Rv1004c Still unknown · low auto-curated
H37Rv Rv1004c · MTBC0 mtbc0_001079 ·
419 aa · 1128225–1129484 (-) ·
RefSeq NP_215520.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 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 |
O05589
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2AV97 |
|---|
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 | 0.456 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.69% of strains (2454) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS36 (PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub), high confidence from genomic context alone (score 867 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0702 rplD |
50S ribosomal protein L4 | 928 | 920 | experimental:827 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 925 | 916 | experimental:829 |
Rv2890c rpsB |
30S ribosomal protein S2 | 916 | 907 | experimental:802 |
Rv0651 rplJ |
50S ribosomal protein L10 | 904 | 900 | experimental:826 |
Rv0715 rplX |
50S ribosomal protein L24 | 905 | 899 | experimental:828 |
Rv0703 rplW |
50S ribosomal protein L23 | 906 | 894 | experimental:829 |
Rv0718 rpsH |
30S ribosomal protein S8 | 904 | 892 | experimental:793 |
Rv0723 rplO |
50S ribosomal protein L15 | 893 | 879 | experimental:826 |
Rv0721 rpsE |
30S ribosomal protein S5 | 892 | 878 | coexpression:402 experimental:801 |
Rv0719 rplF |
50S ribosomal protein L6 | 879 | 871 | experimental:827 |
Rv0701 rplC |
50S ribosomal protein L3 | 883 | 869 | experimental:828 |
Rv3443c rplM |
50S ribosomal protein L13 | 881 | 867 | experimental:827 |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 873 | 867 ctx | cooccurence:761 experimental:463 |
Rv0714 rplN |
50S ribosomal protein L14 | 877 | 863 | experimental:827 |
Rv0716 rplE |
50S ribosomal protein L5 | 874 | 863 | experimental:825 |
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: 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_215520.1)
- 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
2AV97 - Curated reference: UniProt O05589 (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 —
244 functional partner(s); context anchor
PE_PGRS36 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001079|Rv1004c| MSISCRVREGFVMRLAIVGTAAAAAIGGTLAVAPLTLSTPERVAGGTCSAGQQCDRLAAVLMPDTATPSGPAAAEHAVPAPFEPVADTIAPGLVPRPGVPAAAAVPRVGPPAVPGLPNIPGAAGPALPPPPALPNLAAPSVPGVGIPGIGIPGIGIPGIGIPGVPDPITGVNTAAAVVNGVLGVGGTAAGVVTASAVAVTYLVLAVNALESSGILPTARGTASTVASLLLPGAQSAAAALPAVGLPALPGVTPASLLAMAAAAGLPGVGFPSLPGVSPTDLMAMAAAAGLPTSLPGLAGMSPAELTALVAGGLPMLAAAGLPAGLAGVDPATLAAALPALAAGGLPPGLPALPGVDPAALAAALPALAAGLPALPAGLPPLPAVPALPAPPPLPGPPPLPALPSRLCTPGFGPIGVCIP