Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane transport protein |
|---|
| MTBC0 PGAP re-annotation | MHS family MFS transporter |
|---|
| Revised (this work) | MHS 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 |
O05301
TrEMBL · unreviewed
· Predicted
|
|---|
| UniProt name | Probable conserved integral membrane transport protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
G Carbohydrate transport and metabolism
P Inorganic ion transport and metabolism
|
|---|
| eggNOG description | Major facilitator superfamily |
|---|
| Orthologous group | COG0477 |
|---|
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 |
1.501 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 synonymous, 4 missense, 0 nonsense, 2 frameshift
|
|---|
| Disruption |
2 distinct premature-stop/frameshift site(s); most common in
0.75% of strains
(1082) · 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 |
5.8e-23 | 6–215 |
Sugar (and other) transporter |
MFS_1 | PF07690.22 |
4.2e-25 | 29–377 |
Major Facilitator Superfamily |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0157A hyp |
hypothetical protein |
548 |
541 |
database:487 |
Rv1975 hyp |
hypothetical protein |
546 |
539 |
database:487 |
Rv0425c ctpH |
metal cation transporting ATPase H |
476 |
446 |
|
Rv0107c ctpI |
cation-transporter ATPase I |
473 |
443 |
|
Rv1997 ctpF |
cation transporter ATPase F |
471 |
441 |
|
Rv0908 ctpE |
metal cation transporter ATPase E |
471 |
441 |
|
Rv1767 hyp |
hypothetical protein |
440 |
441 |
coexpression:423 |
Rv0771 |
4-carboxymuconolactone decarboxylase |
439 |
439 |
coexpression:421 |
Rv0165c mce1R |
transcriptional regulator Mce1R |
448 |
428 |
coexpression:412 |
Rv1305 atpE |
ATP synthase subunit C |
448 |
427 |
database:425 |
Rv0043c |
HTH-type transcriptional regulator |
442 |
421 |
coexpression:405 |
Rv0751c mmsB |
3-hydroxyisobutyrate dehydrogenase |
414 |
414 |
coexpression:405 |
Rv0770 |
oxidoreductase |
412 |
412 |
coexpression:403 |
Rv1843c guaB1 |
inosine-5'-monophosphate dehydrogenase |
430 |
408 |
|
Rv2443 dctA |
C4-dicarboxylate-transport transmembrane protein DctA |
473 |
394 |
|
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: integral membrane transport protein
- MTBC0 PGAP product: MHS family MFS transporter
- Pfam (hmmscan --cut_ga): Sugar_tr PF00083.31 (E=6e-23), MFS_1 PF07690.22 (E=4e-25)
- (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_215716.1)
- 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
O05301
(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 —
20 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001288|Rv1200|
MKRVALACLVGSAIEFYDFLIYGTAAALVFPTVFFPHLDPTVAAVASMGTFAVAFLSRPFGAAVFGYFGDRLGRKKTLVATLLIMGLATVTVGLVPTTVAIGAAAPLILTTMRLLQGFAVGGEWAGSALLSAEYAPASKRGWYGMFTVVGGGIALVLTSLTFLGVNYTIGESSPTFMQWGWRIPFLVSAALIAVALYVRFNIDETPVFARERADEKTRLGPAETPIAQVLRRQRREIVLAAGSAVCCFGFVYLASTYLASYAQTRLGYSRGSILFDSVLGGLLCIVFTALSSALCDQLGRRRVLLAGWAVALPWSLLVMPLIDSGSPSLFAVAVVGMYAIGGFGFGPTASFIPELFATSYRYTGSALAANLAGVAGGALPPVIAGALVATYGSWAIGVMLAILALISLVCTYRLPETAGSALVSR
Spot an error? Suggest an improvement