Rv1686c Family assigned · medium auto-curated
H37Rv Rv1686c · MTBC0 - ·
226 aa · 1911401–1912081 (-) ·
RefSeq NP_216202.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ABC transporter permease |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | ABC transporter permease. Pfam: ABC2_membrane (PF01061.30), ABC2_membrane_3 (PF12698.14), ABC2_membrane_2 (PF12679.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O33188
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Transport permease protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | Transport permease protein |
| Orthologous group | COG0842 |
| KEGG orthology |
K01990, K01992
|
| KEGG modules |
M00254
|
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 | 0.555 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
ABC2_membrane | PF01061.30 | 3.3e-29 | 4–188 | ABC-2 type transporter |
ABC2_membrane_3 | PF12698.14 | 9.5e-20 | 28–218 | ABC-2 family transporter protein |
ABC2_membrane_2 | PF12679.14 | 2.5e-06 | 46–223 | ABC-2 family transporter protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1687c (ABC transporter ATP-binding protein), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1687c |
ABC transporter ATP-binding protein | 999 | 996 ctx | neighborhood:792 cooccurence:773 coexpression:890 textmining:931 |
Rv1685c hyp |
hypothetical protein | 986 | 965 ctx | neighborhood:882 cooccurence:501 coexpression:449 textmining:638 |
Rv1218c |
tetronasin ABC transporter ATP-binding protein | 917 | 745 ctx | cooccurence:564 coexpression:408 textmining:689 |
Rv1688 mpg |
3-methyladenine DNA glycosylase | 728 | 728 ctx | neighborhood:726 |
Rv1217c |
tetronasin ABC transporter integral membrane protein | 878 | 637 ctx | cooccurence:594 textmining:679 |
Rv1689 tyrS |
tyrosine--tRNA ligase | 631 | 631 ctx | neighborhood:631 |
Rv3131 |
NAD(P)H nitroreductase | 556 | 540 | coexpression:421 |
Rv2936 drrA |
daunorubicin ABC transporter ATP-binding protein DrrA | 578 | 526 | coexpression:405 |
Rv2032 acg |
NAD(P)H nitroreductase | 538 | 522 | coexpression:423 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 534 | 514 | coexpression:405 |
Rv3127 hyp |
hypothetical protein | 527 | 511 | coexpression:421 |
Rv2938 drrC |
daunorubicin ABC transporter permease DrrC | 501 | 501 | |
Rv1863c |
integral membrane protein | 502 | 484 | coexpression:410 |
Rv2937 drrB |
daunorubicin ABC transporter permease DrrB | 474 | 475 | |
Rv1375 hyp |
hypothetical protein | 488 | 457 | coexpression:439 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): ABC transporter permease
- Pfam (hmmscan --cut_ga): ABC2_membrane PF01061.30 (E=3e-29), ABC2_membrane_3 PF12698.14 (E=1e-19), ABC2_membrane_2 PF12679.14 (E=3e-06)
- (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_216202.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC2_membrane (PF01061.30), ABC2_membrane_3 (PF12698.14), ABC2_membrane_2 (PF12679.14)
- 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
COG0842 - Curated reference: UniProt O33188 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
32 functional partner(s); context anchor
Rv1687c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1686c| MILLVPILIITLMYFMFENVPHRPGTPSGFNTACLVLLGLFPLFVMFVITAITMQRERASGTLERILTTPLRRLDLLAGYGTAFSIAAAAQATLACIVAFWFLGFDTAGSPVWVFAIAIVNAVLGVGLGLLCSAFARTEFQAVQFIPLVMVPQLLLAGIIVPRALMPTWLEWISNVMPASYALEALQQVGAHPELTGIAVRDVVVVLSFAVASLCLAAVTLRRRTS