dapF Resolved · high auto-curated
H37Rv Rv2726c · MTBC0 mtbc0_002900 ·
289 aa · 3061346–3062215 (-) ·
RefSeq NP_217242.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | diaminopimelate epimerase |
|---|---|
| MTBC0 PGAP re-annotation | diaminopimelate epimerase |
| Revised (this work) | Diaminopimelate epimerase. Pfam: DAP_epimerase (PF01678.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP19
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Diaminopimelate epimerase |
| EC (curated) |
EC 5.1.1.7
|
| Curated function | Catalyzes the stereoinversion of LL-2,6-diaminopimelate (L,L-DAP) to meso-diaminopimelate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dapF |
| eggNOG description | Catalyzes the stereoinversion of LL-2,6- diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso- DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan |
| Orthologous group | COG0253 |
| EC number |
EC 5.1.1.7
|
| KEGG orthology |
K01778
|
| KEGG pathways |
map00300, map01100, map01110, map01120, map01130, map01230
|
| KEGG modules |
M00016, M00525, M00527
|
| Gene Ontology (50) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006082, GO:0006520, GO:0006553, GO:0006807 +38 more
|
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 | 0.36 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
DAP_epimerase | PF01678.25 | 9.1e-30 | 3–141 | Diaminopimelate epimerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lysA (diaminopimelate decarboxylase), high confidence from genomic context alone (score 972 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1293 lysA |
diaminopimelate decarboxylase | 996 | 972 ctx | cooccurence:643 database:900 textmining:886 |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 997 | 959 ctx | cooccurence:557 database:900 textmining:949 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 979 | 926 | database:900 textmining:730 |
Rv2727c miaA |
tRNA delta(2)-isopentenylpyrophosphate transferase | 850 | 850 ctx | neighborhood:849 |
Rv2728c hyp |
hypothetical protein | 850 | 850 ctx | neighborhood:849 |
Rv2725c hflX |
GTP-binding protein HflX | 927 | 817 ctx | neighborhood:808 textmining:623 |
Rv3708c asd |
aspartate-semialdehyde dehydrogenase | 969 | 767 | coexpression:677 textmining:875 |
Rv2773c dapB |
4-hydroxy-tetrahydrodipicolinate reductase | 969 | 731 ctx | cooccurence:708 textmining:890 |
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 965 | 730 ctx | cooccurence:697 textmining:877 |
Rv3859c gltB |
glutamate synthase large subunit | 835 | 724 ctx | neighborhood:544 coexpression:420 textmining:426 |
Rv1178 dapC |
aminotransferase | 898 | 685 ctx | cooccurence:581 textmining:691 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 609 | 593 ctx | fusion:560 |
Rv3709c ask |
aspartokinase | 932 | 509 ctx | cooccurence:437 textmining:868 |
Rv2729c |
integral membrane protein | 524 | 504 ctx | neighborhood:503 |
Rv2731 hyp |
hypothetical protein | 491 | 491 ctx | neighborhood:483 |
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: diaminopimelate epimerase
- MTBC0 PGAP product: diaminopimelate epimerase
- Pfam (hmmscan --cut_ga): DAP_epimerase PF01678.25 (E=9e-30)
- (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_217242.1)
- Domains: Pfam-A via hmmscan --cut_ga — DAP_epimerase (PF01678.25)
- 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
COG0253 - Curated reference: UniProt P9WP19 (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 —
54 functional partner(s); context anchor
lysA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002900|Rv2726c|dapF MIFAKGHGTQNDFVLLPDVDAELVLTAARVAALCDRRKGLGADGVLRVTTAGAAQAVGVLDSLPEGVRVTDWYMDYRNADGSAAQMCGNGVRVFAHYLRASGLEVRDEFVVGSLAGPRPVTCHHVEAAYADVSVDMGKANRLGAGEAVVGGRRFHGLAVDVGNPHLACVDSQLTVDGLAALDVGAPVSFDGAQFPDGVNVEVLTAPVDGAVWMRVHERGVGETRSCGTGTVAAAVAALAAVGSPTGTLTVHVPGGEVVVTVTDATSFLRGPSVLVARGDLADDWWNAMG