Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | C4-dicarboxylate-transport transmembrane protein DctA |
|---|
| MTBC0 PGAP re-annotation | cation:dicarboxylase symporter family transporter |
|---|
| Revised (this work) | Cation:dicarboxylase symporter family transporter. Pfam: SDF (PF00375.24). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71906
TrEMBL · unreviewed
· Predicted
|
|---|
| UniProt name | Probable C4-dicarboxylate-transport transmembrane protein DctA |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|
| Preferred name | dctA |
|---|
| eggNOG description | Belongs to the dicarboxylate amino acid cation symporter (DAACS) (TC 2.A.23) family |
|---|
| Orthologous group | COG1301 |
|---|
| KEGG orthology |
K11103
|
|---|
| KEGG pathways |
map02020
|
|---|
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 |
0.838 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
4 synonymous, 9 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 |
|---|
SDF | PF00375.24 |
8.8e-96 | 26–418 |
Sodium:dicarboxylate symporter family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit |
845 |
672 |
coexpression:672 textmining:549 |
Rv2124c metH |
methionine synthase |
630 |
606 |
database:588 |
Rv1488 hyp |
hypothetical protein |
627 |
594 |
database:533 |
Rv3090 hyp |
hypothetical protein |
625 |
592 |
database:533 |
Rv3063 cstA |
carbon starvation protein A |
585 |
559 |
coexpression:410 |
Rv1770 hyp |
hypothetical protein |
541 |
541 |
database:539 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL |
540 |
540 |
database:539 |
Rv0350 dnaK |
chaperone protein DnaK |
552 |
535 |
database:463 |
Rv0312 hyp |
hypothetical protein |
551 |
535 |
database:463 |
Rv2264c hyp |
hypothetical protein |
551 |
535 |
database:463 |
Rv3446c hyp |
hypothetical protein |
550 |
534 |
database:463 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase |
651 |
518 |
database:457 |
Rv1389 gmk |
guanylate kinase |
500 |
501 |
database:432 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA |
513 |
496 |
database:493 |
Rv0435c |
ATPase |
512 |
495 |
database:493 |
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: C4-dicarboxylate-transport transmembrane protein DctA
- MTBC0 PGAP product: cation:dicarboxylase symporter family transporter
- Pfam (hmmscan --cut_ga): SDF PF00375.24 (E=9e-96)
- (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_216959.1)
- Domains: Pfam-A via hmmscan --cut_ga — SDF (PF00375.24)
- 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
COG1301
- Curated reference: UniProt
P71906
(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 —
56 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002602|Rv2443|dctA
MTAPLDRAPVTDLPANNKGRDRTHWLYLAVIFAVIAGVIVGLTAPSTGKSLTVLGTVFVNLIKMMIAPVIFCTIVLGIGSVRKAAAVGKVGGLALAYFLTMSSVALGIGLIVGNLLSPGRDLHLRPGAVGSGAALAGQAAESHGIAGFIQQIIPRSLPSALTEGNVLQVLLVALLVGFAVQGLGPAGESILRAVENLQKLVFKVLVMVLWLAPIGAFGAIANIVATTGFNAVTNLLLLMAGFYLTCVVFVFGVLGVLLRIVSGLSIFRLLRYLAREYLLIFATSSSEVVLPRLITKMKHLGVQSSTVGVVVPTGYSFNLDGTAIYLTMASLFIADAMGHRLTWGEQIALLAFMIIASKGAAGVSGAGLATLAGGLQAHRPELLDGVGLIVGIDRFMSEARSLTNFSGNAVATILVASWTKTIDLSKADEVLRGRDPFDESTMVDPHDEEPPAATPHGGGVPTNPALCDFEQVSLGGLVGRPAGPQRADVDG
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