Rv1230c Family assigned · medium auto-curated
H37Rv Rv1230c · MTBC0 mtbc0_001319 ·
411 aa · 1381406–1382641 (-) ·
RefSeq NP_215746.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | lytic transglycosylase domain-containing protein |
| Revised (this work) | Lytic transglycosylase domain-containing protein. Pfam: SLT_2 (PF13406.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86313
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | Transglycosylase SLT domain |
| Orthologous group | COG2951 |
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 | 4.486 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 12 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 |
|---|---|---|---|---|
SLT_2 | PF13406.12 | 9.6e-08 | 194–249 | Transglycosylase SLT domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mrp (multiple resistance/pH adaptation protein), high confidence from genomic context alone (score 809 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1229c mrp |
multiple resistance/pH adaptation protein | 809 | 809 ctx | neighborhood:803 |
Rv1231c |
membrane protein | 913 | 762 ctx | neighborhood:761 textmining:653 |
Rv1232c hyp |
hypothetical protein | 762 | 762 ctx | neighborhood:761 |
Rv3594 hyp |
hypothetical protein | 704 | 685 ctx | cooccurence:683 |
Rv2164c hyp |
hypothetical protein | 588 | 588 ctx | cooccurence:572 |
Rv3365c hyp |
hypothetical protein | 541 | 528 ctx | cooccurence:525 |
Rv1233c hyp |
hypothetical protein | 513 | 513 ctx | neighborhood:510 |
Rv3201c adnB |
ATP-dependent DNA helicase | 510 | 511 ctx | cooccurence:495 |
Rv2542 hyp |
hypothetical protein | 486 | 486 ctx | cooccurence:484 |
Rv0345 hyp |
hypothetical protein | 474 | 474 ctx | cooccurence:448 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 458 | 458 ctx | cooccurence:458 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 453 | 454 ctx | cooccurence:447 |
Rv0867c rpfA |
resuscitation-promoting factor RpfA | 444 | 445 ctx | cooccurence:425 |
Rv1226c |
transmembrane protein | 443 | 444 ctx | cooccurence:442 |
Rv0192 hyp |
hypothetical protein | 435 | 435 ctx | cooccurence:428 |
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: membrane protein
- MTBC0 PGAP product: lytic transglycosylase domain-containing protein
- Pfam (hmmscan --cut_ga): SLT_2 PF13406.12 (E=1e-07)
- (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_215746.1)
- Domains: Pfam-A via hmmscan --cut_ga — SLT_2 (PF13406.12)
- 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
COG2951 - Curated reference: UniProt O86313 (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 —
29 functional partner(s); context anchor
mrp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001319|Rv1230c| MHIGGRWGARPAVAAVRRGACRLTRAPAFGVAAIAPLVFASAVGGAAPVFPGRTAPVHAVITPVAAVAASGIDLSGPVVIAMKRPPTSFRVAVATISAPPPPMIVNSPGALGIPAMALSAYRNAELKMAAAAPGCGVSWNLLAGIGRIESMHANGGATDARGTAIQPIYGPTLDGTLPGNEIIIQSSVGNRVTYARAMGPMQFLPGTWARYATDGDDDGVADPQNLFDSTLAAARYLCSGGLNLRDPAQVMAALLRYNNSMPYAQNVLGWAAGYATGVFPVDLPPITGPPPPLGDAHLENPEGLGPGLPINVNGLTADGPMAHLPLIDLTPRQAALNPPPMFPWMAPDPSAPMPGCTLICIGSHGPPVGAPPFPPTAPPPPFLPAAPPPPDPLAGPPGDAGLAPPAPAPAG