Rv3168 Family assigned · medium auto-curated
H37Rv Rv3168 · MTBC0 mtbc0_003367 ·
378 aa · 3560950–3562086 (+) ·
RefSeq NP_217684.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aminoglycoside phosphotransferase |
|---|---|
| MTBC0 PGAP re-annotation | phosphotransferase family protein |
| Revised (this work) | Phosphotransferase family protein. Pfam: APH (PF01636.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI99
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative aminoglycoside phosphotransferase |
| EC (curated) |
EC 2.7.1.-
|
| Curated function | Might catalyze the phosphorylation of aminoglycosides and confer aminoglycoside antibiotics resistance. |
UniProt still lists this protein as Putative aminoglycoside phosphotransferase; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Aminoglycoside phosphotransferase |
| Orthologous group | COG3173 |
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 | 0.658 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
APH | PF01636.30 | 1.8e-22 | 94–286 | Phosphotransferase enzyme family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3167c (TetR family transcriptional regulator), high confidence from genomic context alone (score 774 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3169 hyp |
hypothetical protein | 997 | 992 ctx | neighborhood:881 cooccurence:765 coexpression:746 textmining:629 |
Rv3167c |
TetR family transcriptional regulator | 953 | 774 ctx | neighborhood:743 textmining:803 |
Rv3761c fadE36 |
acyl-CoA dehydrogenase FadE36 | 676 | 676 ctx | cooccurence:674 |
Rv3170 aofH |
flavin-containing monoamine oxidase | 628 | 628 ctx | neighborhood:540 |
Rv0138 hyp |
hypothetical protein | 626 | 626 ctx | cooccurence:626 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 633 | 620 ctx | cooccurence:536 |
Rv0310c hyp |
hypothetical protein | 595 | 592 ctx | cooccurence:586 |
Rv0311 hyp |
hypothetical protein | 566 | 566 ctx | cooccurence:565 |
Rv1874 hyp |
hypothetical protein | 536 | 536 ctx | cooccurence:532 |
Rv3061c fadE22 |
acyl-CoA dehydrogenase FadE22 | 517 | 500 | |
Rv0273c |
transcriptional regulator | 494 | 494 ctx | cooccurence:491 |
Rv0764c cyp51 |
lanosterol 14-alpha demethylase | 494 | 493 ctx | cooccurence:478 |
Rv3541c chsH1 hyp |
hypothetical protein | 482 | 463 | |
Rv3359 |
oxidoreductase | 457 | 457 ctx | cooccurence:415 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 472 | 454 |
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: aminoglycoside phosphotransferase
- MTBC0 PGAP product: phosphotransferase family protein
- Pfam (hmmscan --cut_ga): APH PF01636.30 (E=2e-22)
- (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_217684.1)
- Domains: Pfam-A via hmmscan --cut_ga — APH (PF01636.30)
- 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
COG3173 - Curated reference: UniProt P9WI99 (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 —
38 functional partner(s); context anchor
Rv3167c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003367|Rv3168| MANEPAIGAIDRLQRSSRDVTTLPAVISRWLSSVLPGGAAPEVTVESGVDSTGMSSETIILTARWQQDGRSIQQKLVARVAPAAEDVPVFPTYRLDHQFEVIRLVGELTDVPVPRVRWIETTGDVLGTPFFLMDYVEGVVPPDVMPYTFGDNWFADAPAERQRQLQDATVAALATLHSIPNAQNTFSFLTQGRTSDTTLHRHFNWVRSWYDFAVEGIGRSPLLERTFEWLQSHWPDDAAAREPVLLWGDARVGNVLYRDFQPVAVLDWEMVALGPRELDVAWMIFAHRVFQELAGLATLPGLPEVMREDDVRATYQALTGVELGDLHWFYVYSGVMWACVFMRTGARRVHFGEIEKPDDVESLFYHAGLMKHLLGEEH