Rv1975 Family assigned · medium auto-curated
H37Rv Rv1975 · MTBC0 mtbc0_002091 ·
221 aa · 2237169–2237834 (+) ·
RefSeq NP_216491.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | CAP domain-containing protein |
| Revised (this work) | CAP domain-containing protein. Pfam: CAP (PF00188.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53976
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | SCP domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Cysteine-rich secretory protein family |
| Orthologous group | COG2340 |
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 | 0.325 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
CAP | PF00188.33 | 5.9e-06 | 45–156 | Cysteine-rich secretory protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1973 (Mce associated membrane protein), high confidence from genomic context alone (score 962 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) |
|---|---|---|---|---|
Rv1973 |
Mce associated membrane protein | 963 | 962 ctx | neighborhood:739 coexpression:780 |
Rv1972 |
Mce associated membrane protein | 928 | 925 ctx | neighborhood:852 |
Rv1974 |
membrane protein | 983 | 882 ctx | neighborhood:863 textmining:868 |
Rv1971 mce3F |
Mce family protein Mce3F | 835 | 836 ctx | neighborhood:825 |
Rv1968 mce3C |
Mce family protein Mce3C | 835 | 835 ctx | neighborhood:825 |
Rv1964 yrbE3A |
integral membrane protein | 828 | 828 ctx | neighborhood:821 |
Rv1966 mce3A |
Mce family protein Mce3A | 826 | 707 ctx | neighborhood:658 textmining:434 |
Rv1967 mce3B |
Mce family protein Mce3B | 697 | 697 ctx | neighborhood:680 |
Rv1965 yrbE3B |
integral membrane protein | 687 | 687 ctx | neighborhood:671 |
Rv1970 lprM |
Mce family lipoprotein LprM | 685 | 685 ctx | neighborhood:666 |
Rv1969 mce3D |
Mce family protein Mce3D | 683 | 683 ctx | neighborhood:665 |
Rv1200 |
integral membrane transport protein | 546 | 539 | database:487 |
Rv1362c |
membrane protein | 480 | 457 | |
Rv1950c hyp |
hypothetical protein | 443 | 444 | coexpression:434 |
Rv3903c cpnT hyp |
hypothetical protein | 441 | 442 | coexpression:432 |
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: CAP domain-containing protein
- Pfam (hmmscan --cut_ga): CAP PF00188.33 (E=6e-06)
- (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_216491.1)
- Domains: Pfam-A via hmmscan --cut_ga — CAP (PF00188.33)
- 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
COG2340 - Curated reference: UniProt O53976 (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 —
28 functional partner(s); context anchor
Rv1973 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002091|Rv1975| MSRRASATCALSATTAVAIMAAPAARADDKRLNDGVVANVYTVQRQAGCTNDVTINPQLQLAAQWHTLDLLNNRHLNDDTGSDGSTPQDRAHAAGFRGKVAETVAINPAVAISGIELINQWYYNPAFFAIMSDCANTQIGVWSENSPDRTVVVAVYGQPDRPSAMPPRGAVTGPPSPVAAQENVPIDPSPDYDASDEIEYGINWLPWILRGVYPPPAMPPQ