mmpS4 Resolved · high auto-curated
H37Rv Rv0451c · MTBC0 mtbc0_000473 ·
140 aa · 544853–545275 (-) ·
RefSeq NP_214965.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein MmpS4 |
|---|---|
| MTBC0 PGAP re-annotation | siderophore RND transporter accessory protein MmpS4 |
| Revised (this work) | Siderophore RND transporter accessory protein MmpS4. Pfam: Mycobact_memb (PF05423.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJS9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Siderophore export accessory protein MmpS4 |
| Curated function | Part of an export system, which is required for biosynthesis and secretion of siderophores. Essential for virulence. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpS4 |
| eggNOG description | Mycobacterium membrane protein |
| Orthologous group | 2BG05 |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
Mycobact_memb | PF05423.19 | 1.3e-74 | 2–140 | Mycobacterium membrane protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL4 (transmembrane transport protein MmpL4), high confidence from genomic context alone (score 909 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0450c mmpL4 |
transmembrane transport protein MmpL4 | 984 | 909 ctx | neighborhood:882 textmining:831 |
Rv0449c hyp |
hypothetical protein | 660 | 659 ctx | neighborhood:659 |
Rv0447c ufaA1 |
cyclopropane-fatty-acyl-phospholipid synthase UfaA | 509 | 510 ctx | neighborhood:508 |
Rv0446c |
transmembrane protein | 509 | 510 ctx | neighborhood:508 |
Rv0448c hyp |
hypothetical protein | 509 | 509 ctx | neighborhood:509 |
Rv0452 |
transcriptional regulator | 821 | 508 ctx | neighborhood:508 textmining:652 |
Rv0445c sigK |
ECF RNA polymerase sigma factor SigK | 440 | 440 ctx | neighborhood:436 |
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 911 | 133 | textmining:902 |
Rv1501 hyp |
hypothetical protein | 419 | 55 | textmining:411 |
Rv3592 mhuD |
heme-degrading monooxygenase | 516 | 51 | textmining:511 |
Rv3533c PPE62 |
PPE family protein PPE62 | 443 | 50 | textmining:438 |
Rv1348 irtA |
iron ABC transporter ATP-binding protein/permease IrtA | 654 | 47 | textmining:652 |
Rv0677c mmpS5 |
membrane protein MmpS5 | 509 | 47 | textmining:506 |
Rv0203 hyp |
hypothetical protein | 437 | 47 | textmining:434 |
Rv3424c hyp |
hypothetical protein | 414 | 47 | textmining:411 |
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 MmpS4
- MTBC0 PGAP product: siderophore RND transporter accessory protein MmpS4
- Pfam (hmmscan --cut_ga): Mycobact_memb PF05423.19 (E=1e-74)
- (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_214965.1)
- Domains: Pfam-A via hmmscan --cut_ga — Mycobact_memb (PF05423.19)
- 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
2BG05 - Curated reference: UniProt P9WJS9 (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 —
23 functional partner(s); context anchor
mmpL4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000473|Rv0451c|mmpS4 MLMRTWIPLVILVVVIVGGFTVHRIRGFFGSENRPSYSDTNLENSKPFNPKHLTYEIFGPPGTVADISYFDVNSEPQRVDGAVLPWSLHITTNDAAVMGNIVAQGNSDSIGCRITVDGKVRAERVSNEVNAYTYCLVKSA