lexA Resolved · high auto-curated
H37Rv Rv2720 · MTBC0 mtbc0_002894 ·
236 aa · 3054203–3054913 (+) ·
RefSeq NP_217236.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | repressor LexA |
|---|---|
| MTBC0 PGAP re-annotation | transcriptional repressor LexA |
| Revised (this work) | Transcriptional repressor LexA. Pfam: LexA_DNA_bind (PF01726.23), Peptidase_S24 (PF00717.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHR7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | LexA repressor |
| EC (curated) |
EC 3.4.21.88
|
| Curated function | Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. Has been shown to bind to the 14 bp palindromic sequence 5'-CGAACNNNNGTTCG-3'. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | lexA |
| eggNOG description | Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair |
| Orthologous group | COG1974 |
| EC number |
EC 3.4.21.88
|
| KEGG orthology |
K01356
|
| KEGG modules |
M00729
|
| Gene Ontology (67) |
GO:0000976, GO:0001067, GO:0001130, GO:0001217, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005575, GO:0005618 +55 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 | 0.12 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
LexA_DNA_bind | PF01726.23 | 1.4e-29 | 25–88 | LexA DNA binding domain |
Peptidase_S24 | PF00717.29 | 3.6e-33 | 118–230 | Peptidase S24-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: chiZ (membrane protein), high confidence from genomic context alone (score 773 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2737c recA |
recombinase A | 998 | 977 | coexpression:855 experimental:829 textmining:958 |
Rv2719c chiZ |
membrane protein | 859 | 773 ctx | neighborhood:723 textmining:408 |
Rv2718c nrdR |
transcriptional regulator NrdR | 799 | 770 ctx | neighborhood:667 |
Rv1537 dinX |
DNA polymerase IV | 925 | 681 | experimental:463 textmining:777 |
Rv1696 recN |
DNA repair protein RecN | 869 | 651 | coexpression:649 textmining:640 |
Rv3056 dinP |
DNA polymerase IV 2 | 832 | 601 | experimental:463 textmining:598 |
Rv3394c hyp |
hypothetical protein | 629 | 589 | experimental:463 |
Rv2717c hyp |
hypothetical protein | 461 | 461 ctx | neighborhood:454 |
Rv1931c |
transcriptional regulator | 454 | 451 | |
Rv0052 hyp |
hypothetical protein | 452 | 450 | |
Rv1930c hyp |
hypothetical protein | 471 | 448 | |
Rv2191 hyp |
hypothetical protein | 646 | 422 | textmining:413 |
Rv3833 |
AraC family transcriptional regulator | 408 | 409 | |
Rv1657 argR |
arginine repressor | 835 | 381 | textmining:745 |
Rv0605 |
IS1536 family serine type transposase | 445 | 380 |
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: repressor LexA
- MTBC0 PGAP product: transcriptional repressor LexA
- Pfam (hmmscan --cut_ga): LexA_DNA_bind PF01726.23 (E=1e-29), Peptidase_S24 PF00717.29 (E=4e-33)
- (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_217236.2)
- Domains: Pfam-A via hmmscan --cut_ga — LexA_DNA_bind (PF01726.23), Peptidase_S24 (PF00717.29)
- 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
COG1974 - Curated reference: UniProt P9WHR7 (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 —
85 functional partner(s); context anchor
chiZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002894|Rv2720|lexA MNDSNDTSVAGGAAGADSRVLSADSALTERQRTILDVIRASVTSRGYPPSIREIGDAVGLTSTSSVAHQLRTLERKGYLRRDPNRPRAVNVRGADDAALPPVTEVAGSDALPEPTFVPVLGRIAAGGPILAEEAVEDVFPLPRELVGEGTLFLLKVIGDSMVEAAICDGDWVVVRQQNVADNGDIVAAMIDGEATVKTFKRAGGQVWLMPHNPAFDPIPGNDATVLGKVVTVIRKV