Rv1972 Resolved · medium auto-curated
H37Rv Rv1972 · MTBC0 mtbc0_002088 ·
191 aa · 2235709–2236284 (+) ·
RefSeq NP_216488.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce associated membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | Mce associated membrane protein |
| Revised (this work) | Mce associated membrane 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 |
O53973
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved Mce associated membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2E5BU |
|---|---|
| KEGG orthology |
K18481
|
| KEGG modules |
M00670
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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: mce3F (Mce family protein Mce3F), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1971 mce3F |
Mce family protein Mce3F | 994 | 994 ctx | neighborhood:851 cooccurence:755 coexpression:860 |
Rv1968 mce3C |
Mce family protein Mce3C | 992 | 992 ctx | neighborhood:851 cooccurence:742 coexpression:808 |
Rv1973 |
Mce associated membrane protein | 991 | 992 ctx | neighborhood:800 cooccurence:762 coexpression:836 |
Rv1970 lprM |
Mce family lipoprotein LprM | 989 | 988 ctx | neighborhood:721 cooccurence:753 coexpression:838 |
Rv1966 mce3A |
Mce family protein Mce3A | 993 | 987 ctx | neighborhood:714 cooccurence:767 coexpression:820 textmining:547 |
Rv1969 mce3D |
Mce family protein Mce3D | 997 | 985 ctx | neighborhood:715 cooccurence:766 coexpression:799 textmining:803 |
Rv1967 mce3B |
Mce family protein Mce3B | 984 | 985 ctx | neighborhood:729 cooccurence:712 coexpression:822 |
Rv1965 yrbE3B |
integral membrane protein | 988 | 976 ctx | neighborhood:715 cooccurence:620 coexpression:793 textmining:548 |
Rv1974 |
membrane protein | 994 | 972 ctx | neighborhood:869 coexpression:797 textmining:803 |
Rv1964 yrbE3A |
integral membrane protein | 946 | 946 ctx | neighborhood:747 cooccurence:492 coexpression:615 |
Rv1975 hyp |
hypothetical protein | 928 | 925 ctx | neighborhood:852 |
Rv0492c |
GMC-type oxidoreductase | 765 | 756 | database:536 |
Rv3494c mce4F |
Mce family protein Mce4 | 755 | 756 ctx | cooccurence:754 |
Rv3492c |
Mce associated protein | 755 | 755 ctx | cooccurence:752 |
Rv1362c |
membrane protein | 752 | 753 ctx | cooccurence:719 |
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: Mce associated membrane protein
- MTBC0 PGAP product: Mce associated membrane 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_216488.1)
- 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
2E5BU - Curated reference: UniProt O53973 (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 —
295 functional partner(s); context anchor
mce3F - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002088|Rv1972| MSVAVDSDAEDDAVSEIAEAAGVSPAPAKPSMSAPRRMLLFGLVVVVALAVLLCCWGFRVQRARHAQDQRGHFLQAARQCALNLTTIDWRNAEADVRRILDGATGEFYNDFAQRSQPFVEVLRHAKASTVGTITEAGLQTQTADTAQALVAVSVQTSNAGEADPVPRAWRMRITVQRVGDRVKVSDVGFVP