Rv1057 Family assigned · low auto-curated
H37Rv Rv1057 · MTBC0 mtbc0_001137 ·
393 aa · 1186735–1187916 (+) ·
RefSeq NP_215573.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YncE family protein |
| Revised (this work) | YncE family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53405
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Seven-bladed beta-propeller protein Rv1057 |
| Curated function | May play an important role in host-pathogen interactions and in ESAT-6 secretion. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | amine dehydrogenase activity |
| Orthologous group | COG3391 |
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 | 1.424 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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: fadD14 (fatty-acid--CoA ligase FadD14), high confidence from genomic context alone (score 774 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) |
|---|---|---|---|---|
Rv1058 fadD14 |
fatty-acid--CoA ligase FadD14 | 774 | 774 ctx | neighborhood:768 |
Rv0978c PE_PGRS17 |
PE-PGRS family protein PE_PGRS17 | 750 | 750 ctx | cooccurence:750 |
Rv0980c PE_PGRS18 |
PE-PGRS family protein PE_PGRS18 | 743 | 743 ctx | cooccurence:743 |
Rv2383c mbtB |
phenyloxazoline synthase | 710 | 710 | coexpression:658 |
Rv1061 hyp |
hypothetical protein | 709 | 709 ctx | neighborhood:656 |
Rv1062 hyp |
hypothetical protein | 706 | 706 ctx | neighborhood:662 |
Rv3604c |
transmembrane protein | 681 | 681 ctx | cooccurence:681 |
Rv2574 hyp |
hypothetical protein | 663 | 664 ctx | cooccurence:660 |
Rv2633c hyp |
hypothetical protein | 653 | 653 ctx | cooccurence:653 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 670 | 650 | experimental:622 |
Rv0955 |
integral membrane protein | 633 | 633 ctx | cooccurence:632 |
Rv1059 hyp |
hypothetical protein | 630 | 630 ctx | neighborhood:548 |
Rv1157c hyp |
hypothetical protein | 609 | 610 | coexpression:419 |
Rv0804 hyp |
hypothetical protein | 588 | 588 ctx | cooccurence:587 |
Rv3896c hyp |
hypothetical protein | 585 | 586 ctx | cooccurence:584 |
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: YncE family protein
- (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_215573.1)
- 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
COG3391 - Curated reference: UniProt O53405 (SwissProt, reviewed; 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 —
68 functional partner(s); context anchor
fadD14 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001137|Rv1057| MSVMNGREVARESRDAQVFEFGTAPGSAVVKIPVQGGPIGGIAISRDGSLLVVTNNGTDTVSVVGTDTCRVTQTVTSVNEPFAIAMGNAEANRAYVSTVSSAYDAIAVIDVATNTVLGTHPLALSVSDLTLSPDDKYLYVSRNGTRGADVAVLDTTTGALIDVVDVSQAPGTTTQCVRMSPDGSVLYVGANGPSGGLLVVITTRAQSDGGRIGSRSRSRQKSSKPRGNQAAAGLRVVATIDIGSSVRDVALSPDGAIAYVASCGSDFGAVVDVIDTRTHQITSSRAISEIGGLVTRVSVSGDADRAYLVSEDRVTVLCTRTHDVIGTIRTGQPSCVVESPDGKYLYIADYSGTITRTAVASTIVSGTEQLALQRRGSMQWFSPELQQYAPALA