Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|
| MTBC0 PGAP re-annotation | DUF808 domain-containing protein |
|---|
| Revised (this work) | Putative ABC-transporter component of the mxyR xylan-utilisation locus. RefSeq leaves it of unknown function. Rv3092c lies in the locus controlled by the MarR-family regulator MxyR (Rv3095), divergent from a hydrolase (rv3094c) and oxidoreductase (rv3093c) and convergent with a xylanase (rv3096); MxyR derepresses the locus in response to xylan/arabinose/galactose (Mauran 2022). Substrate unfixed. |
|---|
Curated reference (UniProt)
| UniProt |
I6Y2I9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable conserved integral membrane protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| Preferred name | yedI |
|---|
| eggNOG description | Protein of unknown function (DUF808) |
|---|
| Orthologous group | COG2354 |
|---|
| KEGG orthology |
K09781
|
|---|
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 |
1.526 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
2 synonymous, 8 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 |
|---|
DUF808 | PF05661.18 |
9.9e-115 | 4–291 |
Protein of unknown function (DUF808) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner:
Rv3095 (HTH-type transcriptional regulator),
high confidence from genomic context alone
(score 877 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3095 |
HTH-type transcriptional regulator |
877 |
877 ctx |
neighborhood:507 coexpression:761 |
Rv2553c mltG |
membrane protein |
733 |
733 |
coexpression:733 |
Rv3093c |
oxidoreductase |
723 |
723 ctx |
neighborhood:707 |
Rv3094c hyp |
hypothetical protein |
711 |
711 ctx |
neighborhood:697 |
Rv3335c yhjD |
integral membrane protein |
425 |
425 |
coexpression:425 |
Rv2707 hyp |
hypothetical protein |
419 |
420 |
coexpression:420 |
Rv2575 |
membrane protein |
408 |
409 |
|
Rv0783c emrB |
multidrug resistance protein EmrB |
871 |
54 |
textmining:870 |
Rv1377c |
transferase |
870 |
47 |
textmining:870 |
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
- ABC transporter of the MxyR (Rv3095) xylan-utilisation locus (Mauran 2022, PMID 35082266)
- 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_217608.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF808 (PF05661.18)
- 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
COG2354
- Curated reference: UniProt
I6Y2I9
(TrEMBL, unreviewed; 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 —
9 functional partner(s); context anchor
Rv3095
- Primary literature: Mauran S, Perera NT, Perera IC (2022). MxyR of Mycobacterium tuberculosis Responds to Xylan; an Unusual Ligand for a MarR Family Transcriptional Regulator Mol Biol (Mosk) 56(1):103-117.
doi:10.31857/S0026898422010074 PMID:35082266
Ancestral MTBC0 protein sequence
>mtbc0_003286|Rv3092c|
MSGGLFGLLDHVAVLARLAAASIDDIGAAAGRATAKAAGVVIDDTAVTPQYVHRITAERELPIIKRIAIGSVRNKLLLILPGALLLSQLVPWLLTPLLMLGATYLCYEGAEKVCGVIGGRGHDAAPQVAERELVAGAIRTDFILSAEIMVIALNEVADQPFVPRLIVLVIVALVITAAVYGVVAVIVQMDDVGLRLTQTASRFGQRIGGGLVAGMPKLLSALSAVGMGAMLWVGGHIVLVGSDHLGWHAPYRLVHHLDDHLVGSAGGALTWLVSTAACAATGLVIGIVVVALVHLVCFRPPRSRSL
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