Rv3096 Resolved · medium auto-curated
H37Rv Rv3096 · MTBC0 mtbc0_003290 ·
379 aa · 3485911–3487050 (+) ·
RefSeq NP_217612.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | 1%2C4-beta-xylanase |
| Revised (this work) | 1%2C4-beta-xylanase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YB54
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 1,4-beta-xylanase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the glycosyl hydrolase 5 (cellulase A) family |
| Orthologous group | COG3934 |
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 | 0.406 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3095 (HTH-type transcriptional regulator), medium confidence from genomic context alone (score 671 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) |
|---|---|---|---|---|
Rv3717 hyp |
hypothetical protein | 797 | 797 | coexpression:797 |
Rv3209 hyp |
hypothetical protein | 730 | 730 | coexpression:730 |
Rv0063 |
oxidoreductase | 730 | 730 | coexpression:730 |
Rv3095 |
HTH-type transcriptional regulator | 670 | 671 ctx | neighborhood:652 |
Rv3094c hyp |
hypothetical protein | 481 | 480 ctx | neighborhood:467 |
Rv2120c |
integral membrane protein | 478 | 478 ctx | cooccurence:478 |
Rv3803c fbpD |
MPT51/MPB51 antigen | 464 | 465 ctx | cooccurence:463 |
Rv0179c lprO |
lipoprotein LprO | 441 | 441 | coexpression:441 |
Rv3093c |
oxidoreductase | 424 | 425 ctx | neighborhood:408 |
Rv0315 |
beta-1,3-glucanase | 718 | 356 | textmining:581 |
Rv2349c plcC |
phospholipase C | 474 | 296 | |
Rv0186 bglS |
beta-glucosidase BglS | 882 | 99 | textmining:875 |
Rv0062 celA1 |
cellulase CelA | 674 | 65 | textmining:666 |
Rv1090 celA2b |
Rv1090, (MTV017.43), len: 151 aa. Probable celA2b,second part of cellulase (endoglucanase), similar to C-terminus of others e.g. O08468 cell | 690 | 60 | textmining:684 |
Rv1754c hyp |
hypothetical protein | 556 | 59 | textmining:548 |
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: 1%2C4-beta-xylanase
- (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_217612.1)
- 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
COG3934 - Curated reference: UniProt I6YB54 (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 —
27 functional partner(s); context anchor
Rv3095 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003290|Rv3096| MHRRTALKLPLLLAAGTVLGQAPRAAAGEPGRWSADRAHRWYQAHGWLVGANYITSNAINQLEMFQPGTYDPRRIDNELGLARFHGFNTVRVFLHDLLWAQDAPGFQTRLAQFVAIAARYHIKPLFVLFDSCWDPLPRPGRQRAPRAGVHNSGWVQSPGAERLDDRRYASTLYNYVTGVLGQFRNDDRVLGWDLWNEPDNPARVYRKVERKDKLERVAELLPQVFRWARTVDPVQPLTSGVWQGNWGDPGRRSTISAIQLDNADVITFHSYAAPAEFEGRIAELAPLQRPILCTEYLARSQGSTVEGILPIAKRHNVGAFNWGLVAGKTQTYLPWDSWDHPYRAPPKVWFHDLLHPNGRPYRDGEVQTIRKLNGMPSQD