Rv3239c Resolved · high auto-curated
H37Rv Rv3239c · MTBC0 mtbc0_003447 ·
1048 aa · 3636600–3639746 (-) ·
RefSeq NP_217756.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane transport protein |
|---|---|
| MTBC0 PGAP re-annotation | MFS transporter |
| Revised (this work) | MFS transporter. Pfam: MFS_1 (PF07690.22), MFS_3 (PF05977.20), cNMP_binding (PF00027.36), Patatin (PF01734.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05884
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable conserved transmembrane transport protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismG Carbohydrate transport and metabolismP Inorganic ion transport and metabolismT Signal transduction mechanisms
|
|---|---|
| eggNOG description | Major facilitator superfamily |
| Orthologous group | COG0477 |
| KEGG orthology |
K07001
|
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 | 0.719 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 17 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.19% of strains (281) · 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 |
|---|---|---|---|---|
MFS_1 | PF07690.22 | 4.0e-35 | 31–200 | Major Facilitator Superfamily |
MFS_3 | PF05977.20 | 3.7e-07 | 76–200 | Transmembrane secretion effector |
cNMP_binding | PF00027.36 | 7.2e-21 | 534–613 | Cyclic nucleotide-binding domain |
Patatin | PF01734.28 | 1.9e-27 | 790–947 | Patatin-like phospholipase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mddA (integral membrane protein), medium confidence from genomic context alone (score 647 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1358 |
transcriptional regulator | 718 | 650 | experimental:440 |
Rv3238c mddA |
integral membrane protein | 647 | 647 ctx | neighborhood:644 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 658 | 627 ctx | neighborhood:544 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 761 | 600 | database:431 textmining:429 |
Rv2048c pks12 |
polyketide synthase | 760 | 597 | database:431 textmining:429 |
Rv1990A |
Rv1990A, len: 111 aa. Possible dehydrogenase (fragment), similar to N-terminal part of several dehydrogenases and hypothetical proteins, e.g | 617 | 596 | database:431 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 758 | 595 | database:431 textmining:429 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 758 | 594 | database:431 textmining:429 |
Rv1527c pks5 |
polyketide synthase | 758 | 594 | database:431 textmining:429 |
Rv0386 |
transcriptional regulator | 672 | 593 | experimental:440 |
Rv2488c |
LuxR family transcriptional regulator | 672 | 593 | experimental:440 |
Rv3240c secA1 |
protein translocase subunit SecA | 609 | 589 ctx | neighborhood:583 |
Rv1004c |
membrane protein | 604 | 578 ctx | cooccurence:530 |
Rv3645 |
transmembrane protein | 614 | 557 | experimental:419 |
Rv3396c guaA |
GMP synthase | 595 | 545 ctx | neighborhood:544 |
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 transport protein
- MTBC0 PGAP product: MFS transporter
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=4e-35), MFS_3 PF05977.20 (E=4e-07), cNMP_binding PF00027.36 (E=7e-21), Patatin PF01734.28 (E=2e-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_217756.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22), MFS_3 (PF05977.20), cNMP_binding (PF00027.36), Patatin (PF01734.28)
- 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 O05884 (TrEMBL, unreviewed; 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 —
113 functional partner(s); context anchor
mddA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003447|Rv3239c| MHISLHGGKGFANLTRRRRPSSASVLLVAGFGAFLAFLDSTIVNIAFPDIQRSFPSYDIGSLSWILNGYNIVFAAFMVAAGRLADLLGRRRTFLSGVLVFTIASGLCAVAGSVEQLVAFRVLQGIGAAILVPASLALVVEGFDAARRAHAIGLWGAAAAIAAGLGPPIGGLLVEWAGWRWVLLVNVPLGIVAAIATKRMLVESRASGRRRMPDLRGALLLAVTLGLVTLGLVKGPDWGWLSVATVGSFLASVLTSVGFVHSSRSHPAPLVEPALLRSRSFVAGNLLTLVAAAGFYCYGLTHVLYLNYVWHYSLLKAGFAIAPAAVVAAVVAAALGRVAGRHGHRVIVLVGALVWAGSLVWYLQRVGSEPDFLRVWLPGQLLQGIGVGATLPVLSSAALAEVAKGGSYATSSAVVSTTRQLGAVLGVAVMVILIGKPEHGTAEEALRRGWAMAAICFIAVAVAAAVLGRTNRNPVQMPAPEPAIAPRLEPPIPQPAAAPIEHWAAGDADPLGNLPLFAGLDAATLAQLGEHVEDVELEAGCYLFHEGDPSDSLYVIRTGRVQVLQDSIVLKELGRGEVLGELGLLIDAPRSATVRALRDTKLVRLTKAQFDEIADHGALAALVKVLATRLREAPPPATDSTSPEVVVSVIGVSGDAPVPAVAAGLLTALSARLRAVDPGRVDRDGLDRAERVADKVVLHAAVEDAGWRDFCLRVADRIVLVAGDPNPQAARLPARARGADLVLAGPAASREHRRQWEELITPRSVHVVHYRRILENVRPLAARIAGRSIGLVLGGGGARGFAHLGVLDELERVGVTIDRFAGTSMGAVIAVFGACGMDAATADAYAYEYFIRHNPLSDYAFPVRGLVRGRRTLTLLEAAFGDRLVEELPKEFRCVSVDLLARRPVVHRRGRLVDVIGCSLRLPGIYPPQVYNGRLHVDGGVLDNLPVSTRASPDGPLIAVSIGLGGGGPGSARQDGSPKVPGIGDTLMRTMTIGSQRGADAALSLAQVVIRPDTGAVGLLEFHQIDAAREAGRVAAREAMPHIMALLNR