Rv0176 Family assigned · medium auto-curated
H37Rv Rv0176 · MTBC0 mtbc0_000189 ·
322 aa · 207800–208768 (+) ·
RefSeq NP_214690.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce associated transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | RDD family protein |
| Revised (this work) | RDD family protein. Pfam: RDD (PF06271.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07420
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved Mce associated transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane protein domain |
| Orthologous group | COG1714 |
| 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) pseudogene candidate
| pN/pS | 2.227 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 29.63% of strains (43030) · clonal |
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 |
|---|---|---|---|---|
RDD | PF06271.19 | 1.9e-14 | 21–144 | RDD family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0175 (Mce associated membrane protein), high confidence from genomic context alone (score 927 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0175 |
Mce associated membrane protein | 948 | 927 ctx | neighborhood:882 coexpression:409 |
Rv0178 |
Mce associated membrane protein | 915 | 887 ctx | neighborhood:801 coexpression:455 |
Rv0174 mce1F |
Mce family protein Mce1F | 926 | 845 ctx | neighborhood:713 cooccurence:408 textmining:543 |
Rv0172 mce1D |
Mce family protein Mce1D | 877 | 836 ctx | neighborhood:666 cooccurence:500 |
Rv0171 mce1C |
Mce family protein Mce1C | 873 | 829 ctx | neighborhood:659 cooccurence:499 |
Rv0169 mce1A |
Mce family protein Mce1A | 850 | 806 ctx | neighborhood:659 cooccurence:428 |
Rv0177 |
Mce associated protein | 952 | 803 ctx | neighborhood:801 textmining:767 |
Rv1797 eccE5 |
ESX-5 type VII secretion system protein EccE | 797 | 797 | coexpression:797 |
Rv0173 lprK |
Mce family lipoprotein LprK | 827 | 790 ctx | neighborhood:695 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 780 | 780 | coexpression:780 |
Rv0170 mce1B |
Mce family protein Mce1B | 864 | 731 ctx | neighborhood:659 textmining:516 |
Rv0167 yrbE1A |
membrane protein | 743 | 675 ctx | neighborhood:657 |
Rv0168 yrbE1B |
membrane protein | 870 | 670 ctx | neighborhood:665 textmining:624 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 659 | 659 | coexpression:651 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 657 | 658 ctx | cooccurence:642 |
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 transmembrane protein
- MTBC0 PGAP product: RDD family protein
- Pfam (hmmscan --cut_ga): RDD PF06271.19 (E=2e-14)
- (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_214690.1)
- Domains: Pfam-A via hmmscan --cut_ga — RDD (PF06271.19)
- 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
COG1714 - Curated reference: UniProt O07420 (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 —
72 functional partner(s); context anchor
Rv0175 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000189|Rv0176| MTVVVEKTPTTLPQATPNGAAPWHVRAGAFAIDVLPGLAVAATMALTALTVPPGSAWRWLCACLLGLTILLLAVNRLLLPTITGWSLGRALTGIRVVRRDGSAIGPWRLLVRDLAHLVDTLSLFVGWLWPLWDSRRRTFADLLLRTEVRRVEPVQRPAVIRRLTAAVALAAAGACASATAVGAAVVYVNEWQTDHTRAQLATRGPKLVVDVLSYDPETVQRDFERARSLATDRYRPQLSIQQDSVRESGPVRNQYWVTDSAVLSATPAQATMLLFMQGERGTPPNQRYISATVRAIFQKSRGQWRLDDLAVVMKPRQPTGEK