Rv1059 Resolved · high auto-curated
H37Rv Rv1059 · MTBC0 mtbc0_001139 ·
354 aa · 1189730–1190794 (+) ·
RefSeq NP_215575.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | dihydrodipicolinate reductase |
| Revised (this work) | Dihydrodipicolinate reductase. Pfam: DapB_N (PF01113.27), DAP_DH_C (PF19328.5). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53407
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | dihydrodipicolinate reductase |
| Orthologous group | COG3804 |
| EC number |
EC 1.4.1.12, EC 1.4.1.26
|
| KEGG orthology |
K21672
|
| KEGG pathways |
map00310, map00330, map00472
|
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 | 0.174 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.23% of strains (338) · 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 |
|---|---|---|---|---|
DapB_N | PF01113.27 | 1.3e-05 | 11–75 | Dihydrodipicolinate reductase, N-terminus |
DAP_DH_C | PF19328.5 | 1.4e-13 | 140–345 | 2,4-diaminopentanoate dehydrogenase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD14 (fatty-acid--CoA ligase FadD14), high confidence from genomic context alone (score 793 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0926c hyp |
hypothetical protein | 925 | 925 | database:900 |
Rv1905c aao |
D-amino acid oxidase | 900 | 900 | database:900 |
Rv1062 hyp |
hypothetical protein | 810 | 810 ctx | neighborhood:772 |
Rv1060 hyp |
hypothetical protein | 809 | 809 ctx | neighborhood:808 |
Rv1061 hyp |
hypothetical protein | 804 | 804 ctx | neighborhood:772 |
Rv1058 fadD14 |
fatty-acid--CoA ligase FadD14 | 793 | 793 ctx | neighborhood:788 |
Rv1057 hyp |
hypothetical protein | 630 | 630 ctx | neighborhood:548 |
Rv0310c hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:537 |
Rv3519 hyp |
hypothetical protein | 508 | 509 ctx | cooccurence:507 |
Rv0273c |
transcriptional regulator | 476 | 477 ctx | cooccurence:474 |
Rv0760c hyp |
hypothetical protein | 475 | 476 ctx | cooccurence:471 |
Rv2042c hyp |
hypothetical protein | 435 | 436 ctx | cooccurence:432 |
Rv2015c hyp |
hypothetical protein | 430 | 430 ctx | cooccurence:430 |
Rv0272c hyp |
hypothetical protein | 425 | 425 ctx | cooccurence:420 |
Rv3577 hyp |
hypothetical protein | 407 | 407 ctx | cooccurence:404 |
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: hypothetical protein
- MTBC0 PGAP product: dihydrodipicolinate reductase
- Pfam (hmmscan --cut_ga): DapB_N PF01113.27 (E=1e-05), DAP_DH_C PF19328.5 (E=1e-13)
- (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_215575.1)
- Domains: Pfam-A via hmmscan --cut_ga — DapB_N (PF01113.27), DAP_DH_C (PF19328.5)
- 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
COG3804 - Curated reference: UniProt O53407 (TrEMBL, unreviewed; 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 —
16 functional partner(s); context anchor
fadD14 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001139|Rv1059| MTMSLRVIQWATGSVGVAAIKGVLQHPELELVGCWVHSAAKSGKDVGEIIGSPPLGVIATNSIDDVLALDADAVIYAPLLPSVDEVAALLRSGKNVVTPLGWFYPSEKEAAPLEVAAQAGNATLHGAGIGPGAVTELFPLLLSVMSTGVTFVRSEEFSDLRSYGAPDVLRYVMGFGGTPDSALTGPMQKILDGGFLQSVRLCVDRLGFAADPQIRTSQEVAVATAPIDSPIGVIEPGQVAGRRFHWEALVEDTVVVQIAVNWLMGSENLDPPWSFGPAGERYEIEVRGSPDTCVTIKGWQPQTVAAGLKSNPGIVATAAHCVNAIPATCAAPAGIQSFFDLPLITGRAAPGLAR