Rv1638A Still unknown · low auto-curated
H37Rv Rv1638A · MTBC0 - ·
85 aa · 1846716–1846973 (-) ·
RefSeq YP_177650.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L7N673
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phage shock protein A |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionT Signal transduction mechanisms
|
|---|---|
| eggNOG description | COG1842 Phage shock protein A (IM30), suppresses sigma54-dependent transcription |
| Orthologous group | COG1842 |
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 | 0.328 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2446c (integral membrane protein), high confidence from genomic context alone (score 709 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) |
|---|---|---|---|---|
Rv1639c hyp |
hypothetical protein | 946 | 947 ctx | neighborhood:741 coexpression:802 |
Rv2468c hyp |
hypothetical protein | 816 | 812 ctx | cooccurence:745 |
Rv3205c hyp |
hypothetical protein | 737 | 737 ctx | cooccurence:737 |
Rv2474c hyp |
hypothetical protein | 733 | 734 ctx | cooccurence:732 |
Rv1083 hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:732 |
Rv2700 cei hyp |
hypothetical protein | 727 | 727 ctx | cooccurence:727 |
Rv3605c hyp |
hypothetical protein | 714 | 714 ctx | cooccurence:714 |
Rv0358 hyp |
hypothetical protein | 709 | 710 ctx | cooccurence:708 |
Rv2446c |
integral membrane protein | 709 | 709 ctx | cooccurence:709 |
Rv1109c hyp |
hypothetical protein | 704 | 704 ctx | cooccurence:700 |
Rv1209 hyp |
hypothetical protein | 705 | 701 ctx | cooccurence:696 |
Rv2091c |
membrane protein | 697 | 697 ctx | cooccurence:688 |
Rv2179c |
3'-5' exoribonuclease | 682 | 682 ctx | cooccurence:681 |
Rv0948c |
chorismate mutase | 672 | 673 ctx | cooccurence:668 |
Rv3212 hyp |
hypothetical protein | 668 | 668 ctx | cooccurence:667 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical 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 YP_177650.1)
- 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
COG1842 - Curated reference: UniProt L7N673 (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 —
92 functional partner(s); context anchor
Rv2446c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1638A| MPDEPTPPEATTPNSESDPRYDSAGVPTFESVREKIETRYGTALGATELDAESPQGRRLEDQYAQRQRAAAERLAQIRESMHTDE