Rv3773c Family assigned · low auto-curated
H37Rv Rv3773c · MTBC0 mtbc0_004000 ·
194 aa · 4242362–4242946 (-) ·
RefSeq NP_218290.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR03086 family metal-binding protein |
| Revised (this work) | TIGR03086 family metal-binding 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 |
P72040
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG3832 |
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 | 0.208 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 13.46% of strains (19551) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA21 (enoyl-CoA hydratase EchA21), high confidence from genomic context alone (score 792 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) |
|---|---|---|---|---|
Rv3774 echA21 |
enoyl-CoA hydratase EchA21 | 792 | 792 ctx | neighborhood:790 |
Rv0048c |
membrane protein | 744 | 744 ctx | cooccurence:744 |
Rv0736 rslA |
anti-sigma-L factor RslA | 711 | 712 ctx | cooccurence:701 |
Rv3779 |
transmembrane protein | 703 | 703 ctx | cooccurence:703 |
Rv3775 lipE |
lipase LipE | 644 | 644 ctx | neighborhood:640 |
Rv3435c |
transmembrane protein | 636 | 636 ctx | cooccurence:634 |
Rv3481c |
integral membrane protein | 570 | 571 ctx | cooccurence:568 |
Rv2423 hyp |
hypothetical protein | 567 | 568 ctx | cooccurence:565 |
Rv3202c adnA |
ATP-dependent DNA helicase | 567 | 567 ctx | cooccurence:553 |
Rv0738 hyp |
hypothetical protein | 556 | 556 ctx | cooccurence:552 |
Rv3830c |
TetR family transcriptional regulator | 545 | 545 ctx | cooccurence:534 |
Rv1353c |
HTH-type transcriptional regulator | 533 | 534 ctx | cooccurence:530 |
Rv0188 |
transmembrane protein | 531 | 532 ctx | cooccurence:525 |
Rv2067c hyp |
hypothetical protein | 522 | 523 ctx | cooccurence:516 |
Rv2248 hyp |
hypothetical protein | 509 | 510 ctx | cooccurence:507 |
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: TIGR03086 family metal-binding 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_218290.1)
- 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
COG3832 - Curated reference: UniProt P72040 (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 —
30 functional partner(s); context anchor
echA21 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004000|Rv3773c| MPPESRPGPDSPPTDELACAEAALQVLQQVLHTIGRQDKAKQTPCPGYDVKKLTEHLLNSIMVLGGMVGAEFSLRADIDSVERLVSGAARSALDAWHRHGLEGDVSLGPGSMSAKVAVSVFSVEFLVHAWDYAVAVGSELKAADSLAEYVLELARKLIKPEERSVAGFNEPVDVPEDGGALERLIAFTGRNPAR