lppK Family assigned · medium auto-curated
H37Rv Rv2116 · MTBC0 mtbc0_002248 ·
189 aa · 2403834–2404403 (+) ·
RefSeq NP_216632.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppK |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains Mtb12_C (PF26580.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK75
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LppK |
UniProt still lists this protein as Putative lipoprotein LppK; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | lppK |
|---|---|
| Orthologous group | 2A0RD |
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, 5 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 |
|---|---|---|---|---|
Mtb12_C | PF26580.1 | 3.2e-28 | 53–170 | Low molecular weight antigen MTB12, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1629 polA |
DNA polymerase I | 995 | 993 | coexpression:414 experimental:970 database:630 |
Rv2090 |
5'-3' exonuclease | 948 | 944 | experimental:772 database:630 |
Rv0001 dnaA |
chromosomal replication initiator protein DnaA | 932 | 924 | coexpression:707 experimental:737 |
Rv2101 helZ |
helicase HelZ | 919 | 911 | experimental:769 database:614 |
Rv3731 ligC |
DNA ligase C | 893 | 887 | experimental:629 database:609 |
Rv3062 ligB |
DNA ligase | 892 | 886 | experimental:629 database:609 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 895 | 885 | experimental:629 database:609 |
Rv2117 hyp |
hypothetical protein | 884 | 884 ctx | neighborhood:882 |
Rv2737c recA |
recombinase A | 898 | 859 | coexpression:430 experimental:436 database:564 |
Rv1537 dinX |
DNA polymerase IV | 862 | 853 | experimental:627 database:612 |
Rv3056 dinP |
DNA polymerase IV 2 | 861 | 852 | experimental:627 database:612 |
Rv3394c hyp |
hypothetical protein | 861 | 852 | experimental:627 database:612 |
Rv2902c rnhB |
ribonuclease HII | 860 | 842 | coexpression:419 experimental:738 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 850 | 834 | experimental:414 database:653 |
Rv2413c hyp |
hypothetical protein | 851 | 832 | experimental:829 |
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: lipoprotein LppK
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): Mtb12_C PF26580.1 (E=3e-28)
- (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_216632.1)
- Domains: Pfam-A via hmmscan --cut_ga — Mtb12_C (PF26580.1)
- 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
2A0RD - Curated reference: UniProt P9WK75 (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 — 143 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002248|Rv2116|lppK MRRNIRVTLGAATIVAALGLSGCSHPEFKRSSPPAPSLPPVTSSPLEAAPITPLPAPEALIDVLSRLADPAVPGTNKVQLIEGATPENAAALDRFTTALRDGSYLPMTFAANDIAWSDNKPSDVMATVVVTTAHPDNREFTFPMEFVSFKGGWQLSRQTAEMLLAMGNSPDSTPSATSPAPAPSPTPPG