pmmB Resolved · high auto-curated
H37Rv Rv3308 · MTBC0 mtbc0_003516 ·
534 aa · 3717002–3718606 (+) ·
RefSeq NP_217825.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphomannomutase PmmB |
|---|---|
| MTBC0 PGAP re-annotation | phospho-sugar mutase |
| Revised (this work) | Phospho-sugar mutase. 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 |
O53360
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable phosphomannomutase PmmB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | pmmB |
| eggNOG description | phosphomannomutase |
| Orthologous group | COG1109 |
| EC number |
EC 5.4.2.8
|
| KEGG orthology |
K01840
|
| KEGG pathways |
map00051, map00520, map01100, map01110, map01130
|
| KEGG modules |
M00114
|
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 | 2.63 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 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 | 4.0e-39 | 36–170 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I |
PGM_PMM_II | PF02879.23 | 3.1e-20 | 205–291 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II |
PGM_PMM_III | PF02880.23 | 3.0e-15 | 304–424 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deoD (purine nucleoside phosphorylase), high confidence from genomic context alone (score 956 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3307 deoD |
purine nucleoside phosphorylase | 958 | 956 ctx | neighborhood:881 cooccurence:438 |
Rv3264c manB |
D-alpha-D-mannose-1-phosphate guanylyltransferase ManB | 964 | 941 | coexpression:414 database:900 textmining:419 |
Rv3255c manA |
mannose-6-phosphate isomerase | 982 | 905 | database:900 textmining:822 |
Rv3257c pmmA |
phosphomannomutase PmmA | 914 | 901 | database:900 |
Rv3305c amiA1 |
N-acyl-L-amino acid amidohydrolase AmiA | 790 | 791 ctx | neighborhood:786 |
Rv3306c amiB1 |
amidase AmiB | 788 | 788 ctx | neighborhood:786 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 797 | 766 ctx | fusion:638 |
Rv3336c trpS |
tryptophan--tRNA ligase | 629 | 629 ctx | fusion:611 |
Rv2417c |
DegV domain-containing protein | 512 | 513 | coexpression:409 |
Rv3315c cdd |
cytidine deaminase | 475 | 456 | |
Rv2101 helZ |
helicase HelZ | 474 | 453 | database:416 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 483 | 449 | coexpression:431 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 478 | 446 | coexpression:427 |
Rv1402 priA |
primosomal protein N' | 436 | 437 | |
Rv0707 rpsC |
30S ribosomal protein S3 | 464 | 410 |
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: phosphomannomutase PmmB
- MTBC0 PGAP product: phospho-sugar mutase
- Pfam (hmmscan --cut_ga): PGM_PMM_I PF02878.23 (E=4e-39), PGM_PMM_II PF02879.23 (E=3e-20), PGM_PMM_III PF02880.23 (E=3e-15)
- (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_217825.1)
- 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
COG1109 - Curated reference: UniProt O53360 (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 —
29 functional partner(s); context anchor
deoD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003516|Rv3308|pmmB MTPENWIAHDPDPQTAAELAACGPDELKARFSRPLAFGTAGLRGHLRGGPDAMNLAVVLRATWAVARVLTDRGLAGSPVIVGRDARHGSPAFAAAAAEVLAAAGFSVLLLPDPAPTPVVAFAVRHTGAAAGIQITASHNPATDNGYKVYVDGGLQLLAPTDRQIEAAMATAPPADQIARKTVNPSENRASDLIDRYIQRAAGVRRCAGSVRVALTPLHGVGGAMAVETLRRAGFTEVHTVATQFAPNPDFPTVTLPNPEEPGATDALLTLATDVDADVAIALDPDADRCAVGIPTVSGWRMLSGDETGWLLGDYILSQTDDRASPPETRVVASTVVSSRMLAAIAAHHAAVHVETLTGFKWLARADANLPGTLVYAYEEAIGHCVDPTAVRDKDGISAAVLVCDLVAALKGQGRSVTDALDELARCYGVHEVAALSRPVGGAVETTDLMRRLREDPPRRLAGFPATVTDIGDTLILTGGDDNMLVRVAVRPSGTEPKLKCYLEIRCAVTGDLPAARQLVRARIDELSASVRRWW