nanT Family assigned · medium auto-curated
H37Rv Rv1902c · MTBC0 mtbc0_002017 ·
422 aa · 2167116–2168384 (-) ·
RefSeq NP_216418.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sialic acid-transport integral membrane protein NanT |
|---|---|
| MTBC0 PGAP re-annotation | sialate:H+ symport family MFS transporter |
| Revised (this work) | Sialate:H+ symport family MFS transporter. Pfam: Sugar_tr (PF00083.31), MFS_1 (PF07690.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07730
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable sialic acid-transport integral membrane protein NanT |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismG Carbohydrate transport and metabolismP Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | nanT |
| eggNOG description | Sugar (and other) transporter |
| Orthologous group | COG0477 |
| KEGG orthology |
K03290, K08178, K08369
|
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 | 0.357 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.53% of strains (763) · 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 |
|---|---|---|---|---|
Sugar_tr | PF00083.31 | 7.2e-26 | 14–210 | Sugar (and other) transporter |
MFS_1 | PF07690.22 | 1.4e-26 | 21–234 | Major Facilitator Superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1903 (membrane protein), medium confidence from genomic context alone (score 620 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1903 |
membrane protein | 620 | 620 ctx | neighborhood:612 |
Rv1191 hyp |
hypothetical protein | 550 | 550 ctx | neighborhood:544 |
Rv1900c lipJ |
lignin peroxidase LipJ | 545 | 545 ctx | neighborhood:541 |
Rv1672c |
integral membrane transport protein | 557 | 541 ctx | cooccurence:530 |
Rv3913 trxB2 |
thioredoxin reductase | 502 | 484 | |
Rv2856 nicT |
nickel-transport integral membrane protein NicT | 471 | 472 ctx | cooccurence:459 |
Rv1904 hyp |
hypothetical protein | 424 | 424 ctx | neighborhood:416 |
Rv1634 |
multidrug-efflux transporter | 417 | 418 ctx | cooccurence:412 |
Rv2127 ansP1 |
L-asparagine permease | 528 | 208 | textmining:429 |
Rv0346c ansP2 |
L-asparagine permease | 430 | 206 | |
Rv1410c |
aminoglycosides/tetracycline-transport integral membrane protein | 411 | 159 | |
Rv1272c |
drug ABC transporter ATP-binding protein | 455 | 47 | textmining:452 |
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: sialic acid-transport integral membrane protein NanT
- MTBC0 PGAP product: sialate:H+ symport family MFS transporter
- Pfam (hmmscan --cut_ga): Sugar_tr PF00083.31 (E=7e-26), MFS_1 PF07690.22 (E=1e-26)
- (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_216418.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sugar_tr (PF00083.31), MFS_1 (PF07690.22)
- 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
COG0477 - Curated reference: UniProt O07730 (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 —
12 functional partner(s); context anchor
Rv1903 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002017|Rv1902c|nanT MAAPRLTGDQRNAFMASFLGWTMDAFDYFLVVLVYADIATTFHHTKTDVAFLTTATLAMRPVGALLFGLWADRVGRRVPLMVDVSFYSVIGFLCAFAPNFTVLVILRLLYGIGMGGEWGLGAALSMEKVPAERRGVFSGLLQEGYAFGYLLASVAALVVMNWLGLSWRWLFGLSIIPALISLIIRYRVKESEVWEAAQDRMRLTKTRIRDVLGNPAIVRRFVYLVLLMTAFNWMSHGTQDVYPTFLTATTDHGAGLSSLTARWIVVIYNIGAIIGGLAFGTLSQRFSRRYTIVFCAALGLPIVPLFAYSRTAAMLCLGSFLMQVFVQGAWGVIPAHLTEMSPDAIRGVYPGVTYQLGNLLAAFNLPIQERLAESHGYPFALAATIVPVLLVVAVLTAIGKDATGIRFGTTETAFLVRHRNRH