Rv0175 Still unknown · low auto-curated
H37Rv Rv0175 · MTBC0 mtbc0_000188 ·
213 aa · 207162–207803 (+) ·
RefSeq NP_214689.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce associated membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| 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.
Curated reference (UniProt)
| UniProt |
O07419
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved Mce associated membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ANQH |
|---|---|
| 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 | 0.498 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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: Rv0178 (Mce associated membrane protein), high confidence from genomic context alone (score 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0178 |
Mce associated membrane protein | 992 | 971 ctx | neighborhood:881 coexpression:770 textmining:751 |
Rv0176 |
Mce associated transmembrane protein | 948 | 927 ctx | neighborhood:882 coexpression:409 |
Rv0177 |
Mce associated protein | 881 | 881 ctx | neighborhood:881 |
Rv0174 mce1F |
Mce family protein Mce1F | 887 | 839 ctx | neighborhood:829 |
Rv0171 mce1C |
Mce family protein Mce1C | 829 | 829 ctx | neighborhood:824 |
Rv0170 mce1B |
Mce family protein Mce1B | 858 | 828 ctx | neighborhood:820 |
Rv3671c marP |
serine protease | 783 | 783 | coexpression:783 |
Rv2190c ripC |
endopeptidase | 732 | 732 | coexpression:732 |
Rv0721 rpsE |
30S ribosomal protein S5 | 732 | 732 | coexpression:732 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 731 | 731 | coexpression:731 |
Rv0701 rplC |
50S ribosomal protein L3 | 729 | 729 | coexpression:729 |
Rv0167 yrbE1A |
membrane protein | 794 | 710 ctx | neighborhood:696 |
Rv0173 lprK |
Mce family lipoprotein LprK | 750 | 708 ctx | neighborhood:695 |
Rv0172 mce1D |
Mce family protein Mce1D | 779 | 692 ctx | neighborhood:674 |
Rv0168 yrbE1B |
membrane protein | 883 | 676 ctx | neighborhood:667 textmining:654 |
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: 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 NP_214689.3)
- 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
2ANQH - Curated reference: UniProt O07419 (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 —
39 functional partner(s); context anchor
Rv0178 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000188|Rv0175| MKAADSAESDAGADQTGPQVKAADSAESDAGELGEDACPEQALVERRPSRLRRGWLVGIAATLLALAGGLGAAGYFALRSHQESQSIAREDLAAIEAAKDCVAATQAPDAGAMSASMQKIIECGTGDFGAQASLYTSMLVEAYQAASVHVQVTDMRAAVERNNNDGSVDVLVALRVKVSNTDSDAHEVGYRLRVRMALDEGRYKIAKLDQVTK