glnX Resolved · high auto-curated
H37Rv Rv0412c · MTBC0 mtbc0_000432 ·
439 aa · 501665–502984 (-) ·
RefSeq NP_214926.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | protein kinase G-activating protein GlnX |
| Revised (this work) | Protein kinase G-activating protein GlnX. Pfam: Sensor_actino (PF28326.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96258
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | phosphoserine phosphatase activity |
| Orthologous group | COG5278 |
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 | 0.498 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
Sensor_actino | PF28326.1 | 1.8e-43 | 65–199 | Actinobacterial sensor domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pknG (serine/threonine-protein kinase PknG), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0410c pknG |
serine/threonine-protein kinase PknG | 994 | 994 ctx | neighborhood:881 cooccurence:746 coexpression:815 |
Rv0411c glnH |
glutamine-binding lipoprotein GlnH | 994 | 990 ctx | neighborhood:881 cooccurence:451 coexpression:860 textmining:489 |
Rv0129c fbpC |
diacylglycerol acyltransferase/mycolyltransferase Ag85C | 683 | 671 ctx | cooccurence:445 coexpression:414 |
Rv1886c fbpB |
diacylglycerol acyltransferase/mycolyltransferase Ag85B | 665 | 652 ctx | cooccurence:420 coexpression:407 |
Rv0413 mutT3 |
8-oxo-dGTP diphosphatase | 640 | 640 ctx | neighborhood:635 |
Rv3804c fbpA |
diacylglycerol acyltransferase/mycolyltransferase Ag85A | 645 | 631 | coexpression:410 |
Rv2743c hyp |
hypothetical protein | 630 | 631 ctx | cooccurence:627 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 618 | 618 ctx | cooccurence:607 |
Rv0383c ttfA hyp |
hypothetical protein | 615 | 615 ctx | cooccurence:603 |
Rv0996 |
transmembrane protein | 594 | 594 ctx | cooccurence:590 |
Rv0774c hyp |
hypothetical protein | 608 | 593 | coexpression:407 |
Rv3803c fbpD |
MPT51/MPB51 antigen | 601 | 586 | coexpression:407 |
Rv3655c hyp |
hypothetical protein | 570 | 570 ctx | cooccurence:570 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 569 | 570 ctx | cooccurence:567 |
Rv2695 hyp |
hypothetical protein | 553 | 554 ctx | cooccurence:544 |
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: protein kinase G-activating protein GlnX
- Pfam (hmmscan --cut_ga): Sensor_actino PF28326.1 (E=2e-43)
- (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_214926.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sensor_actino (PF28326.1)
- 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
COG5278 - Curated reference: UniProt P96258 (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 —
56 functional partner(s); context anchor
pknG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000432|Rv0412c|glnX MTVELAHPSTEPLGSRSPAEPAHPRRWFISTTPGRIMTIGIVLAALGVASAFATSTTIEHRQQVLTAVLDHTEPLSFAAGRLYTTLSVADAAAATAFIAQAEPGGVRLRYEQAITDASVAVTRASSGLTDESLVQLLGRINAELAVYTGLVEIARANNRAGNPVGSSYLSEASGLMQSTILPDAQRLYQATSARVDRETTASTQIPAPVILVVATTVVFGAFAHRWLARRTRRRINPGLVVGALGILVMVVWVGTALTISTTASRSAKDTAAESLKTITNLAITAQQARADETLSLIRRGDEEVRKQAFYQRIDAMQRQLNDYMARRHAVDKPDLQGADQLLVRWRQANDRINSYISVGNYRAATQVALGKGEDDATPAFDKLDEALTKAMGQSRTQLRHDILNAHRGLAGAQVGGVVLSLGAAIAVALGLWPRLKEYR