Rv2205c Resolved · high auto-curated
H37Rv Rv2205c · MTBC0 mtbc0_002341 ·
358 aa · 2495544–2496620 (-) ·
RefSeq NP_216721.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | glycerate kinase |
| Revised (this work) | Glycerate kinase. Pfam: Gly_kinase (PF02595.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMT7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2205c |
UniProt still lists this protein as Uncharacterized protein Rv2205c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | glxK |
| eggNOG description | Belongs to the glycerate kinase type-1 family |
| Orthologous group | COG1929 |
| EC number |
EC 2.7.1.165
|
| KEGG orthology |
K00865
|
| KEGG pathways |
map00260, map00561, map00630, map01100, map01120, map01130
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.666 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.11% of strains (1608) · 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 |
|---|---|---|---|---|
Gly_kinase | PF02595.21 | 2.2e-54 | 155–348 | Glycerate kinase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2206 (transmembrane protein), high confidence from genomic context alone (score 770 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) |
|---|---|---|---|---|
Rv0768 aldA |
aldehyde dehydrogenase AldA | 906 | 903 | database:900 |
Rv0147 |
aldehyde dehydrogenase | 906 | 903 | database:900 |
Rv0223c |
aldehyde dehydrogenase | 906 | 903 | database:900 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 906 | 902 | database:900 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 905 | 900 | database:900 |
Rv2204c hyp |
hypothetical protein | 774 | 774 ctx | neighborhood:773 |
Rv2206 |
transmembrane protein | 770 | 770 ctx | neighborhood:769 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 721 | 711 ctx | neighborhood:709 |
Rv2207 cobT |
nicotinate-nucleotide-dimethylbenzimidazol phosphoribosyltransferase | 710 | 710 ctx | neighborhood:709 |
Rv3752c tadA |
cytidine/deoxycytidylate deaminase | 630 | 630 ctx | fusion:610 |
Rv1088 PE9 |
PE family protein PE9 | 414 | 415 | coexpression:415 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 418 | 41 | textmining:418 |
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: glycerate kinase
- Pfam (hmmscan --cut_ga): Gly_kinase PF02595.21 (E=2e-54)
- (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_216721.2)
- Domains: Pfam-A via hmmscan --cut_ga — Gly_kinase (PF02595.21)
- 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
COG1929 - Curated reference: UniProt P9WMT7 (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 —
12 functional partner(s); context anchor
Rv2206 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002341|Rv2205c| MRVLVAPDCYGDSLSAVEAAAAIATGWTRSRPGDSFIVAPQSDGGPGFVEVLGSRLGETRRLRVCGPLNTVVNAAWVFDPGSATAYLECAQACGLGLLGGPPTPETALAAHSKGVGQLIAAALRAGAARIVVGLGGSACTDGGKGMIAELGGLDAARRQLADVEVIAASDVEYPLLGPWGTARVFAPQKGADMATVAVLEGRLAAWAIELDAAAGRGVSAEPGAGAAGGIGAGLLAVGGRYQSGAAIIAEHTHFADDLADAELIVTGEGRFDEQSLHGKVVGAIAAAARPLAIPVIVLAGQVSLDKSALRSAGIMAALSIAEYAGSVRLALADAANQLMGLASQVAARLGNSGPSGYR