Rv1096 Family assigned · medium auto-curated
H37Rv Rv1096 · MTBC0 mtbc0_001179 ·
291 aa · 1232825–1233700 (+) ·
RefSeq NP_215612.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycosyl hydrolase |
|---|---|
| MTBC0 PGAP re-annotation | polysaccharide deacetylase family protein |
| Revised (this work) | Polysaccharide deacetylase family protein. Pfam: Polysacc_deac_1 (PF01522.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53444
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible glycosyl hydrolase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | polysaccharide deacetylase |
| Orthologous group | COG0726 |
| EC number |
EC 3.5.1.104
|
| KEGG orthology |
K22278
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
Polysacc_deac_1 | PF01522.27 | 6.4e-39 | 47–161 | Polysaccharide deacetylase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: phoH2 (phosphate starvation-inducible protein PsiH), medium confidence from genomic context alone (score 621 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0696 mftF |
mycofactocin biosynthesis glycosyltransferase MftF | 815 | 759 | coexpression:739 |
Rv1095 phoH2 |
phosphate starvation-inducible protein PsiH | 621 | 621 ctx | neighborhood:601 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 503 | 472 | coexpression:428 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 481 | 452 | coexpression:421 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 484 | 435 | |
Rv3404c hyp |
hypothetical protein | 445 | 392 | |
Rv0062 celA1 |
cellulase CelA | 509 | 364 | |
Rv2164c hyp |
hypothetical protein | 791 | 174 | textmining:758 |
Rv1887 hyp |
hypothetical protein | 659 | 83 | textmining:644 |
Rv2688c |
antibiotic ABC transporter ATP-binding protein | 553 | 71 | textmining:539 |
Rv0186 bglS |
beta-glucosidase BglS | 400 | 71 | |
Rv0815c cysA2 |
thiosulfate sulfurtransferase CysA | 451 | 70 | textmining:435 |
Rv0175 |
Mce associated membrane protein | 523 | 64 | textmining:512 |
Rv3117 cysA3 |
thiosulfate sulfurtransferase | 552 | 63 | textmining:542 |
Rv0831c hyp |
hypothetical protein | 663 | 55 | textmining:659 |
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: glycosyl hydrolase
- MTBC0 PGAP product: polysaccharide deacetylase family protein
- Pfam (hmmscan --cut_ga): Polysacc_deac_1 PF01522.27 (E=6e-39)
- (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_215612.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polysacc_deac_1 (PF01522.27)
- 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
COG0726 - Curated reference: UniProt O53444 (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 —
21 functional partner(s); context anchor
phoH2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001179|Rv1096| MPKRPDNQTWRYWRTVTGVVVAGAVLVVGGLSGRVTRAENLSCSVIKCVALTFDDGPGPYTDRLLHILTDNDAKATFFLIGNKVAANPAGARRIADAGMEIGSHTWEHPNMTTIPPEDIPGQFSRANDVIAAATGRTPTLYRPAGGLSNDAVRQAAAKVGQAEILWDVIPFDWINDSNTAATRHMLMTQIKPGSVVLFHDTYSSTVDVVYQFIPVLKANGYRLVTVSELLGPRAPGSSYGSRENGPPVNELRDIPASEIPPLPNTSSPKPMPNFPITDIAGQNSGGPNNGA