Rv1002c Resolved · high auto-curated
H37Rv Rv1002c · MTBC0 mtbc0_001077 ·
503 aa · 1125764–1127275 (-) ·
RefSeq NP_215518.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dolichyl-phosphate-mannose--protein mannosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | dolichyl-phosphate-mannose--protein mannosyltransferase |
| Revised (this work) | Dolichyl-phosphate-mannose--protein mannosyltransferase. Pfam: PMT_2 (PF13231.13), PMT (PF02366.25), PMT_4TMC (PF16192.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN05
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Polyprenol-phosphate-mannose--protein mannosyltransferase |
| EC (curated) |
EC 2.4.1.-
|
| Curated function | Protein O-mannosyltransferase that catalyzes the transfer of a single mannose residue from a polyprenol phospho-mannosyl lipidic donor to the hydroxyl group of selected serine and threonine residues in acceptor proteins. Sec-translocation of the acceptor proteins is required for protein mannosylation, suggesting that O-mannosylation should affect only extracytoplasmic proteins. Is crucial for virulence. It may play a role in adaptive regulation of the mannoproteome during host cell infection..; FUNCTION: Overexpression in M.smegmatis decreases the cell envelope permeability and promotes microb. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | pmt |
| eggNOG description | Dolichyl-phosphate-mannose--protein O-mannosyl transferase |
| Orthologous group | COG4346 |
| EC number |
EC 2.4.1.109
|
| KEGG orthology |
K00728
|
| KEGG pathways |
map00514, map00515, map01100
|
| CAZy family |
GT39
|
| Gene Ontology (39) |
GO:0000030, GO:0003674, GO:0003824, GO:0006464, GO:0006486, GO:0006493, GO:0006807, GO:0008150, GO:0008152, GO:0009058, GO:0009059, GO:0009100 +27 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 | 0.256 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 5 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 |
|---|---|---|---|---|
PMT_2 | PF13231.13 | 1.7e-08 | 83–171 | Dolichyl-phosphate-mannose-protein mannosyltransferase |
PMT | PF02366.25 | 5.1e-12 | 100–281 | Dolichyl-phosphate-mannose-protein mannosyltransferase |
PMT_4TMC | PF16192.11 | 1.3e-13 | 310–502 | C-terminal four TMM region of protein-O-mannosyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsmI (rRNA small subunit methyltransferase I), high confidence from genomic context alone (score 786 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1003 rsmI |
rRNA small subunit methyltransferase I | 786 | 786 ctx | neighborhood:783 |
Rv2219 |
transmembrane protein | 698 | 699 ctx | cooccurence:696 |
Rv2413c hyp |
hypothetical protein | 696 | 697 ctx | cooccurence:696 |
Rv3311 hyp |
hypothetical protein | 642 | 643 ctx | cooccurence:641 |
Rv2146c |
transmembrane protein | 638 | 638 ctx | cooccurence:637 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 635 | 636 ctx | cooccurence:634 |
Rv2708c hyp |
hypothetical protein | 634 | 635 ctx | cooccurence:633 |
Rv2680 hyp |
hypothetical protein | 631 | 632 ctx | cooccurence:630 |
Rv0883c sepH hyp |
hypothetical protein | 619 | 619 ctx | cooccurence:617 |
Rv3212 hyp |
hypothetical protein | 613 | 614 ctx | cooccurence:610 |
Rv3438 hyp |
hypothetical protein | 605 | 606 ctx | cooccurence:600 |
Rv0004 hyp |
hypothetical protein | 592 | 592 ctx | cooccurence:592 |
Rv0528 |
transmembrane protein | 579 | 580 ctx | cooccurence:577 |
Rv2446c |
integral membrane protein | 569 | 570 ctx | cooccurence:565 |
Rv0813c hyp |
hypothetical protein | 567 | 567 ctx | cooccurence:540 |
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: dolichyl-phosphate-mannose--protein mannosyltransferase
- MTBC0 PGAP product: dolichyl-phosphate-mannose--protein mannosyltransferase
- Pfam (hmmscan --cut_ga): PMT_2 PF13231.13 (E=2e-08), PMT PF02366.25 (E=5e-12), PMT_4TMC PF16192.11 (E=1e-13)
- (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_215518.1)
- Domains: Pfam-A via hmmscan --cut_ga — PMT_2 (PF13231.13), PMT (PF02366.25), PMT_4TMC (PF16192.11)
- 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
COG4346 - Curated reference: UniProt P9WN05 (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 —
66 functional partner(s); context anchor
rsmI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001077|Rv1002c| MVPVVSPGPLVPVADFGPLDRLRGWIVTGLITLLATVTRFLNLGSLTDAGTPIFDEKHYAPQAWQVLNNHGVEDNPGYGLVVHPPVGKQLIAIGEAIFGYNGFGWRFTGALLGVVLVALVVRIVRRISRSTLVGAIAGVLLICDGVSFVTARTALLDGFLTFFVVAAFGALIVDRDQVRERMHIALLAGRSAATVWGPRVGVRWWRFGAGVLLGLACATKWSGVYFVLFFGAMALAFDVAARRQYQVQRPWLGTVRRDVLPSGYALGLIPFAVYLATYAPWFASETAIDRHAVGQAVGRNSVVPLPDAVRSLWHYTAKAFHFHAGLTNSAGNYHPWESKPWTWPMSLRPVLYAIDQQDVAGCGAQSCVKAEMLVGTPAMWWLAVPVLAYAGWRMFVRRDWRYAVVLVGYCAGWLPWFADIDRQMYFFYAATMAPFLVMGISLVLGDILYHPGQGSERRTLGLIVVCCYVALVVTNFAWLYPVLTGLPISQQTWNLEIWLPSWR