Rv1903 Family assigned · medium auto-curated
H37Rv Rv1903 · MTBC0 mtbc0_002018 ·
134 aa · 2168474–2168878 (+) ·
RefSeq NP_216419.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | phage holin family protein |
| Revised (this work) | Phage holin family protein. Pfam: Phage_holin_4_2 (PF04020.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07729
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG1950 |
| KEGG orthology |
K08972
|
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 | 0.083 · 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 |
|---|---|---|---|---|
Phage_holin_4_2 | PF04020.19 | 1.9e-27 | 4–119 | Mycobacterial 4 TMS phage holin, superfamily IV |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nanT (sialic acid-transport integral membrane protein NanT), medium confidence from genomic context alone (score 620 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1902c nanT |
sialic acid-transport integral membrane protein NanT | 620 | 620 ctx | neighborhood:612 |
Rv1904 hyp |
hypothetical protein | 839 | 558 ctx | neighborhood:553 textmining:652 |
Rv0944 fpg2 |
formamidopyrimidine-DNA glycosylase | 556 | 557 ctx | neighborhood:544 |
Rv0945 |
oxidoreductase | 546 | 547 ctx | neighborhood:544 |
Rv1001 arcA |
arginine deiminase | 409 | 409 | coexpression:409 |
Rv1912c fadB5 |
oxidoreductase FadB | 812 | 83 | textmining:804 |
Rv1905c aao |
D-amino acid oxidase | 806 | 58 | textmining:803 |
Rv1906c hyp |
hypothetical protein | 870 | 47 | textmining:870 |
Rv1910c hyp |
hypothetical protein | 870 | 45 | textmining:870 |
Rv1911c lppC |
lipoprotein LppC | 808 | 44 | textmining:808 |
Rv1907c hyp |
hypothetical protein | 807 | 41 | textmining:807 |
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: membrane protein
- MTBC0 PGAP product: phage holin family protein
- Pfam (hmmscan --cut_ga): Phage_holin_4_2 PF04020.19 (E=2e-27)
- (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_216419.1)
- Domains: Pfam-A via hmmscan --cut_ga — Phage_holin_4_2 (PF04020.19)
- 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
COG1950 - Curated reference: UniProt O07729 (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 —
11 functional partner(s); context anchor
nanT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002018|Rv1903| MVPFLMRAAVTGFALWVVTLFVPGMRFAGGDTTLQRVAIIFVVAVIFGLVNAFIKPIVQILSIPLYILTLGLFHVVVNASMLWLTAWITEHTTHWGLQIDHFWWTAIWAAILLSIVSWILSLLARDFRRVTRAH