Rv3811 Family assigned · medium auto-curated
H37Rv Rv3811 · MTBC0 - ·
539 aa · 4274798–4276417 (+) ·
RefSeq YP_178018.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Rv3811_N (PF27503.1), Amidase_2 (PF01510.31), LGFP (PF08310.18) 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
Q79F96
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Peptidoglycan recognition protein family domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | csp |
| eggNOG description | N-acetylmuramoyl-L-alanine amidase |
| Orthologous group | COG5479 |
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) pseudogene candidate
| pN/pS | 0.452 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 8 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 3.97% of strains (5762) · clonal |
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 |
|---|---|---|---|---|
Rv3811_N | PF27503.1 | 3.4e-29 | 28–139 | Rv3811 N-terminal galactose-binding domain-like |
Amidase_2 | PF01510.31 | 7.6e-14 | 220–374 | N-acetylmuramoyl-L-alanine amidase |
LGFP | PF08310.18 | 4.2e-16 | 420–471 | LGFP repeat |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pirG (cell surface protein), high confidence from genomic context alone (score 779 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) |
|---|---|---|---|---|
Rv3810 pirG |
cell surface protein | 787 | 779 ctx | neighborhood:714 |
Rv0207c hyp |
hypothetical protein | 561 | 561 ctx | cooccurence:555 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 553 | 537 | |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 536 | 536 ctx | neighborhood:536 |
Rv3492c |
Mce associated protein | 472 | 472 | |
Rv3808c glfT2 |
galactofuranosyl transferase GlfT | 466 | 466 | |
Rv3668c |
protease | 458 | 458 ctx | cooccurence:458 |
Rv3809c glf |
UDP-galactopyranose mutase | 466 | 447 ctx | neighborhood:422 |
Rv1363c |
membrane protein | 423 | 423 | |
Rv3268 hyp |
hypothetical protein | 416 | 414 | |
Rv1972 |
Mce associated membrane protein | 404 | 405 | |
Rv3802c |
membrane protein | 400 | 400 | |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 459 | 351 | |
Rv3707c hyp |
hypothetical protein | 515 | 258 | |
Rv3594 hyp |
hypothetical protein | 920 | 179 | textmining:907 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): Rv3811_N PF27503.1 (E=3e-29), Amidase_2 PF01510.31 (E=8e-14), LGFP PF08310.18 (E=4e-16)
- (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 YP_178018.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv3811_N (PF27503.1), Amidase_2 (PF01510.31), LGFP (PF08310.18)
- 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
COG5479 - Curated reference: UniProt Q79F96 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
29 functional partner(s); context anchor
pirG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3811| MAATVVIVAWIANRPPASSHEPSPTPNTQLAEQPLIGLGGGVTVRELTQDTPFSLVALTGDLAGTSARVRAKRPDGDWGPWYQTEYETEPRDPAGTDGSVELGGLNPGPRSTDPVFVGTTTTVQVAVTRPIDAPITQPPAGRPPNDLLDSGLGYRPATKEQPFGQNISAILISPPQAPPGTQWTPPTAVTMAGQPPAIISRAEWGADESLRCETPEYDRGVRAAVVHHTAGSNDYSPLESAGIVKAIYTYHSKTLGWCDIAYNALVDKYGQVFEGSAGGLTKPVEGFHTGGFNRNTWGVAMIGNFDDVAPTPIQIRTVGRLLGWRLGMDDVDPRSMVDLQSAGSSYTTFPGGAIARLPAIFTHRDVGNTDCPGNAAYAVMDEIRDIAAHFNDPPEELIKALEGGAIYQRWQALGGMNSALGAPTSPEADAADGARYATFAKGAMYWSPVTDAQPITGAIYEAWASQSYERGPLGLPTSAEIQEPLQITQNFQHGTLNFERLTGNVTEVVDGITTPLATRPPSGPTVPPEHFTLPTHPIT