lsr2 Resolved · high auto-curated
H37Rv Rv3597c · MTBC0 mtbc0_003816 ·
112 aa · 4064685–4065023 (-) ·
RefSeq NP_218114.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | iron-regulated H-NS-like protein |
|---|---|
| MTBC0 PGAP re-annotation | histone-like nucleoid-structuring protein Lsr2 |
| Revised (this work) | Histone-like nucleoid-structuring protein Lsr2. Pfam: Lsr2 (PF11774.15), Lsr2_DNA-bd (PF23359.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nucleoid-associated protein Lsr2 |
| Curated function | DNA-bridging protein that has both architectural and regulatory roles. Influences the organization of chromatin and gene expression by binding non-specifically to DNA, with a preference for AT-rich sequences, and bridging distant DNA segments. Binds in the minor groove of AT-rich DNA. Represses expression of multiple genes involved in a broad range of cellular processes, including major virulence factors or antibiotic-induced genes, such as iniBAC or efpA, and genes important for adaptation of changing O(2) levels. May also activate expression of some gene. May coordinate global gene regulatio. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lsr2 |
| eggNOG description | pathogenesis |
| Orthologous group | 2C4MW |
| Gene Ontology (82) |
GO:0000302, GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +70 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 | 0.698 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Lsr2 | PF11774.15 | 1.2e-28 | 1–59 | Lsr2 dimerization domain |
Lsr2_DNA-bd | PF23359.2 | 2.0e-19 | 76–111 | Lsr2 DNA-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: clpC1 (ATP-dependent protease ATP-binding subunit ClpC), high confidence from genomic context alone (score 724 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3596c clpC1 |
ATP-dependent protease ATP-binding subunit ClpC | 724 | 724 ctx | neighborhood:721 |
Rv3601c panD |
aspartate 1-decarboxylase | 703 | 704 ctx | neighborhood:702 |
Rv3602c panC |
pantothenate synthetase | 703 | 703 ctx | neighborhood:702 |
Rv3600c coaX |
type III pantothenate kinase | 703 | 703 ctx | neighborhood:702 |
Rv3603c hyp |
hypothetical protein | 702 | 702 ctx | neighborhood:702 |
Rv3604c |
transmembrane protein | 663 | 650 ctx | neighborhood:645 |
Rv3610c ftsH |
zinc metalloprotease FtsH | 687 | 620 ctx | neighborhood:561 |
Rv3598c lysS |
lysine--tRNA ligase | 607 | 607 ctx | neighborhood:606 |
Rv3607c folB |
dihydroneopterin aldolase | 596 | 596 ctx | neighborhood:593 |
Rv3605c hyp |
hypothetical protein | 596 | 596 ctx | neighborhood:596 |
Rv2256c hyp |
hypothetical protein | 590 | 591 ctx | cooccurence:575 |
Rv3608c folP1 |
dihydropteroate synthase | 579 | 578 ctx | neighborhood:577 |
Rv0786c hyp |
hypothetical protein | 546 | 546 ctx | cooccurence:546 |
Rv2239c hyp |
hypothetical protein | 543 | 543 ctx | cooccurence:539 |
Rv0498 hyp |
hypothetical protein | 523 | 523 ctx | cooccurence:520 |
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: iron-regulated H-NS-like protein
- MTBC0 PGAP product: histone-like nucleoid-structuring protein Lsr2
- Pfam (hmmscan --cut_ga): Lsr2 PF11774.15 (E=1e-28), Lsr2_DNA-bd PF23359.2 (E=2e-19)
- (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_218114.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lsr2 (PF11774.15), Lsr2_DNA-bd (PF23359.2)
- 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
2C4MW - Curated reference: UniProt P9WIP7 (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 —
56 functional partner(s); context anchor
clpC1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003816|Rv3597c|lsr2 MAKKVTVTLVDDFDGSGAADETVEFGLDGVTYEIDLSTKNATKLRGDLKQWVAAGRRVGGRRRGRSGSGRGRGAIDREQSAAIREWARRNGHNVSTRGRIPADVIDAYHAAT