Rv2864c Family assigned · medium auto-curated
H37Rv Rv2864c · MTBC0 mtbc0_003046 ·
603 aa · 3196120–3197931 (-) ·
RefSeq NP_217380.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | penicillin-binding lipoprotein |
|---|---|
| MTBC0 PGAP re-annotation | penicillin-binding protein |
| Revised (this work) | Penicillin-binding protein. Pfam: MecA_N (PF05223.18), Transpeptidase (PF00905.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33346
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible penicillin-binding lipoprotein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | pbp2B |
| eggNOG description | penicillin-binding protein |
| Orthologous group | COG0768 |
| EC number |
EC 3.4.16.4
|
| KEGG orthology |
K01286
|
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 | 0.152 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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 |
|---|---|---|---|---|
MecA_N | PF05223.18 | 1.3e-27 | 32–139 | NTF2-like N-terminal transpeptidase domain |
Transpeptidase | PF00905.28 | 7.2e-33 | 326–581 | Penicillin binding protein transpeptidase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ponA2 (bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase), high confidence from genomic context alone (score 785 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2151c ftsQ |
cell division protein FtsQ | 872 | 858 | experimental:781 |
Rv2154c ftsW |
lipid II flippase FtsW | 800 | 787 | experimental:589 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 941 | 785 ctx | cooccurence:599 experimental:419 textmining:738 |
Rv0017c rodA |
cell division protein RodA | 782 | 768 | experimental:589 |
Rv2091c |
membrane protein | 680 | 670 ctx | cooccurence:670 |
Rv2867c |
GCN5-like N-acetyltransferase | 614 | 614 ctx | neighborhood:544 |
Rv0185 hyp |
hypothetical protein | 562 | 562 ctx | cooccurence:561 |
Rv2868c gcpE |
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) | 556 | 556 ctx | neighborhood:544 |
Rv2869c rip |
zinc metalloprotease | 579 | 554 ctx | neighborhood:528 |
Rv2870c dxr |
1-deoxy-D-xylulose 5-phosphate reductoisomerase | 550 | 551 ctx | neighborhood:539 |
Rv2446c |
integral membrane protein | 547 | 548 ctx | cooccurence:540 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 551 | 522 | coexpression:443 |
Rv0863 hyp |
hypothetical protein | 518 | 519 ctx | cooccurence:517 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 880 | 515 | experimental:419 textmining:762 |
Rv0556 |
transmembrane protein | 493 | 494 ctx | cooccurence:491 |
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: penicillin-binding lipoprotein
- MTBC0 PGAP product: penicillin-binding protein
- Pfam (hmmscan --cut_ga): MecA_N PF05223.18 (E=1e-27), Transpeptidase PF00905.28 (E=7e-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_217380.1)
- Domains: Pfam-A via hmmscan --cut_ga — MecA_N (PF05223.18), Transpeptidase (PF00905.28)
- 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
COG0768 - Curated reference: UniProt O33346 (TrEMBL, unreviewed; Predicted)
- 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 —
63 functional partner(s); context anchor
ponA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003046|Rv2864c| MVTKTTLASATSGLLLLAVVAMSGCTPRPQGPGPAAEKFFAALAIGDTASAAQLSDNPNEAREALNAAWAGLQAAHLDAQVLSAKYAEDTGTVAYRFSWHLPKDRIWTYDGQLKMARDEGRWHVRWTTSGLHPKLGEHQTFALRADPPRRASVNEVGGTDVLVPGYLYHYSLDAGQAGRELFGTAHAVVGALHPFDDTLNDPQLLAEQASSSTQPLDLVTLHADDSNRVAAAIGQLPGVVITPQAELLPTDKHFAPAVLNDVKKAVVDELDGKAGWRVVSVNQNGVDVSVLHEVAPSPASSVSITLDRVVQNAAQHAVNTRGGKAMIVVIKPSTGEILAIAQNAGADADGPVATTGLYPPGSTFKMITAGAAVERDLATPETLLGCPGEIDIGHRTIPNYGGFDLGVVPMSRAFASSCNTTFAELSSRLPPRGLTQAARRYGIGLDYQVDGITTVTGSVPPTVDLAERTEDGFGQGKVLASPFGMALVAATVAAGKTPVPQLIAGRPTAVEGDATPISQKMIDALRPMMRLVVTNGTAKEIAGCGEVFGKTGEAEFPGGSHSWFAGYRGDLAFASLIVGGGSSEYAVRMTKVMFESLPPGYLA