Rv0192 Family assigned · medium auto-curated
H37Rv Rv0192 · MTBC0 - ·
366 aa · 223564–224664 (+) ·
RefSeq NP_214706.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Big_10 (PF17964.8), YkuD (PF03734.20) 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 |
O07436
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L,D-transpeptidase 4 |
| EC (curated) |
EC 2.3.2.-
|
| Curated function | Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ErfK YbiS YcfS YnhG family protein |
| Orthologous group | COG1376 |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 13 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 28.93% of strains (42010) · 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 |
|---|---|---|---|---|
Big_10 | PF17964.8 | 2.0e-22 | 137–209 | Bacterial Ig domain |
YkuD | PF03734.20 | 3.0e-23 | 224–348 | L,D-transpeptidase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0191 (MFS-type transporter), medium confidence from genomic context alone (score 678 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) |
|---|---|---|---|---|
Rv0191 |
MFS-type transporter | 678 | 678 ctx | neighborhood:672 |
Rv3015c hyp |
hypothetical protein | 635 | 635 ctx | cooccurence:635 |
Rv3330 dacB1 |
penicillin-binding protein DacB | 598 | 576 | database:500 |
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 546 | 521 | database:500 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 578 | 517 | database:500 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 540 | 503 | database:500 |
Rv0190 ricR hyp |
hypothetical protein | 452 | 452 ctx | neighborhood:449 |
Rv1024 |
membrane protein | 450 | 450 ctx | cooccurence:427 |
Rv2413c hyp |
hypothetical protein | 444 | 444 ctx | cooccurence:443 |
Rv1230c |
membrane protein | 435 | 435 ctx | cooccurence:428 |
Rv3201c adnB |
ATP-dependent DNA helicase | 430 | 430 ctx | cooccurence:423 |
Rv1312 hyp |
hypothetical protein | 403 | 403 ctx | cooccurence:403 |
Rv3835 hyp |
hypothetical protein | 414 | 348 |
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): Big_10 PF17964.8 (E=2e-22), YkuD PF03734.20 (E=3e-23)
- (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_214706.1)
- Domains: Pfam-A via hmmscan --cut_ga — Big_10 (PF17964.8), YkuD (PF03734.20)
- 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
COG1376 - Curated reference: UniProt O07436 (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 —
13 functional partner(s); context anchor
Rv0191 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0192| MPHWAEERHRRESNYVALEAGLDEGESIRRSEHSRSGCGADAGCWRCRGGPGRGSRRSRRSRGPGGTAGPVDPPAVDLLAPPPDPLALPPALDPLAPPPPDPLAPPPPDPLAVPVAAGPVAGQDPTSFVGPPPFRPPTFNPVDGAMVGVAKPIVINFAVPIADRAMAESAIHISSIPPVPGKFYWMSPTQVRWRPFEFWPANTAVNIDAAGTKSSFRTGDSLVATADDATHQMTITRNGVVQKTFPMSMGMVSGGHQTPNGTYYVLEKFATVVMDSSTYGVPVNSAQGYKLTVSDAVRIDNSGNFVHSAPWSVADQGKRNVTHGCINLSPANAKWFYDNFGSGDPVVVKNSVGTYNKNDGAQDWQI