amt Resolved · high auto-curated
H37Rv Rv2920c · MTBC0 mtbc0_003102 ·
477 aa · 3251902–3253335 (-) ·
RefSeq NP_217436.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ammonium transporter integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | ammonium transporter |
| Revised (this work) | Ammonium transporter. Pfam: Ammonium_transp (PF00909.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ65
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Ammonium transporter |
| Curated function | Involved in the uptake of ammonium/ammonia (NH(4)(+)/NH(3)). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | amtB |
| eggNOG description | Ammonium Transporter |
| Orthologous group | COG0004 |
| KEGG orthology |
K03320
|
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) pseudogene candidate
| pN/pS | 0.943 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.38% of strains (2009) · clonal |
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 |
|---|---|---|---|---|
Ammonium_transp | PF00909.27 | 9.6e-132 | 16–441 | Ammonium Transporter Family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glnB (nitrogen regulatory protein P-II), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2919c glnB |
nitrogen regulatory protein P-II | 999 | 1000 ctx | neighborhood:881 fusion:899 cooccurence:632 coexpression:859 experimental:911 textmining:634 |
Rv2918c glnD |
bifunctional uridylyltransferase/uridylyl-removing enzyme | 937 | 842 ctx | neighborhood:805 textmining:621 |
Rv3859c gltB |
glutamate synthase large subunit | 947 | 801 ctx | neighborhood:544 cooccurence:438 textmining:745 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 673 | 658 ctx | neighborhood:651 |
Rv2923c hyp |
hypothetical protein | 655 | 655 ctx | neighborhood:647 |
Rv2922c smc |
chromosome partition protein Smc | 627 | 613 ctx | neighborhood:613 |
Rv2922A acyP |
acylphosphatase | 516 | 517 ctx | neighborhood:514 |
Rv1475c acn |
iron-regulated aconitate hydratase | 577 | 514 | coexpression:443 |
Rv1626 pdtaR |
two-component system transcriptional regulator | 528 | 461 | coexpression:417 |
Rv1858 modB |
molybdenum ABC transporter permease ModB | 436 | 436 | coexpression:426 |
Rv1857 modA |
molybdate ABC transporter substrate-binding lipoprotein ModA | 480 | 420 | coexpression:417 |
Rv0133 |
GCN5-like N-acetyltransferase | 412 | 413 | coexpression:402 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 647 | 412 | textmining:424 |
Rv2222c glnA2 |
glutamine synthetase | 748 | 409 | textmining:591 |
Rv2860c glnA4 |
glutamine synthetase | 744 | 406 | textmining:587 |
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: ammonium transporter integral membrane protein
- MTBC0 PGAP product: ammonium transporter
- Pfam (hmmscan --cut_ga): Ammonium_transp PF00909.27 (E=1e-131)
- (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_217436.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ammonium_transp (PF00909.27)
- 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
COG0004 - Curated reference: UniProt P9WQ65 (SwissProt, reviewed; Inferred from homology)
- 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 —
28 functional partner(s); context anchor
glnB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003102|Rv2920c|amt MDQFPIMGVPDGGDTAWMLVSSALVLLMTPGLAFFYGGMVRSKSVLNMIMMSISAMGVVTVLWALYGYSIAFGDDVGNIAGNPSQYWGLKGLIGVNAVAADPSTQTAAVNIPLAGTLPATVFVAFQLMFAIITVALISGAVADRLKFGAWLLFAGLWATFVYFPVAHWVFAFDGFAAEHGGWIANKLHAIDFAGGTAVHINAGVAALMLAIVLGKRRGWPATLFRPHNLPFVMLGAALLWFGWYGFNAGSATTANGVAGATFVTTTIATAAAMLGWLLTERVRDGKATTLGAASGIVAGLVAITPSCSSVNVLGALAVGVSAGVLCALAVGLKFKLGFDDSLDVVGVHLVGGLVGTLLVGLLAAPEAPAINGVAGVSKGLFYGGGFAQLERQALGACSVLVYSGIITLILALILKFTIGLRLDAEQESTGIDEAEHAESGYDFAVASGSVLPPRVTVEDSRNGIQERIGQKVEAEPK