Rv1101c Family assigned · medium auto-curated
H37Rv Rv1101c · MTBC0 mtbc0_001184 ·
385 aa · 1237831–1238988 (-) ·
RefSeq NP_215617.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | AI-2E family transporter |
| Revised (this work) | AI-2E family transporter. Pfam: AI-2E_transport (PF01594.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFM3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative transport protein Rv1101c |
UniProt still lists this protein as Putative transport protein Rv1101c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | AI-2E family transporter |
| Orthologous group | COG0628 |
| Gene Ontology (19) |
GO:0003674, GO:0005215, GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0006810, GO:0008150, GO:0016020, GO:0016021, GO:0031224, GO:0031226 +7 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) pseudogene candidate
| pN/pS | 0.716 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 12.01% of strains (17438) · 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 |
|---|---|---|---|---|
AI-2E_transport | PF01594.23 | 2.0e-65 | 15–346 | AI-2E family transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL11 (transmembrane transport protein MmpL11), medium confidence from genomic context alone (score 661 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) |
|---|---|---|---|---|
Rv3835 hyp |
hypothetical protein | 702 | 703 ctx | cooccurence:702 |
Rv3909 hyp |
hypothetical protein | 690 | 691 ctx | cooccurence:690 |
Rv0202c mmpL11 |
transmembrane transport protein MmpL11 | 660 | 661 ctx | cooccurence:621 |
Rv2264c hyp |
hypothetical protein | 643 | 643 ctx | cooccurence:630 |
Rv0262c aac |
aminoglycoside 2'-N-acetyltransferase | 610 | 610 ctx | cooccurence:609 |
Rv0538 |
membrane protein | 607 | 607 ctx | cooccurence:606 |
Rv1024 |
membrane protein | 583 | 584 ctx | cooccurence:562 |
Rv3494c mce4F |
Mce family protein Mce4 | 565 | 565 ctx | cooccurence:552 |
Rv0312 hyp |
hypothetical protein | 548 | 549 ctx | cooccurence:529 |
Rv2164c hyp |
hypothetical protein | 544 | 544 ctx | cooccurence:525 |
Rv1648 |
transmembrane protein | 536 | 536 ctx | cooccurence:536 |
Rv1102c mazF3 |
mRNA interferase MazF3 | 535 | 535 ctx | neighborhood:528 |
Rv1103c mazE3 |
antitoxin MazE3 | 529 | 528 ctx | neighborhood:528 |
Rv0007 |
membrane protein | 525 | 525 ctx | cooccurence:522 |
Rv3810 pirG |
cell surface protein | 524 | 524 ctx | cooccurence:520 |
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: hypothetical protein
- MTBC0 PGAP product: AI-2E family transporter
- Pfam (hmmscan --cut_ga): AI-2E_transport PF01594.23 (E=2e-65)
- (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_215617.1)
- Domains: Pfam-A via hmmscan --cut_ga — AI-2E_transport (PF01594.23)
- 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
COG0628 - Curated reference: UniProt P9WFM3 (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 —
27 functional partner(s); context anchor
mmpL11 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001184|Rv1101c| MNTEFTLTQKRALAILTLIALLFGAYFLRNYFVLIVVAAVGAYLFTPLFKWFTKRFNTGLSAACTLLSALAAVVVPVGALVGLAIVQIARMVDSVADWVRTTDLSTLGDKILQFVNGLFDRVPFLHITVTADALRKAMISVAQNVGEWLLHFLRDAAGSLAGVITSAIIFVYVFVALLVNREKLRTLIGQLNPLGEDVTDLYLQKMGSMVRGTVNGQFVIAACQGVAGAASIYIAGFHHGFFIFAIVLTALSIIPLGGGIVTIPFGIGMIFYGNIAGGIFVLLWHLLVVTNIDNVLRPILVPRDARLNSALMLLSVFAGITMFGPWGIIIGPVLMILIVTTIDVYLAVYKGVELEQFEAPPVRRRWLPRRGPATSRNAPPPSTAE