Rv3400 Family assigned · medium auto-curated
H37Rv Rv3400 · MTBC0 mtbc0_003613 ·
262 aa · 3842678–3843466 (+) ·
RefSeq NP_217917.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hydrolase |
|---|---|
| MTBC0 PGAP re-annotation | beta-phosphoglucomutase family hydrolase |
| Revised (this work) | Beta-phosphoglucomutase family hydrolase. Pfam: Hydrolase (PF00702.33), HAD_2 (PF13419.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKZ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Beta-phosphoglucomutase |
| EC (curated) |
EC 5.4.2.6
|
| Curated function | Catalyzes the interconversion of D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), forming beta-D-glucose 1,6-(bis)phosphate (beta-G16P) as an intermediate. Does not show phosphatase and pyrophosphatase activity. Is probably one of the key enzymes involved in the metabolism of trehalose, a disaccharide abundantly present in mycobacteria and which plays a crucial role in bacterial physiology and virulence. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Beta-phosphoglucomutase family hydrolase |
| Orthologous group | COG0637 |
| Gene Ontology (6) |
GO:0003674, GO:0003824, GO:0008801, GO:0016853, GO:0016866, GO:0016868
|
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 | 0.528 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
Hydrolase | PF00702.33 | 8.5e-24 | 23–225 | haloacid dehalogenase-like hydrolase |
HAD_2 | PF13419.13 | 7.9e-12 | 27–231 | Haloacid dehalogenase-like hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3401 (glycosyl hydrolase), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3401 |
glycosyl hydrolase | 997 | 997 ctx | neighborhood:865 fusion:898 cooccurence:773 |
Rv3396c guaA |
GMP synthase | 785 | 778 ctx | neighborhood:706 |
Rv3399 |
S-adenosylmethionine-dependent methyltransferase | 638 | 638 ctx | neighborhood:633 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 560 | 467 | |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 455 | 456 ctx | neighborhood:449 |
Rv3397c phyA |
phytoene synthase | 443 | 423 ctx | neighborhood:416 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 427 | 399 | |
Rv3406 |
dioxygenase | 873 | 70 | textmining:870 |
Rv3405c |
HTH-type transcriptional regulator | 870 | 47 | textmining:870 |
Rv1980c mpt64 |
immunogenic protein Mpt64 | 443 | 47 | textmining:440 |
Rv1984c cfp21 |
cutinase | 442 | 47 | textmining:439 |
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: hydrolase
- MTBC0 PGAP product: beta-phosphoglucomutase family hydrolase
- Pfam (hmmscan --cut_ga): Hydrolase PF00702.33 (E=9e-24), HAD_2 PF13419.13 (E=8e-12)
- (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_217917.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase (PF00702.33), HAD_2 (PF13419.13)
- 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
COG0637 - Curated reference: UniProt P9WKZ7 (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 —
11 functional partner(s); context anchor
Rv3401 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003613|Rv3400| MANWYRPNYPEVRSRVLGLPEKVRACLFDLDGVLTDTASLHTKAWKAMFDAYLAERAERTGEKFVPFDPAADYHTYVDGKKREDGVRSFLSSRAIEIPDGSPDDPGAAETVYGLGNRKNDMLHKLLRDDGAQVFDGSRRYLEAVTAAGLGVAVVSSSANTRDVLATTGLDRFVQQRVDGVTLREEHIAGKPAPDSFLRAAELLGVTPDAAAVFEDALSGVAAGRAGNFAVVVGINRTGRAAQAAQLRRHGADVVVTDLAELL