Rv3434c Family assigned · medium auto-curated
H37Rv Rv3434c · MTBC0 mtbc0_003653 ·
237 aa · 3879101–3879814 (-) ·
RefSeq NP_217951.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | rhomboid-like protein |
| Revised (this work) | Rhomboid-like protein. Pfam: Rhomboid_2 (PF20401.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YC44
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2CJZS |
|---|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 2.29% of strains (3325) · 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 |
|---|---|---|---|---|
Rhomboid_2 | PF20401.4 | 4.9e-65 | 20–214 | Rhomboid-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3435c (transmembrane protein), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3435c |
transmembrane protein | 903 | 884 ctx | neighborhood:832 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 945 | 883 ctx | neighborhood:882 textmining:550 |
Rv3432c gadB |
glutamate decarboxylase GadB | 830 | 831 ctx | neighborhood:829 |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 895 | 732 ctx | neighborhood:730 textmining:625 |
Rv0180c |
transmembrane protein | 706 | 707 ctx | cooccurence:705 |
Rv2423 hyp |
hypothetical protein | 669 | 669 ctx | cooccurence:669 |
Rv3166c hyp |
hypothetical protein | 664 | 664 ctx | cooccurence:662 |
Rv2638 hyp |
hypothetical protein | 652 | 653 ctx | cooccurence:650 |
Rv2729c |
integral membrane protein | 624 | 624 ctx | cooccurence:624 |
Rv3899c hyp |
hypothetical protein | 599 | 599 ctx | cooccurence:597 |
Rv2963 |
integral membrane protein | 568 | 568 ctx | cooccurence:568 |
Rv0090 |
membrane protein | 535 | 535 ctx | cooccurence:535 |
Rv2042c hyp |
hypothetical protein | 525 | 526 ctx | cooccurence:515 |
Rv1635c |
mannosyltransferase | 517 | 518 ctx | cooccurence:516 |
Rv2777c hyp |
hypothetical protein | 499 | 499 ctx | cooccurence:478 |
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: rhomboid-like protein
- Pfam (hmmscan --cut_ga): Rhomboid_2 PF20401.4 (E=5e-65)
- (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_217951.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rhomboid_2 (PF20401.4)
- 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
2CJZS - Curated reference: UniProt I6YC44 (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 —
54 functional partner(s); context anchor
Rv3435c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003653|Rv3434c| MADASVVARLRSWALAVWHFVSNAPLTYAWLVVLVITTIIQNNLTGSQLHFVLLHRSTNIAELGRDPLEVLFSSLLWIDGRNLEPYLLLFTLFLAPAEHWLGHLRWLTVGLTAHIGATYLSEGLLYLAIQHRDASERMVHARDIGVSYFLVGVMAVLTYHIAKPWRWGYLGVLLVIFGFPLIAMDKAELDFTAVGHFASILIGLLFYPMARERDGRLWNPARIKSLLHRRGTRGRRA