Rv1006 Family assigned · low
H37Rv Rv1006 · MTBC0 mtbc0_001081 ·
567 aa · 1131050–1132753 (+) ·
RefSeq NP_215522.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Glycoside-hydrolase-like fold (GH2, PDB 5T99); putative glycosidase. |
Curated reference (UniProt)
| UniProt |
O05592
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Secreted protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Beta-galactosidase |
| Orthologous group | COG1874 |
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 | 0.558 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 82.4 (confident). 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 |
|---|---|---|---|---|
5t99-assembly2_B |
1.00 | 0.46 | 4.4e-04 sig | 5t99-assembly2_B Crystal structure of BuGH2Awt in complex with Galactoisofagomine |
5t99-assembly1_A |
1.00 | 0.47 | 1.0e-03 sig | 5t99-assembly1_A Crystal structure of BuGH2Awt in complex with Galactoisofagomine |
5t98-assembly2_B |
1.00 | 0.44 | 1.1e-03 sig | 5t98-assembly2_B Crystal structure of BuGH2Awt |
3fn9-assembly2_C |
0.99 | 0.50 | 2.6e-03 sig | 3fn9-assembly2_C Crystal structure of putative beta-galactosidase from bacteroides fragilis |
3bga-assembly1_B |
0.99 | 0.41 | 3.9e-04 sig | 3bga-assembly1_B Crystal structure of beta-galactosidase from Bacteroides thetaiotaomicron VPI-5482 |
5g50-assembly1_B |
0.97 | 0.43 | 5.0e-03 sig | 5g50-assembly1_B Vibrio cholerae scaffolding protein RbmA in complex with magnesium. |
4kkq-assembly1_B |
0.97 | 0.43 | 5.0e-03 sig | 4kkq-assembly1_B Crystal structure of Vibrio cholerae RbmA (crystal form 1) |
4be6-assembly1_A |
0.95 | 0.42 | 3.7e-03 sig | 4be6-assembly1_A V. cholera biofilm scaffolding protein RbmA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0180c (transmembrane protein), high confidence from genomic context alone (score 741 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) |
|---|---|---|---|---|
Rv1435c hyp |
hypothetical protein | 775 | 775 ctx | cooccurence:774 |
Rv1868 hyp |
hypothetical protein | 774 | 774 ctx | cooccurence:774 |
Rv2047c hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:770 |
Rv3033 hyp |
hypothetical protein | 765 | 765 ctx | cooccurence:764 |
Rv2114 hyp |
hypothetical protein | 761 | 761 ctx | cooccurence:759 |
Rv2598 hyp |
hypothetical protein | 750 | 751 ctx | cooccurence:749 |
Rv0180c |
transmembrane protein | 741 | 741 ctx | cooccurence:741 |
Rv3899c hyp |
hypothetical protein | 738 | 739 ctx | cooccurence:737 |
Rv1364c |
sigma factor regulatory protein | 737 | 738 ctx | cooccurence:736 |
Rv1005c pabB |
para-aminobenzoate synthase component I | 786 | 726 ctx | neighborhood:725 |
Rv3166c hyp |
hypothetical protein | 714 | 714 ctx | cooccurence:714 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 709 | 709 ctx | cooccurence:705 |
Rv2571c |
transmembrane protein | 702 | 703 ctx | cooccurence:701 |
Rv2597 |
membrane protein | 702 | 703 ctx | cooccurence:701 |
Rv3263 |
DNA methylase | 698 | 698 ctx | cooccurence:695 |
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: hypothetical protein
- Foldseek best: 5t99-assembly2_B Crystal structure of BuGH2Awt in complex with Galactoisofagomin (prob 1.00, E=4e-04, TM=0.46)
- (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_215522.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG1874 - Curated reference: UniProt O05592 (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 82.4, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
92 functional partner(s); context anchor
Rv0180c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001081|Rv1006| MVLRSRKSTLGVVVCLALVLGGPLNGCSSSASHRGPLNAMGSPAIPSTAQEIPNPLRGQYEDLMEPLFPQGNPAQQRYPPWPASYDASLRVSWRQLQPTDPRTLPPDAPDDRKYDFSVIDNALTRLADRGMRLTLRVYAYSSCCKASYPDGTNIAIPDWERAIASTNTSYPGPATDPSTGVVQVVPNFNDSTYLNDFAQLLAALGRRYDGDERLSVFEFSGYGDFSENHVAYLRDTLGAPGPGPDESVATLGYYSQFRDQNITTASIKQLIAANVSAFPHTQLVTSPANPEIVRELFADEVTNKLAAPVGVRSDCLGVDAPLPAWAESSTSHYVQTKDPVVAALRQRLATAPVITEWCELPTGSSPRAYYEKGLRDVIRYHVSMTSSVNFPDQTATSPMDPALYLVWAQANAAAGYRYSVEAQPGSQALAGKVATISVTWTNYGAAAATEKWVPGYRLVDSTGQVVRTLPAAVDLKTLVSDQRGDRSSDQPTPASVAETVRVDLSGLPAGHYTLRAAIDWQQHKPNGSHVVNYPPMLLSRDGRDDSGFYPVATLDIPRDAQTAVNAS