Rv3906c Resolved · medium auto-curated
H37Rv Rv3906c · MTBC0 mtbc0_004140 ·
169 aa · 4415349–4415858 (-) ·
RefSeq NP_218423.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | pullulanase |
| Revised (this work) | Pullulanase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05439
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Pullulanase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ETCM |
|---|
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 | 0.967 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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: pcnA (poly(A) polymerase PcnA), high confidence from genomic context alone (score 851 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) |
|---|---|---|---|---|
Rv3907c pcnA |
poly(A) polymerase PcnA | 851 | 851 ctx | neighborhood:849 |
Rv3910 murJ |
peptidoglycan biosynthesis protein | 830 | 830 ctx | neighborhood:618 cooccurence:569 |
Rv3909 hyp |
hypothetical protein | 811 | 804 ctx | neighborhood:669 |
Rv0383c ttfA hyp |
hypothetical protein | 741 | 741 ctx | cooccurence:741 |
Rv1125 hyp |
hypothetical protein | 724 | 724 ctx | cooccurence:723 |
Rv0513 |
transmembrane protein | 721 | 721 ctx | cooccurence:717 |
Rv2719c chiZ |
membrane protein | 715 | 715 ctx | cooccurence:712 |
Rv1836c hyp |
hypothetical protein | 714 | 715 ctx | cooccurence:709 |
Rv0756c hyp |
hypothetical protein | 714 | 713 ctx | cooccurence:708 |
Rv2743c hyp |
hypothetical protein | 700 | 701 ctx | cooccurence:699 |
Rv3810 pirG |
cell surface protein | 690 | 691 ctx | cooccurence:683 |
Rv3707c hyp |
hypothetical protein | 690 | 691 ctx | cooccurence:689 |
Rv0138 hyp |
hypothetical protein | 688 | 689 ctx | cooccurence:688 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 688 | 689 ctx | cooccurence:687 |
Rv2905 lppW |
lipoprotein LppW | 684 | 685 ctx | cooccurence:666 |
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: pullulanase
- (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_218423.1)
- 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
2ETCM - Curated reference: UniProt O05439 (TrEMBL, unreviewed; Predicted)
- 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 —
77 functional partner(s); context anchor
pcnA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004140|Rv3906c| MEYCIAGDDGSAGIWNRPFDVDLDGDGRLDAIGLDLDGDGLRDDALADFDGDDVADHAVFDVDNDGTPESYFIDDGSGTWAVAVDRGGQLRWYGLDGVEHTGGPLVDFDGFGGLDDRLLDTDGDGLADRVLCAGEQRVTGYVDTDGDGRWDVRLTDTDGDGTADGASSL