Rv0390 Family assigned · medium auto-curated
H37Rv Rv0390 · MTBC0 mtbc0_000409 ·
140 aa · 472955–473377 (+) ·
RefSeq NP_214904.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | rhodanese-like domain-containing protein |
| Revised (this work) | Rhodanese-like domain-containing protein. Pfam: Rhodanese (PF00581.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95198
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | sulfurtransferase |
| Orthologous group | COG0607 |
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 | 0.108 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
Rhodanese | PF00581.26 | 2.8e-08 | 9–117 | Rhodanese-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: metZ (O-succinylhomoserine sulfhydrylase), high confidence from genomic context alone (score 921 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) |
|---|---|---|---|---|
Rv0391 metZ |
O-succinylhomoserine sulfhydrylase | 925 | 921 ctx | neighborhood:882 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 882 | 882 ctx | neighborhood:881 |
Rv3846 sodA |
superoxide dismutase | 634 | 611 | experimental:573 |
Rv2367c ybeY |
endoribonuclease | 582 | 582 | experimental:573 |
Rv3456c rplQ |
50S ribosomal protein L17 | 516 | 516 | experimental:466 |
Rv3443c rplM |
50S ribosomal protein L13 | 510 | 510 | experimental:453 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 506 | 506 | experimental:476 |
Rv2442c rplU |
50S ribosomal protein L21 | 500 | 501 | experimental:466 |
Rv0640 rplK |
50S ribosomal protein L11 | 491 | 492 | experimental:461 |
Rv0701 rplC |
50S ribosomal protein L3 | 491 | 491 | experimental:450 |
Rv0715 rplX |
50S ribosomal protein L24 | 485 | 486 | experimental:453 |
Rv0723 rplO |
50S ribosomal protein L15 | 481 | 482 | experimental:453 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 465 | 441 | |
Rv2582 ppiB |
peptidyl-prolyl cis-trans isomerase B | 437 | 438 | experimental:426 |
Rv0009 ppiA |
iron-regulated peptidyl-prolyl cis-trans isomerase PpiA | 436 | 437 | experimental:426 |
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: rhodanese-like domain-containing protein
- Pfam (hmmscan --cut_ga): Rhodanese PF00581.26 (E=3e-08)
- (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_214904.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rhodanese (PF00581.26)
- 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
COG0607 - Curated reference: UniProt P95198 (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 —
32 functional partner(s); context anchor
metZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000409|Rv0390| MSYAGDITPLQAWEMLSDNPRAVLVDVRCEAEWRFVGVPDLSSLGREVVYVEWATSDGTHNDNFLAELRDRIPADADQHERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFEGHLDAEGHRGATGWRAVGLPWRQG