Rv2417c Family assigned · medium auto-curated
H37Rv Rv2417c · MTBC0 mtbc0_002573 ·
280 aa · 2739740–2740582 (-) ·
RefSeq NP_216933.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DegV domain-containing protein |
|---|---|
| MTBC0 PGAP re-annotation | DegV family protein |
| Revised (this work) | DegV family protein. Pfam: DegV (PF02645.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP05
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DegV domain-containing protein Rv2417c |
| Curated function | May bind long-chain fatty acids, such as palmitate, and may play a role in lipid transport or fatty acid metabolism. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | DegV family |
| Orthologous group | COG1307 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
DegV | PF02645.22 | 1.5e-74 | 3–272 | Uncharacterised protein, DegV family COG1307 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gpgP (glucosyl-3-phosphoglycerate phosphatase), high confidence from genomic context alone (score 825 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2974c hyp |
hypothetical protein | 930 | 928 ctx | cooccurence:774 experimental:652 |
Rv2419c gpgP |
glucosyl-3-phosphoglycerate phosphatase | 976 | 825 ctx | neighborhood:786 textmining:870 |
Rv2418c octT hyp |
hypothetical protein | 973 | 797 ctx | neighborhood:786 textmining:875 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 794 | 794 ctx | neighborhood:786 |
Rv2420c rsfS hyp |
hypothetical protein | 787 | 788 ctx | neighborhood:786 |
Rv2975c hyp |
hypothetical protein | 762 | 753 | experimental:652 |
Rv2425c hyp |
hypothetical protein | 606 | 606 ctx | neighborhood:544 |
Rv0499 hyp |
hypothetical protein | 562 | 563 | coexpression:494 |
Rv2426c hyp |
hypothetical protein | 553 | 554 ctx | neighborhood:544 |
Rv2427c proA |
gamma-glutamyl phosphate reductase | 546 | 547 ctx | neighborhood:544 |
Rv3308 pmmB |
phosphomannomutase PmmB | 512 | 513 | coexpression:409 |
Rv2416c eis |
enhanced intracellular survival protein | 691 | 499 ctx | neighborhood:494 textmining:410 |
Rv2414c hyp |
hypothetical protein | 428 | 428 ctx | neighborhood:415 |
Rv2415c hyp |
hypothetical protein | 424 | 425 ctx | neighborhood:420 |
Rv2413c hyp |
hypothetical protein | 416 | 417 |
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: DegV domain-containing protein
- MTBC0 PGAP product: DegV family protein
- Pfam (hmmscan --cut_ga): DegV PF02645.22 (E=2e-74)
- (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_216933.1)
- Domains: Pfam-A via hmmscan --cut_ga — DegV (PF02645.22)
- 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
COG1307 - Curated reference: UniProt P9WP05 (SwissProt, reviewed; Evidence at protein level)
- 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 —
21 functional partner(s); context anchor
gpgP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002573|Rv2417c| MTVVVVTDTSCRLPADLREQWSIRQVPLHILLDGLDLRDGVDEIPDDIHKRHATTAGATPVELSAAYQRALADSGGDGVVAVHISSALSGTFRAAELTAAELGPAVRVIDSRSAAMGVGFAALAAGRAAAAGDELDTVARAAAAAVSRIHAFVAVARLDNLRRSGRISGAKAWLGTALALKPLLSVDDGKLVLVQRVRTVSNATAVMIDRVCQLVGDRPAALAVHHVADPAAANDVAAALAERLPACEPAMVTAMGPVLALHVGAGAVGVCVDVGASPPA