Rv3200c Family assigned · medium auto-curated
H37Rv Rv3200c · MTBC0 mtbc0_003404 ·
355 aa · 3594744–3595811 (-) ·
RefSeq NP_217716.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane cation transporter |
|---|---|
| MTBC0 PGAP re-annotation | potassium channel family protein |
| Revised (this work) | Potassium channel family protein. Pfam: Ion_trans_2 (PF07885.23), TrkA_N (PF02254.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53346
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible transmembrane cation transporter |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | kch |
| eggNOG description | transport |
| Orthologous group | COG1226 |
| KEGG orthology |
K10716
|
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 | 0.654 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 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 |
|---|---|---|---|---|
Ion_trans_2 | PF07885.23 | 2.4e-14 | 48–129 | Ion channel |
TrkA_N | PF02254.25 | 2.6e-27 | 150–266 | TrkA-N domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nudC (NADH pyrophosphatase), high confidence from genomic context alone (score 810 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3199c nudC |
NADH pyrophosphatase | 810 | 810 ctx | neighborhood:804 |
Rv3202c adnA |
ATP-dependent DNA helicase | 813 | 806 ctx | neighborhood:801 |
Rv3201c adnB |
ATP-dependent DNA helicase | 812 | 804 ctx | neighborhood:801 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 675 | 675 | coexpression:578 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 553 | 554 | coexpression:454 |
Rv0948c |
chorismate mutase | 544 | 544 ctx | cooccurence:531 |
Rv3013 hyp |
hypothetical protein | 478 | 478 ctx | cooccurence:460 |
Rv0260c |
transcriptional regulator | 470 | 470 | coexpression:452 |
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 | 465 | 466 | coexpression:465 |
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 464 | 463 | coexpression:458 |
Rv0813c hyp |
hypothetical protein | 462 | 463 ctx | cooccurence:461 |
Rv0866 moaE2 |
molybdopterin synthase catalytic subunit 2 | 461 | 462 | coexpression:461 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 454 | 454 | coexpression:423 |
Rv3753c hyp |
hypothetical protein | 421 | 422 ctx | cooccurence:420 |
Rv3311 hyp |
hypothetical protein | 411 | 411 ctx | cooccurence:409 |
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: transmembrane cation transporter
- MTBC0 PGAP product: potassium channel family protein
- Pfam (hmmscan --cut_ga): Ion_trans_2 PF07885.23 (E=2e-14), TrkA_N PF02254.25 (E=3e-27)
- (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_217716.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ion_trans_2 (PF07885.23), TrkA_N (PF02254.25)
- 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
COG1226 - Curated reference: UniProt O53346 (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 —
30 functional partner(s); context anchor
nudC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003404|Rv3200c| MAGSWRRLRGLDEKLTAQPGYALVGVLRIPQRRASPARVISRRVVVAVVALLLTAGIVYVDRDGYLDAQGDRLTFLDCLYYAAVTLSTTGYGDITPISEFARAINIFVITPLRIAFLILLVGTTLEVLTETSRQAYKIQRWRSRVRNHTVVIGYGTKGKTAVAAMVSDELVPGEIVVVDTDSGVLERAAAAGLVTVHGDATKSDVLRLAGTQHASSIIVATSRDDTAVLVTLTAREIAPKAKIVASIREAENQHLLRQSGADTVVVSSETAGRLLGIATTTPSVVEMIEDLLTPEAGLAVAEREVEQAEVGGSPRHLRDIVLGVVRDGQLLRIGAPEVDAIEASDRLLYIRQVGR