Rv2411c Resolved · high auto-curated
H37Rv Rv2411c · MTBC0 mtbc0_002567 ·
551 aa · 2732578–2734233 (-) ·
RefSeq NP_216927.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | circularly permuted type 2 ATP-grasp protein |
| Revised (this work) | Circularly permuted type 2 ATP-grasp protein. Pfam: CP_ATPgrasp_1 (PF04174.19), CP_ATPgrasp_2 (PF14403.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLA9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2411c |
UniProt still lists this protein as Uncharacterized protein Rv2411c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | gcs2 |
| eggNOG description | Circularly permuted ATP-grasp type 2 |
| Orthologous group | COG2308 |
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 | 0.34 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 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 |
|---|---|---|---|---|
CP_ATPgrasp_1 | PF04174.19 | 1.5e-169 | 100–431 | A circularly permuted ATPgrasp |
CP_ATPgrasp_2 | PF14403.12 | 9.6e-163 | 100–476 | Circularly permuted ATP-grasp type 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0433 (carboxylate-amine ligase), high confidence from genomic context alone (score 876 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) |
|---|---|---|---|---|
Rv2410c hyp |
hypothetical protein | 997 | 998 ctx | neighborhood:882 cooccurence:774 coexpression:885 |
Rv2409c hyp |
hypothetical protein | 993 | 993 ctx | neighborhood:882 cooccurence:774 coexpression:754 |
Rv0433 |
carboxylate-amine ligase | 876 | 876 ctx | fusion:868 |
Rv2566 hyp |
hypothetical protein | 852 | 847 ctx | neighborhood:526 cooccurence:660 |
Rv2569c hyp |
hypothetical protein | 807 | 801 ctx | cooccurence:774 |
Rv2412 rpsT |
30S ribosomal protein S20 | 632 | 632 ctx | neighborhood:630 |
Rv2567 hyp |
hypothetical protein | 520 | 498 | |
Rv2568c hyp |
hypothetical protein | 430 | 430 |
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: circularly permuted type 2 ATP-grasp protein
- Pfam (hmmscan --cut_ga): CP_ATPgrasp_1 PF04174.19 (E=1e-169), CP_ATPgrasp_2 PF14403.12 (E=1e-162)
- (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_216927.1)
- Domains: Pfam-A via hmmscan --cut_ga — CP_ATPgrasp_1 (PF04174.19), CP_ATPgrasp_2 (PF14403.12)
- 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
COG2308 - Curated reference: UniProt P9WLA9 (SwissProt, reviewed; 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 —
8 functional partner(s); context anchor
Rv0433 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002567|Rv2411c| MRRVSLPNQLNETRRRSPTRGERIFGGYNTSDVYAMAFDEMFDAQGIVRGPYKGIYAELAPSDASELKARADALGRAFIDQGITFSLSGQERPFPLDLVPRVISAPEWTRLERGITQRVKALECYLDDIYGDQEILRDGVIPRRLVTSCEHFHRQAVGIVPPNGVRIHVAGIDLIRDHRGDFRVLEDNLRSPSGVSYVMENRRTMARVFPNLFATHRVRAVDDYASHLLRALRNSAATNEADPTVVVLTPGVYNSAYFEHSLLARQMGVELVEGRDLFCRDNQVYMRTTEGERQVDVIYRRIDDAFLDPLQFRADSVLGVAGLVNAARAGNVVLSSAIGNGVGDDKLVYTYVPTMIEYYLHEKPLLANVETLRCWLDDEREEVLDRIRELVLKPVEGSGGYGIVFGPEASQAELAAVSQKIRDDPRSWIAQPMMELSTVPTRIEGTLAPRYVDLRPFAVNDGNEVWVLPGGLTRVALVEGSRVVNSSQGGGSKDTWVLAPRASAAARELGAAQIVRSLPQPLCDPTVDASGYEPHDQQPQQQQQQQQQAFH