lcp1 Resolved · high auto-curated
H37Rv Rv3267 · MTBC0 mtbc0_003475 ·
498 aa · 3670028–3671524 (+) ·
RefSeq NP_217784.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | phosphotransferase Lcp1 |
| Revised (this work) | Phosphotransferase Lcp1. Pfam: LytR_cpsA_psr (PF03816.20), LytR_C (PF13399.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96872
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 |
K Transcription
|
|---|---|
| Preferred name | lytR2 |
| eggNOG description | cell envelope-related transcriptional attenuator |
| Orthologous group | COG1316 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 |
|---|---|---|---|---|
LytR_cpsA_psr | PF03816.20 | 1.6e-42 | 95–263 | LytR_cpsA_psr family |
LytR_C | PF13399.12 | 2.6e-14 | 365–449 | LytR cell envelope-related transcriptional attenuator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: manB (D-alpha-D-mannose-1-phosphate guanylyltransferase ManB), high confidence from genomic context alone (score 847 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) |
|---|---|---|---|---|
Rv3268 hyp |
hypothetical protein | 951 | 951 ctx | neighborhood:825 coexpression:734 |
Rv3264c manB |
D-alpha-D-mannose-1-phosphate guanylyltransferase ManB | 847 | 847 ctx | neighborhood:783 |
Rv3265c wbbL1 |
N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase | 919 | 831 ctx | neighborhood:783 textmining:545 |
Rv3266c rmlD |
dTDP-4-dehydrorhamnose reductase | 931 | 787 ctx | neighborhood:784 textmining:693 |
Rv1697 steA hyp |
hypothetical protein | 766 | 766 | coexpression:732 |
Rv3270 ctpC |
manganese/zinc-exporting P-type ATPase | 716 | 717 ctx | neighborhood:715 |
Rv3269 hyp |
hypothetical protein | 688 | 689 ctx | neighborhood:687 |
Rv3311 hyp |
hypothetical protein | 649 | 649 ctx | cooccurence:644 |
Rv3212 hyp |
hypothetical protein | 602 | 603 ctx | cooccurence:597 |
Rv0996 |
transmembrane protein | 599 | 599 ctx | cooccurence:512 |
Rv3438 hyp |
hypothetical protein | 581 | 581 ctx | cooccurence:581 |
Rv3794 embA |
arabinosyltransferase A | 589 | 539 ctx | cooccurence:533 |
Rv3795 embB |
arabinosyltransferase B | 551 | 521 ctx | cooccurence:517 |
Rv3244c lpqB |
lipoprotein LpqB | 520 | 521 ctx | cooccurence:492 |
Rv3793 embC |
arabinosyltransferase C | 530 | 519 ctx | cooccurence:512 |
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: phosphotransferase Lcp1
- Pfam (hmmscan --cut_ga): LytR_cpsA_psr PF03816.20 (E=2e-42), LytR_C PF13399.12 (E=3e-14)
- (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_217784.1)
- Domains: Pfam-A via hmmscan --cut_ga — LytR_cpsA_psr (PF03816.20), LytR_C (PF13399.12)
- 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
COG1316 - Curated reference: UniProt P96872 (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 —
54 functional partner(s); context anchor
manB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003475|Rv3267|lcp1 MMSAQRVVRTVRTARAISTALAVAIVLGTGVAWSSVRSFEDGIFHMSAPSLGHGGDDGAIDILLVGLDSRTDAHGNPLSAEELATLHAGDEEATNTDTIILIRVPNNGKSATAISIPRDSYVAAPGLGKTKINGVYGQTRETKRAGLVQAGASPTEAAAAGTEAGREALIKTVADLTGVTVDHYAEIGLLGFALIADALGGVDVCLKEPVYEPLSGADFPAGRQKLNGPQALSFVRQRHDLPRGDLDRVVRQQAVMAALAHRVISGQTLSSPATLKRLEQAVQRSVVLSSGWDIMDFVRQLQKLAGGNVAFATIPVLDGAGWSDDGMQSVVRVDPRQVQDWVVGLLHEQDQGKTDELAYTPAKTTANVVNDTDINGLAAAVSKVLSSKGFTTGSVGNNDGDHVPGSQVRAAKADDLGAQQVAKELGGLPVVADASIAPGSVRVVLANDYSGPGSGLGGSDPNGVVSPARAFNLGSADDTTPPPSPILTAGSDAPECIN