Rv3888c Family assigned · low auto-curated
H37Rv Rv3888c · MTBC0 mtbc0_004122 ·
341 aa · 4395927–4396952 (-) ·
RefSeq NP_218405.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | MinD/ParA family protein |
| Revised (this work) | MinD/ParA family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05456
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | bacterial-type flagellum organization |
| Orthologous group | COG0455 |
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 | 0.884 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 13 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 1.13% of strains (1646) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD2 (ESX-2 secretion system protein EccD), high confidence from genomic context alone (score 949 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 993 | 949 ctx | neighborhood:881 cooccurence:568 textmining:870 |
Rv3886c mycP2 |
membrane-anchored mycosin | 930 | 930 ctx | neighborhood:881 cooccurence:410 |
Rv3885c eccE2 |
ESX-2 secretion system protein EccE | 884 | 885 ctx | neighborhood:881 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 876 | 850 ctx | neighborhood:794 |
Rv1796 mycP5 |
membrane-anchored mycosin MycP | 625 | 626 ctx | cooccurence:608 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 634 | 620 ctx | cooccurence:540 |
Rv3889c espG2 |
ESX-2 secretion-associated protein EspG2 | 946 | 606 ctx | neighborhood:590 textmining:870 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 663 | 595 ctx | cooccurence:505 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 588 | 588 ctx | cooccurence:586 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 551 | 540 ctx | cooccurence:524 |
Rv1783 eccC5 |
ESX-5 type VII secretion system protein EccC5 | 685 | 502 ctx | cooccurence:478 |
Rv3286c sigF |
RNA polymerase sigma factor SigF | 468 | 435 | coexpression:416 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 427 | 427 ctx | neighborhood:419 |
Rv3883c mycP1 |
membrane-anchored mycosin | 433 | 418 ctx | neighborhood:407 |
Rv3890c esxC |
ESAT-6 like protein EsxC | 787 | 412 ctx | neighborhood:403 textmining:652 |
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: MinD/ParA family protein
- (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_218405.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0455 - Curated reference: UniProt O05456 (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 —
16 functional partner(s); context anchor
eccD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004122|Rv3888c| MTNPWNDPNMLDDGAIGRGDPSVRHHFRDSVSDTMRITDLAAPRKIPPGTGWRKFVYSVSFHKINPGESPRERHYRNLQGRIRRHIRRQYVITVVSGKGGVGVTTMAACIGGVFRECRPENVIAIDAVPSFGTLADRIDESPPGDYAAIINDTDVQGYADIREHLGQNTVGLDVLAGNRTSDQPRPLVPAMFSAVLSRLRRTHTVIVIDTSPDLEHDVMKAVLQSTDTLVFVSGITADRSRPVLRAVDYLRAQGYHELVSRSTVILNHTDSITDKDALAYLTERFTKVGAIVEAMPFDPHLAKGGIIDTVHELNKKSRLRLFEITAGLADKYVPDAERAAQ