Rv0540 Family assigned · low
H37Rv Rv0540 · MTBC0 mtbc0_000569 ·
220 aa · 635923–636585 (+) ·
RefSeq NP_215054.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2064 domain-containing protein |
| Revised (this work) | DUF2064; fold of a putative nucleotide-diphospho-sugar transferase (PDB 3CGX); putative sugar/nucleotidyl transferase. |
Curated reference (UniProt)
| UniProt |
O06406
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycosyltransferase involved in cell wall biogenesis |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterized protein conserved in bacteria (DUF2064) |
| Orthologous group | COG3222 |
| KEGG orthology |
K09931
|
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 | 0.19 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 2 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 |
|---|---|---|---|---|
DUF2064 | PF09837.16 | 4.1e-29 | 44–165 | Uncharacterized protein conserved in bacteria (DUF2064) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 97.8 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
3cgx-assembly1_A |
1.00 | 0.83 | 2.1e-15 sig | 3cgx-assembly1_A Crystal structure of putative nucleotide-diphospho-sugar transferase (YP_389115.1) from Desulfovibrio desulfuricans G20 at 1.90 A resolution |
6bwg-assembly1_A |
1.00 | 0.74 | 1.6e-09 sig | 6bwg-assembly1_A Crystal structure of native Rv2983 from Mycobacterium tuberculosis |
7p97-assembly2_BBB |
1.00 | 0.71 | 5.6e-10 sig | 7p97-assembly2_BBB Structure of 3-phospho-D-glycerate guanylyltransferase with product 3-GPPG bound |
2i5e-assembly1_B |
1.00 | 0.77 | 3.8e-08 sig | 2i5e-assembly1_B Crystal Structure of a Protein of Unknown Function MM2497 from Methanosarcina mazei Go1, Probable Nucleotidyltransferase |
6bwh-assembly3_C |
1.00 | 0.76 | 2.0e-08 sig | 6bwh-assembly3_C Crystal structure of Mycoibacterium tuberculosis Rv2983 in complex with PEP |
6bwg-assembly2_B |
1.00 | 0.73 | 3.8e-08 sig | 6bwg-assembly2_B Crystal structure of native Rv2983 from Mycobacterium tuberculosis |
2wee-assembly2_B |
1.00 | 0.63 | 1.2e-06 sig | 2wee-assembly2_B Crystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv |
2wee-assembly1_A |
1.00 | 0.64 | 1.6e-06 sig | 2wee-assembly1_A Crystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0539 (dolichyl-phosphate sugar synthase), high confidence from genomic context alone (score 985 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0539 |
dolichyl-phosphate sugar synthase | 997 | 985 ctx | neighborhood:882 fusion:499 cooccurence:766 textmining:870 |
Rv0218 |
transmembrane protein | 885 | 886 ctx | neighborhood:521 cooccurence:771 |
Rv0536 galE3 |
UDP-glucose 4-epimerase GalE | 975 | 817 ctx | cooccurence:770 textmining:870 |
Rv0541c |
integral membrane protein | 974 | 811 ctx | cooccurence:771 textmining:870 |
Rv0538 |
membrane protein | 806 | 806 ctx | neighborhood:804 |
Rv0219 |
transmembrane protein | 684 | 684 ctx | cooccurence:637 |
Rv2963 |
integral membrane protein | 453 | 453 ctx | cooccurence:453 |
Rv0535 pnp |
5'-methylthioadenosine phosphorylase | 920 | 410 | textmining:870 |
Rv2855 mtr |
mycothione reductase | 735 | 81 | textmining:724 |
Rv2051c ppm1 |
polyprenol-monophosphomannose synthase | 663 | 78 | textmining:650 |
Rv3631 |
transferase | 874 | 77 | textmining:870 |
Rv0091 mtn |
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | 808 | 47 | textmining:807 |
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
- MTBC0 PGAP product: DUF2064 domain-containing protein
- Pfam: DUF2064 PF09837.16
- Foldseek best: 3cgx-assembly1_A Crystal structure of putative nucleotide-diphospho-sugar transf (prob 1.00, E=2e-15, TM=0.83)
- (structure-only promotion reviewed by hand, 2026-06-01)
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_215054.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2064 (PF09837.16)
- 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
COG3222 - Curated reference: UniProt O06406 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 97.8, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
12 functional partner(s); context anchor
Rv0539 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000569|Rv0540| MSCLPVSVLVVAKAPEPGRVKTRLAAAIGDKVAADIAAAALLDTLDAVAAAPVTARAVALTGDLDSAADSAEIRRRLKSFTVFRQRGDAFADRLANAHVDAADGYPVLQIGMDTPQVTAELLADCARLLLQIPAVLGLAFDGGWWVLGIRTPTAAECLRAVPMSQPDTGELTLKALRDNGIDVTLVQRLGDFDIVDDIALVRDCCAPGSRFAQATRAAGL