Rv3604c Still unknown · low auto-curated
H37Rv Rv3604c · MTBC0 mtbc0_003822 ·
397 aa · 4070007–4071200 (-) ·
RefSeq NP_218121.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF6779 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF6779. 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 |
O06278
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein rich in alanine and arginine and proline |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2F5G1 |
|---|
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 | 2.25 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 12 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 |
|---|---|---|---|---|
DUF6779 | PF20570.4 | 1.9e-28 | 45–150 | Domain of unknown function (DUF6779) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0955 (integral membrane protein), high confidence from genomic context alone (score 776 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3605c hyp |
hypothetical protein | 780 | 780 ctx | neighborhood:734 |
Rv0955 |
integral membrane protein | 776 | 776 ctx | cooccurence:773 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 769 | 770 ctx | cooccurence:769 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 769 | 769 ctx | cooccurence:754 |
Rv0804 hyp |
hypothetical protein | 747 | 747 ctx | cooccurence:746 |
Rv0256c PPE2 |
PPE family protein PPE2 | 745 | 745 ctx | cooccurence:744 |
Rv3602c panC |
pantothenate synthetase | 741 | 741 ctx | neighborhood:740 |
Rv3600c coaX |
type III pantothenate kinase | 741 | 741 ctx | neighborhood:740 |
Rv3603c hyp |
hypothetical protein | 740 | 740 ctx | neighborhood:740 |
Rv3601c panD |
aspartate 1-decarboxylase | 740 | 740 ctx | neighborhood:740 |
Rv3607c folB |
dihydroneopterin aldolase | 738 | 738 ctx | neighborhood:734 |
Rv3606c folK |
2-amino-4-hydroxy-6-hydroxymethyldihydropteridinepyrophosphokinase | 737 | 737 ctx | neighborhood:734 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 737 | 737 ctx | cooccurence:737 |
Rv3608c folP1 |
dihydropteroate synthase | 736 | 737 ctx | neighborhood:734 |
Rv3609c folE |
GTP cyclohydrolase I | 735 | 736 ctx | neighborhood:734 |
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: transmembrane protein
- MTBC0 PGAP product: DUF6779 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF6779 PF20570.4 (E=2e-28)
- (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_218121.2)
- Domains: Pfam-A via hmmscan --cut_ga — DUF6779 (PF20570.4)
- 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
2F5G1 - Curated reference: UniProt O06278 (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 —
112 functional partner(s); context anchor
Rv0955 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003822|Rv3604c| MTVLSRGARVRRGGRRPGWVLLTALLVLAIGASSALVFTDRVELLKLAVLLALWAAVAGAFVSVLYRRQSDVDQARVRDLKLVYDLQLDREISARREYELTLESQLRRELASELRAPAADEVAALRAELAALRTSLEILFDADLEHRPALGTVEKEARAARALDGESPPADWVSSDRVMAVRGGDGASRTDEASIIDVPEVGVPPVSGGPRHYEAPPPPQPEPLFEPRHRPPPLPPQQERPVWQPVTSHGQWLPAETPGSQWASVEPETTPAAPPPGRRRRARHASPADQAYNPPAYVELAAQYGESGRRSRHSAEHRDHDIGGSGAGTGERPPSPPMAPPPPAEPTRRHRTADTPPDDSGGLHARDPLTGGQSVADLMARLQVESTGGGRRRRRGE