pmmA Resolved · high auto-curated
H37Rv Rv3257c · MTBC0 mtbc0_003465 ·
465 aa · 3659455–3660852 (-) ·
RefSeq NP_217774.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphomannomutase PmmA |
|---|---|
| MTBC0 PGAP re-annotation | phosphomannomutase/phosphoglucomutase |
| Revised (this work) | Phosphomannomutase/phosphoglucomutase. Pfam: PGM_PMM_I (PF02878.23), PGM_PMM_II (PF02879.23), PGM_PMM_III (PF02880.23), PGM_PMM_IV (PF00408.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86374
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable phosphomannomutase PmmA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | manB |
| eggNOG description | the resulting product is then converted to GDP-mannose by ManC which is then used in the synthesis of mannose-containing glycoconjugates that are important for mediating entry into host cells |
| Orthologous group | COG1109 |
| EC number |
EC 5.4.2.8
|
| KEGG orthology |
K01840
|
| KEGG pathways |
map00051, map00520, map01100, map01110, map01130
|
| KEGG modules |
M00114
|
| Gene Ontology (60) |
GO:0000271, GO:0000287, GO:0003674, GO:0003824, GO:0004614, GO:0004615, GO:0005488, GO:0005975, GO:0005976, GO:0006082, GO:0006629, GO:0008150 +48 more
|
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 | 0.349 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 | 2.2e-32 | 11–128 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I |
PGM_PMM_II | PF02879.23 | 9.6e-24 | 160–259 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II |
PGM_PMM_III | PF02880.23 | 1.2e-26 | 269–373 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III |
PGM_PMM_IV | PF00408.27 | 5.4e-09 | 378–450 | Phosphoglucomutase/phosphomannomutase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: manA (mannose-6-phosphate isomerase), high confidence from genomic context alone (score 990 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3255c manA |
mannose-6-phosphate isomerase | 994 | 990 ctx | neighborhood:882 database:900 textmining:417 |
Rv3264c manB |
D-alpha-D-mannose-1-phosphate guanylyltransferase ManB | 967 | 951 | coexpression:435 database:900 |
Rv3308 pmmB |
phosphomannomutase PmmB | 914 | 901 | database:900 |
Rv3256c hyp |
hypothetical protein | 902 | 896 ctx | neighborhood:881 |
Rv1328 glgP |
glycogen phosphorylase | 752 | 725 ctx | fusion:672 |
Rv3259 hyp |
hypothetical protein | 704 | 704 ctx | neighborhood:658 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 668 | 633 ctx | fusion:532 |
Rv3258c hyp |
hypothetical protein | 629 | 630 ctx | neighborhood:618 |
Rv2101 helZ |
helicase HelZ | 473 | 452 | database:416 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 496 | 449 | |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 478 | 446 | coexpression:427 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 477 | 444 | coexpression:425 |
Rv0486 mshA |
D-inositol 3-phosphate glycosyltransferase | 447 | 421 | |
Rv0707 rpsC |
30S ribosomal protein S3 | 433 | 412 | |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 430 | 396 |
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 PmmA
- MTBC0 PGAP product: phosphomannomutase/phosphoglucomutase
- Pfam (hmmscan --cut_ga): PGM_PMM_I PF02878.23 (E=2e-32), PGM_PMM_II PF02879.23 (E=1e-23), PGM_PMM_III PF02880.23 (E=1e-26), PGM_PMM_IV PF00408.27 (E=5e-09)
- (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_217774.1)
- Domains: Pfam-A via hmmscan --cut_ga — PGM_PMM_I (PF02878.23), PGM_PMM_II (PF02879.23), PGM_PMM_III (PF02880.23), PGM_PMM_IV (PF00408.27)
- 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 O86374 (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 —
20 functional partner(s); context anchor
manA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003465|Rv3257c|pmmA MSWPAAAVDRVIKAYDVRGLVGEEIDESLVTDLGAAFARLMRTEDARPVVIGHDMRDSSPSLADAFAAGVTGQGLDVVRVGLASTDQLYFASGLLDCPGAMFTASHNPAAYNGIKMCRAAAKPVGADTGLTAIRDDLIAGVARYDGTPGTIADQDVLVDYGAFLRSLVDTSGLRPLRVAVDAGNGMAGHTAPAVLGVIDSITLLPLYFELDGSFPNHEANPLDPANLVDLQAYVRDTGADIGLAFDGDADRCFVVDERGQPVSPSTVTALVAARELNREIGATIIHNVITSRAVPELVAERGGTPLRSRVGHSYIKALMAETGAIFGGEHSAHYYFRDFWGADSGMLAALHVLAALGEQSRPLSELTADYQRYESSGEINFTVVDSSACVEAVLKSFGNRIVSIDHLDGVTVDLGDDSWFNLRSSNTEPLLRLNVEGRSVGDVDAVVRQVSAEIAAQSAHAKAGP