Rv1273c Family assigned · medium auto-curated
H37Rv Rv1273c · MTBC0 mtbc0_001363 ·
582 aa · 1431285–1433033 (-) ·
RefSeq NP_215789.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | drug ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter ATP-binding protein |
| Revised (this work) | ABC transporter ATP-binding protein. Pfam: ABC_membrane (PF00664.29), ABC_tran (PF00005.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQJ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Drug eflux ATP-binding/permease protein Rv1273c |
| EC (curated) |
EC 7.6.2.-
|
| Curated function | ABC transporter that contributes to drug efflux. Transmembrane domains (TMD) form a pore in the membrane and the ATP-binding domain (NBD) is responsible for energy generation (Probable). Could contribute to efflux-mediated low-level tolerance to antimicrobials of various families and might play a role in biofilm formation. Overexpression of Rv1273c in E.coli and M.smegmatis increases biofilm formation and the tolerance of the cells to a multitude of antimicrobials..; FUNCTION: Rv1273c may promote mycobacterial intracellular survival within macrophages via modulating the host cell immune respon. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | ABC transporter |
| Orthologous group | COG1132 |
| KEGG orthology |
K06147
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.439 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 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_membrane | PF00664.29 | 1.5e-54 | 18–288 | ABC transporter transmembrane region |
ABC_tran | PF00005.34 | 6.1e-28 | 352–501 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1272c (drug ABC transporter ATP-binding protein), high confidence from genomic context alone (score 911 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1272c |
drug ABC transporter ATP-binding protein | 921 | 911 ctx | neighborhood:881 |
Rv1274 lprB |
lipoprotein LprB | 775 | 776 ctx | neighborhood:772 |
Rv1275 lprC |
lipoprotein LprC | 775 | 775 ctx | neighborhood:772 |
Rv1218c |
tetronasin ABC transporter ATP-binding protein | 755 | 690 | database:536 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 686 | 666 | database:528 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 683 | 664 | database:528 |
Rv0435c |
ATPase | 679 | 664 | database:528 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 682 | 663 | database:528 |
Rv1687c |
ABC transporter ATP-binding protein | 722 | 655 | database:536 |
Rv2115c mpa |
proteasome-associated ATPase | 652 | 652 | database:539 |
Rv1458c |
antibiotic ABC transporter ATP-binding protein | 689 | 633 | database:536 |
Rv2936 drrA |
daunorubicin ABC transporter ATP-binding protein DrrA | 648 | 632 | database:536 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 690 | 629 | database:536 |
Rv2688c |
antibiotic ABC transporter ATP-binding protein | 630 | 614 | database:536 |
Rv1527c pks5 |
polyketide synthase | 652 | 595 |
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: drug ABC transporter ATP-binding protein
- MTBC0 PGAP product: ABC transporter ATP-binding protein
- Pfam (hmmscan --cut_ga): ABC_membrane PF00664.29 (E=2e-54), ABC_tran PF00005.34 (E=6e-28)
- (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_215789.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_membrane (PF00664.29), ABC_tran (PF00005.34)
- 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
COG1132 - Curated reference: UniProt P9WQJ1 (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 —
98 functional partner(s); context anchor
Rv1272c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001363|Rv1273c| MLLALLRQHIRPYRRLVAMLMMLQLVSTLASLYLPTVNAAIVDDGVAKGDTATIVRLGAVMLGVTGLQVLCAIGAVYLGSRTGAGFGRDLRSAMFEHIITFSERETARFGAPTLLTRSTNDVRQILFLVQMTATVLVTAPIMCVGGIIMAIHQEAALTWLLLVSVPILAVANYWIISHMLPLFRRMQSLIDGINRVMRDQLSGVRVVRAFTREGYERDKFAQANTALSNAALSAGNWQALMLPVTTLTINASSVALIWFGGLRIDSGQMQVGSLIAFLSYFAQILMAVLMATMTLAVLPRASVCAERITEVLSTPAALGNPDNPKFPTDGVTGVVRLAGATFTYPGADCPVLQDISLTARPGTTTAIVGSTGSGKSTLVSLICRLYDVTAGAVLVDGIDVREYHTERLWSAIGLVPQRSYLFSGTVADNLRYGGGPDQVVTEQEMWEALRVAAADGFVQTDGLQTRVAQGGVNFSGGQRQRLAIARAVIRRPAIYVFDDAFSALDVHTDAKVHASLRQVSGDATIIVVTQRISNAAQADQVIVVDNGKIVGTGTHETLLADCPTYAEFAASQSLSATVGGVG