 |
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 | 0.855 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 12 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 |
|---|---|---|---|---|
TfuA | PF07812.19 | 5.9e-43 | 53–172 | TfuA-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS28 (PE-PGRS family protein PE_PGRS28), medium confidence from genomic context alone (score 688 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) |
|---|---|---|---|---|
Rv1375 hyp |
hypothetical protein | 988 | 986 ctx | neighborhood:882 cooccurence:774 coexpression:533 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 688 | 688 ctx | cooccurence:688 |
Rv3347c PPE55 |
PPE family protein PPE55 | 675 | 676 ctx | cooccurence:674 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 670 | 670 ctx | cooccurence:670 |
Rv3350c PPE56 |
PPE family protein PPE56 | 669 | 669 ctx | cooccurence:668 |
Rv0355c PPE8 |
PPE family protein PPE8 | 668 | 668 ctx | cooccurence:667 |
Rv2337c hyp |
hypothetical protein | 648 | 649 ctx | cooccurence:636 |
Rv2209 |
integral membrane protein | 648 | 648 ctx | cooccurence:646 |
Rv3343c PPE54 |
PPE family protein PPE54 | 641 | 641 ctx | cooccurence:639 |
Rv1917c PPE34 |
PPE family protein PPE34 | 637 | 637 ctx | cooccurence:635 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 634 | 634 ctx | cooccurence:634 |
Rv1004c |
membrane protein | 628 | 628 ctx | cooccurence:628 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 626 | 626 ctx | cooccurence:621 |
Rv0304c PPE5 |
PPE family protein PPE5 | 612 | 612 ctx | cooccurence:612 |
Rv2293c hyp |
hypothetical protein | 588 | 589 ctx | cooccurence:586 |
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: TfuA-like protein
- Pfam (hmmscan --cut_ga): TfuA PF07812.19 (E=6e-43)
- (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_215892.1)
- Domains: Pfam-A via hmmscan --cut_ga — TfuA (PF07812.19)
- 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
COG3482 - Curated reference: UniProt P71804 (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 —
65 functional partner(s); context anchor
PE_PGRS28 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001477|Rv1376| MTACGRIVVTAGPTISAADIRSVVPDAEVAPPIAFGQALSYDLRSGDTLLIVDGLFFQQPSVRHKELLTLMADGVRVVGSSSMGALRAAELHPFGMEGYGWVFESYRDGVLEADDEVGVVHGDADDGYPVFVDALVNMRHTLARAVATGVVCSELAERIIETARATPFTMRTWARLLSEVGAPDQRGLAAQLRSLRVDVKHADALLALRQLGQRPRVEPLRPGPPPTVWSRRWRQRWAPPTSVAASADHGESFVDVTDLEVLSFLSVSSVDYWAYRPALQQVAAWYWTLKHPEQSGSVGERAARAVAEVASEGYGRALEFIAYRYALATGIIDETGFPEAVAAHWLTTEERHGLGNDPISISARVITRTLFVVRLLPAIDHFLDLLRKDSRLPRWRAMAAHALCKRDDLARQKPHLNLGRPDPTQLKRLFGARWGTQVNRIELARRGLMTEDAFYAAATPFAVAAVDDQLPRIEVGTLGPAPLSADVPERHFDFGSV