Rv1717 Family assigned · medium auto-curated
H37Rv Rv1717 · MTBC0 mtbc0_001827 ·
116 aa · 1956421–1956771 (+) ·
RefSeq NP_216233.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | cupin domain-containing protein |
| Revised (this work) | Cupin domain-containing protein. Pfam: Cupin_2 (PF07883.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86372
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Beta-D-galactosidase Rv1717 |
| EC (curated) |
EC 3.2.1.23
|
| Curated function | Beta-D-galactopyranosidase that specifically recognizes the beta-glycosidic bonds formed with beta-D-galactopyranose (beta-D-Gal) or N-acetylgalactosamine (beta-D-GalNAc). May target the galactoside linkages in the exopolysaccharide component of the mycobacterial extracellular polymeric substance (EPS) and help dispersal of Mtb bacteria from a deteriorating biofilm. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Cupin domain |
| Orthologous group | COG3837 |
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) pseudogene candidate
| pN/pS | 0.559 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.21% of strains (14829) · clonal |
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 |
|---|---|---|---|---|
Cupin_2 | PF07883.18 | 8.7e-09 | 41–107 | Cupin domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadB3 (3-hydroxybutyryl-CoA dehydrogenase FadB), high confidence from genomic context alone (score 983 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) |
|---|---|---|---|---|
Rv1716 hyp |
hypothetical protein | 992 | 993 ctx | neighborhood:882 cooccurence:615 coexpression:853 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 982 | 983 ctx | neighborhood:881 coexpression:815 |
Rv1714 |
oxidoreductase | 976 | 976 ctx | neighborhood:881 coexpression:767 |
Rv1718 hyp |
hypothetical protein | 969 | 970 ctx | neighborhood:717 coexpression:845 |
Rv1719 |
transcriptional regulator | 784 | 785 ctx | neighborhood:698 |
Rv3859c gltB |
glutamate synthase large subunit | 544 | 544 ctx | neighborhood:544 |
Rv0355c PPE8 |
PPE family protein PPE8 | 535 | 535 ctx | cooccurence:534 |
Rv3347c PPE55 |
PPE family protein PPE55 | 527 | 527 ctx | cooccurence:525 |
Rv3350c PPE56 |
PPE family protein PPE56 | 525 | 525 ctx | cooccurence:524 |
Rv2209 |
integral membrane protein | 514 | 514 ctx | cooccurence:511 |
Rv1713 engA |
GTPase Der | 513 | 513 ctx | neighborhood:488 |
Rv3343c PPE54 |
PPE family protein PPE54 | 510 | 510 ctx | cooccurence:503 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 510 | 510 ctx | cooccurence:510 |
Rv1917c PPE34 |
PPE family protein PPE34 | 506 | 506 ctx | cooccurence:502 |
Rv1712 cmk |
cytidylate kinase | 495 | 495 ctx | neighborhood:482 |
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: hypothetical protein
- MTBC0 PGAP product: cupin domain-containing protein
- Pfam (hmmscan --cut_ga): Cupin_2 PF07883.18 (E=9e-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_216233.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cupin_2 (PF07883.18)
- 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
COG3837 - Curated reference: UniProt O86372 (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 —
42 functional partner(s); context anchor
fadB3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001827|Rv1717| MKLTRASQAPRYVAPAHHEVSTMRLQGREAGRTERFWVGLSVYRPGGTAEPAPTREETVYVVLDGELVVTVDGAETVLGWLDSVHLAKGELRSIHNRTDRQALLLVTVAHPVAEVA