Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
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| MTBC0 PGAP re-annotation | DUF5336 domain-containing protein |
|---|
| Revised (this work) | Component of the mycobacterial cell-division complex (divisome). RefSeq leaves this locus 'hypothetical protein'. The previously uncharacterised Rv0954 protein localises to the mid-cell during cell division and interacts with the division-related proteins LamA, PbpA and PknH; transposon mutagenesis shows genetic interactions with cell-division genes, indicating that Rv0954 participates in cell division and is a candidate divisome component (Wang & Ehrt 2021). Also identified as a glycoprotein of the cell envelope. Experimentally characterised. |
|---|
Curated reference (UniProt)
| UniProt |
P9WIR9
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | 34 kDa antigenic protein homolog |
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Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
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| eggNOG description | Family of unknown function (DUF5336) |
|---|
| Orthologous group | 2EGIB |
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| Gene Ontology (14) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0044425, GO:0044459 +2 more
|
|---|
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 |
0.361 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
8 synonymous, 8 missense, 0 nonsense, 1 frameshift
|
|---|
| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.51% of strains
(737) · 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 |
|---|
DUF5336 | PF17270.9 |
1.9e-32 | 36–166 |
Family of unknown function (DUF5336) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner:
Rv0955 (integral membrane protein),
high confidence from genomic context alone
(score 828 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0955 |
integral membrane protein |
828 |
828 ctx |
neighborhood:823 |
Rv0953c |
oxidoreductase |
767 |
768 ctx |
neighborhood:768 |
Rv3442c rpsI |
30S ribosomal protein S9 |
735 |
735 |
coexpression:734 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase |
732 |
732 ctx |
neighborhood:729 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha |
731 |
731 |
coexpression:731 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN |
730 |
730 ctx |
neighborhood:729 |
Rv0959 hyp |
hypothetical protein |
673 |
674 ctx |
neighborhood:673 |
Rv0958 |
magnesium chelatase |
672 |
673 ctx |
neighborhood:671 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta |
540 |
540 |
coexpression:514 |
Rv1274 lprB |
lipoprotein LprB |
479 |
479 |
coexpression:470 |
Rv1388 mihF |
integration host factor MihF |
457 |
458 |
coexpression:458 |
Rv1078 pra hyp |
hypothetical protein |
449 |
449 |
coexpression:449 |
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
- RefSeq: hypothetical protein
- Mid-cell localisation during division; interacts with LamA, PbpA, PknH; genetic interactions with cell-division genes (Wang & Ehrt 2021, PMID 33959103)
- Identified among M. tuberculosis cell-envelope glycoproteins (Yari 2023, PMID 38092899)
- Curated from the literature crible (project 'Still unknown gene function', 2026-06-09)
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_215469.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF5336 (PF17270.9)
- 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
2EGIB
- Curated reference: UniProt
P9WIR9
(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 —
12 functional partner(s); context anchor
Rv0955
- Primary literature: Wang R, Ehrt S (2021). Rv0954 Is a Member of the Mycobacterial Cell Division Complex Front Microbiol 12:626461.
doi:10.3389/fmicb.2021.626461 PMID:33959103
Ancestral MTBC0 protein sequence
>mtbc0_001018|Rv0954|
MTYSPGNPGYPQAQPAGSYGGVTPSFAHADEGASKLPMYLNIAVAVLGLAAYFASFGPMFTLSTELGGGDGAVSGDTGLPVGVALLAALLAGVALVPKAKSHVTVVAVLGVLGVFLMVSATFNKPSAYSTGWALWVVLAFIVFQAVAAVLALLVETGAITAPAPRPKFDPYGQYGRYGQYGQYGVQPGGYYGQQGAQQAAGLQSPGPQQSPQPPGYGSQYGGYSSSPSQSGSGYTAQPPAQPPAQSGSQQSHQGPSTPPTGFPSFSPPPPVSAGTGSQAGSAPVNYSNPSGGEQSSSPGGAPV
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