recN Resolved · high auto-curated
H37Rv Rv1696 · MTBC0 mtbc0_001804 ·
587 aa · 1931698–1933461 (+) ·
RefSeq NP_216212.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA repair protein RecN |
|---|---|
| MTBC0 PGAP re-annotation | DNA repair protein RecN |
| Revised (this work) | DNA repair protein RecN. Pfam: SMC_N (PF02463.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHI7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA repair protein RecN |
| Curated function | May be involved in recombinational repair of damaged DNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recN |
| eggNOG description | May be involved in recombinational repair of damaged DNA |
| Orthologous group | COG0497 |
| KEGG orthology |
K03631
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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 | 0.249 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
SMC_N | PF02463.26 | 4.3e-15 | 2–535 | RecF/RecN/SMC N terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tlyA (16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA), high confidence from genomic context alone (score 895 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 917 | 895 ctx | neighborhood:867 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 978 | 882 ctx | neighborhood:867 textmining:821 |
Rv1693 hyp |
hypothetical protein | 981 | 869 ctx | neighborhood:867 textmining:861 |
Rv1691 hyp |
hypothetical protein | 981 | 869 ctx | neighborhood:867 textmining:866 |
Rv1692 |
phosphatase | 980 | 867 ctx | neighborhood:867 textmining:861 |
Rv1698 mctB |
copper transporter MctB | 761 | 761 ctx | neighborhood:756 |
Rv2737c recA |
recombinase A | 937 | 708 | coexpression:689 textmining:793 |
Rv1690 lprJ |
lipoprotein LprJ | 668 | 668 ctx | neighborhood:668 |
Rv1697 steA hyp |
hypothetical protein | 654 | 654 ctx | neighborhood:651 |
Rv2720 lexA |
repressor LexA | 869 | 651 | coexpression:649 textmining:640 |
Rv1713 engA |
GTPase Der | 579 | 579 | |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 691 | 569 ctx | neighborhood:440 |
Rv3423c alr |
alanine racemase | 591 | 551 ctx | cooccurence:546 |
Rv1700 |
NUDIX hydrolase | 549 | 521 ctx | neighborhood:514 |
Rv1699 pyrG |
CTP synthase | 569 | 518 ctx | neighborhood:513 |
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 repair protein RecN
- MTBC0 PGAP product: DNA repair protein RecN
- Pfam (hmmscan --cut_ga): SMC_N PF02463.26 (E=4e-15)
- (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_216212.1)
- Domains: Pfam-A via hmmscan --cut_ga — SMC_N (PF02463.26)
- 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
COG0497 - Curated reference: UniProt P9WHI7 (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 —
88 functional partner(s); context anchor
tlyA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001804|Rv1696|recN MLTELRIESLGAISVATAEFDRGFTVLTGETGTGKTMVVTGLHLLGGARADATRVRSGADRAVVEGRFTTTDLDDATVAGLQAVLDSSGAERDEDGSVIALRSISRDGPSRAYLGGRGVPAKSLSGFTNELLTLHGQNDQLRLMRPDEQRGALDRFAAAGEAVQRYRKLRDAWLTARRDLVDRRNRARELAQEADRLKFALNEIDTVDPQPGEDVALVADIARLSELDTLREAATTARATLCGTPDADAFDRGAVDSLGRARAALQSSDDAALRGLAEQVGEALTVVVDAVAELGAYLDELPADASALDAKLARQAQLRTLTRKYAADIDGVLRWADEARARLAQLDVSEEGLAALERRTGELAHELGQAAVDLSTIRRKAAKRLAKEVSAELSALAMADAEFTIGVTTELADHGDPVALALASGELARAGADGVDAVEFGFVAHRGMTVLPLAKSASGGELSRVMLSLEVVLATSRKQAAGTTMVFDEIDAGVGGWAAVQIGRRLARLARTHQVIVVTHLPQVAAYADVHLMVQRTGRDGASGVRRLTSEDRVAELARMLAGLGDSDSGRAHARELLETAQNDELT