pgmA Resolved · high auto-curated
H37Rv Rv3068c · MTBC0 mtbc0_003261 ·
547 aa · 3453343–3454986 (-) ·
RefSeq NP_217584.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoglucomutase PgmA |
|---|---|
| MTBC0 PGAP re-annotation | phosphoglucomutase (alpha-D-glucose-1%2C6-bisphosphate-dependent) |
| Revised (this work) | Phosphoglucomutase (alpha-D-glucose-1%2C6-bisphosphate-dependent). Pfam: PGM_PMM_I (PF02878.23), PGM_PMM_II (PF02879.23), PGM_PMM_III (PF02880.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y2G3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable phosphoglucomutase PgmA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | pgm |
| eggNOG description | Phosphoglucomutase |
| Orthologous group | COG0033 |
| EC number |
EC 5.4.2.2
|
| KEGG orthology |
K01835
|
| KEGG pathways |
map00010, map00030, map00052, map00230, map00500, map00520, map00521, map01100, map01110, map01120, map01130
|
| KEGG modules |
M00549
|
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 | 0.153 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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 |
|---|---|---|---|---|
PGM_PMM_I | PF02878.23 | 3.4e-32 | 41–181 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I |
PGM_PMM_II | PF02879.23 | 3.4e-08 | 209–317 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II |
PGM_PMM_III | PF02880.23 | 1.6e-28 | 323–441 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glgB (1,4-alpha-glucan branching protein), high confidence from genomic context alone (score 906 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1328 glgP |
glycogen phosphorylase | 988 | 983 | coexpression:818 database:900 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 990 | 979 | coexpression:749 database:900 textmining:590 |
Rv1212c glgA |
capsular glucan synthase | 943 | 940 | database:900 |
Rv1449c tkt |
transketolase | 954 | 938 | database:900 |
Rv1781c malQ |
4-alpha-glucanotransferase | 943 | 924 | database:900 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 952 | 913 | database:900 textmining:484 |
Rv2436 rbsK |
ribokinase RbsK | 940 | 912 | database:900 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 934 | 908 | database:900 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 917 | 906 ctx | fusion:687 coexpression:696 |
Rv0334 rmlA |
glucose-1-phosphate thymidylyltransferase | 914 | 906 | database:900 |
Rv2702 ppgK |
polyphosphate glucokinase | 939 | 904 | database:900 |
Rv0650 |
sugar kinase | 930 | 903 | database:900 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 910 | 901 | database:900 |
Rv0046c ino1 |
inositol-3-phosphate synthase | 946 | 900 | database:900 textmining:489 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 900 | 900 | database:900 |
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: phosphoglucomutase PgmA
- MTBC0 PGAP product: phosphoglucomutase (alpha-D-glucose-1%2C6-bisphosphate-dependent)
- Pfam (hmmscan --cut_ga): PGM_PMM_I PF02878.23 (E=3e-32), PGM_PMM_II PF02879.23 (E=3e-08), PGM_PMM_III PF02880.23 (E=2e-28)
- (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_217584.1)
- Domains: Pfam-A via hmmscan --cut_ga — PGM_PMM_I (PF02878.23), PGM_PMM_II (PF02879.23), PGM_PMM_III (PF02880.23)
- 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
COG0033 - Curated reference: UniProt I6Y2G3 (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 —
84 functional partner(s); context anchor
glgB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003261|Rv3068c|pgmA MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPTPAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANEILLARSMVKRLPLARALRTAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGASVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRERYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSIIDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIMALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELAGEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQTAREVVDRVIG