dinF Family assigned · medium auto-curated
H37Rv Rv2836c · MTBC0 mtbc0_003015 ·
439 aa · 3162975–3164294 (-) ·
RefSeq NP_217352.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-damage-inducible protein DinF |
|---|---|
| MTBC0 PGAP re-annotation | MATE family efflux transporter |
| Revised (this work) | MATE family efflux transporter. Pfam: MatE (PF01554.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71616
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Possible DNA-damage-inducible protein F DinF |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | dinF |
| eggNOG description | Efflux protein, MATE family |
| Orthologous group | COG0534 |
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 | 0.649 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 11 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (348) · 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 |
|---|---|---|---|---|
MatE | PF01554.24 | 5.5e-28 | 19–178 | MatE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: infB (translation initiation factor IF-2), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2839c infB |
translation initiation factor IF-2 | 896 | 883 ctx | neighborhood:881 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 895 | 882 ctx | neighborhood:881 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 927 | 881 ctx | neighborhood:881 textmining:414 |
Rv2840c hyp |
hypothetical protein | 898 | 810 ctx | neighborhood:782 textmining:489 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 781 | 782 ctx | neighborhood:782 |
Rv3397c phyA |
phytoene synthase | 790 | 777 | coexpression:751 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 730 | 712 | coexpression:704 |
Rv1630 rpsA |
30S ribosomal protein S1 | 703 | 703 | coexpression:694 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 673 | 674 ctx | neighborhood:668 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 668 | 668 ctx | neighborhood:668 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 569 | 569 ctx | neighborhood:569 |
Rv0955 |
integral membrane protein | 510 | 511 ctx | cooccurence:476 |
Rv2842c rimP |
ribosome maturation factor RimP | 512 | 492 ctx | neighborhood:492 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 492 | 492 ctx | neighborhood:492 |
Rv3604c |
transmembrane protein | 463 | 464 ctx | cooccurence:460 |
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: DNA-damage-inducible protein DinF
- MTBC0 PGAP product: MATE family efflux transporter
- Pfam (hmmscan --cut_ga): MatE PF01554.24 (E=5e-28)
- (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_217352.1)
- Domains: Pfam-A via hmmscan --cut_ga — MatE (PF01554.24)
- 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
COG0534 - Curated reference: UniProt P71616 (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 —
35 functional partner(s); context anchor
infB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003015|Rv2836c|dinF MSQVGHRAGGRQIAQLALPALGVLAAEPLYLLFDIAVVGRLGAISLAGLAIGSLVLGLVGSQATFLSYGTTARAARRYGAGNRVAAVTEGVQATWLALGLGALVVVVVEATATPLVSAIASGDGITAAALPWLRIAILGTPAILVSLAGNGWLRGVQDTVRPLRYVVAGFGSSALLCPLLVYGWLGLPRWGLTGSAVANLVGQWLAALLFAGALLAERVSLRPDRAVLGAQLMMARDLIVRTLAFQVCYVSAAAVAARFGAAALAAHQVVLQLWGLLALVLDSLAIAAQSLVGAALGAGDAGHAKAVAWRVTAFSLLAAGILAAALGLGSSVLPGLFTDDRSVLAAIGVPWWFMVVQLPFAGIVFAVDGVLLGAGDAAFMRTATVASALVGFLPLVWLSLAYGWGLAGIWSGLGTFIVLRLIFVGWRAYSGRWAVTGAA