Rv2688c Family assigned · medium auto-curated
H37Rv Rv2688c · MTBC0 mtbc0_002862 ·
301 aa · 3027160–3028065 (-) ·
RefSeq NP_217204.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antibiotic ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter ATP-binding protein |
| Revised (this work) | ABC transporter ATP-binding protein. Pfam: ABC_tran (PF00005.34), AAA_21 (PF13304.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQL7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Fluoroquinolones export ATP-binding protein Rv2688c |
| EC (curated) |
EC 7.6.2.-
|
| Curated function | Part of the ABC transporter complex Rv2686c/Rv2687c/Rv2688c involved in fluoroquinolones export. Confers resistance to ciprofloxacin and, to a lesser extent, norfloxacin, moxifloxacin and sparfloxacin. Probably responsible for energy coupling to the transport system. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | ABC transporter |
| Orthologous group | COG1131 |
| KEGG orthology |
K16907
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00224
|
| Gene Ontology (14) |
GO:0003674, GO:0005215, GO:0006810, GO:0008150, GO:0015562, GO:0015893, GO:0022857, GO:0042221, GO:0042493, GO:0042891, GO:0050896, GO:0051179 +2 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)
| pN/pS | 1.369 · 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 |
|---|---|---|---|---|
ABC_tran | PF00005.34 | 3.3e-25 | 36–175 | ABC transporter |
AAA_21 | PF13304.13 | 4.0e-08 | 147–208 | AAA domain, putative AbiEii toxin, Type IV TA system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2686c (antibiotic ABC transporter permease), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2686c |
antibiotic ABC transporter permease | 999 | 998 ctx | neighborhood:781 cooccurence:765 coexpression:740 database:900 textmining:860 |
Rv2687c |
antibiotic ABC transporter permease | 996 | 996 ctx | neighborhood:781 cooccurence:765 database:900 |
Rv1272c |
drug ABC transporter ATP-binding protein | 698 | 661 | database:536 |
Rv1349 irtB |
iron ABC transporter ATP-binding protein/permease IrtB | 673 | 658 | database:536 |
Rv1348 irtA |
iron ABC transporter ATP-binding protein/permease IrtA | 667 | 647 | database:536 |
Rv0194 |
multidrug ABC transporter ATPase/permease | 679 | 614 | database:536 |
Rv1273c |
drug ABC transporter ATP-binding protein | 630 | 614 | database:536 |
Rv1978 hyp |
hypothetical protein | 581 | 582 ctx | cooccurence:578 |
Rv3488 hyp |
hypothetical protein | 536 | 536 | |
Rv1305 atpE |
ATP synthase subunit C | 532 | 523 | |
Rv1310 atpD |
ATP synthase subunit beta | 487 | 459 | experimental:457 |
Rv2689c hyp |
hypothetical protein | 459 | 459 ctx | neighborhood:454 |
Rv1308 atpA |
ATP synthase subunit alpha | 475 | 457 | experimental:456 |
Rv1311 atpC |
ATP synthase subunit epsilon | 453 | 454 | experimental:444 |
Rv2938 drrC |
daunorubicin ABC transporter permease DrrC | 511 | 441 | coexpression: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: antibiotic ABC transporter ATP-binding protein
- MTBC0 PGAP product: ABC transporter ATP-binding protein
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=3e-25), AAA_21 PF13304.13 (E=4e-08)
- (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_217204.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), AAA_21 (PF13304.13)
- 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
COG1131 - Curated reference: UniProt P9WQL7 (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 —
38 functional partner(s); context anchor
Rv2686c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002862|Rv2688c| MTALNRAVASARVGTEVIRVRGLTFRYPKAAEPAVRGMEFTVGRGEIFGLLGPSGAGKSTTQKLLIGLLRDHGGQATVWDKEPAEWGPDYYERIGVSFELPNHYQKLTGYENLRFFASLYAGATADPMQLLAAVGLADDAHTLVGKYSKGMQMRLTFARSLINDPELLFLDEPTSGLDPVNARKIKDIIVDLKARGRTIFLTTHDMATADELCDRVAFVVDGRIVALDSPTELKIARSRRRVRVEYRGDGGGLETAEFGMDGLADDPAFHSVLRNHHVETIHSREASLDDVFVEVTGRQLT