Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | multidrug ABC transporter ATPase/permease |
|---|
| 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 |
O53645
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Multidrug efflux ATP-binding/permease protein Rv0194 |
|---|
| EC (curated) |
EC 7.6.2.-
|
|---|
| Curated function | Overexpression in M.smegmatis increases resistance to erythromycin, ampicillin, novobiocin and vancomycin. It also reduces accumulation of ethidium bromide in the cell. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|
| eggNOG description | ABC transporter |
|---|
| Orthologous group | COG1132 |
|---|
| KEGG orthology |
K06147, K18894
|
|---|
| KEGG pathways |
map02010
|
|---|
| Gene Ontology (41) |
GO:0003674, GO:0003824, GO:0005215, GO:0005319, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006810, GO:0006869, GO:0008150, GO:0010876 +29 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 |
0.458 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
36 synonymous, 43 missense, 0 nonsense, 1 frameshift
|
|---|
| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.11% of strains
(158) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|
ABC_membrane | PF00664.29 |
5.0e-38 | 20–285 |
ABC transporter transmembrane region |
ABC_tran | PF00005.34 |
3.7e-29 | 350–499 |
ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0193c hyp |
hypothetical protein |
955 |
877 |
coexpression:804 textmining:653 |
Rv1674c |
transcriptional regulator |
850 |
844 |
coexpression:772 |
Rv0195 |
two component transcriptional regulator |
866 |
831 |
coexpression:826 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr |
827 |
821 |
coexpression:801 |
Rv3082c virS |
HTH-type transcriptional regulator VirS |
810 |
802 |
coexpression:798 |
Rv0603 hyp |
hypothetical protein |
801 |
801 |
coexpression:801 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA |
804 |
797 |
coexpression:797 |
Rv1190 hyp |
hypothetical protein |
783 |
783 |
coexpression:775 |
Rv2488c |
LuxR family transcriptional regulator |
776 |
755 |
coexpression:730 |
Rv3840 |
transcriptional regulator |
751 |
751 |
coexpression:751 |
Rv3446c hyp |
hypothetical protein |
746 |
734 |
coexpression:538 |
Rv3167c |
TetR family transcriptional regulator |
736 |
734 |
coexpression:734 |
Rv0494 |
HTH-type transcriptional regulator |
733 |
733 |
coexpression:733 |
Rv1776c |
transcriptional regulator |
734 |
732 |
coexpression:732 |
Rv0894 |
transcriptional regulator |
740 |
731 |
coexpression:731 |
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: multidrug ABC transporter ATPase/permease
- MTBC0 PGAP product: ABC transporter ATP-binding protein
- Pfam (hmmscan --cut_ga): ABC_membrane PF00664.29 (E=5e-38), ABC_tran PF00005.34 (E=4e-29)
- (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_214708.1)
- 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
O53645
(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 —
134 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000208|Rv0194|
MRTNCWWRLSGYVMRHRRDLLLGFGAALAGTVIAVLVPLVTKRVIDDAIAADHRPLAPWAVVLVAAAGATYLLTYVRRYYGGRIAHLVQHDLRMDAFQALLRWDGRQQDRWSSGQLIVRTTNDLQLVQALLFDVPNVLRHVLTLLLGVAVMTWLSVPLALLAVLLVPVIGLIAHRSRRLLAAATHCAQEHKAAVTGVVDAAVCGIRVVKAFGQEERETVKLVTASRALYAAQLRVARLNAHFGPLLQTLPALGQMAVFALGGWMAAQGSITVGTFVAFWACLTLLARPACDLAGMLTIAQQARAGAVRVLELIDSRPTLVDGTKPLSPEARLSLEFQRVSFGYVADRPVLREISLSVRAGETLAVVGAPGSGKSTLASLATRCYDVTQGAVRIGGQDVRELTLDSLRSAIGLVPEDAVLFSGTIGANIAYGRPDATPEQIATAARAAHIEEFVNTLPDGYQTAVGARGLTLSGGQRQRIALARALLHQPRLLIMDDPTSAVDAVIECGIQEVLREAIADRTAVIFTRRRSMLTLADRVAVLDSGRLLDVGTPDEVWERCPRYRELLSPAPDLADDLVVAERSPVCRPVAGLGTKAAQHTNVHNPGPHDHPPGPDPLRRLLREFRGPLALSLLLVAVQTCAGLLPPLLIRHGIDVGIRRHVLSALWWAALAGTATVVIRWVVQWGSAMVAGYTGEQVLFRLRSVVFAHAQRLGLDAFEDDGDAQIVTAVTADVEAIVAFLRTGLVVAVISVVTLVGILVALLAIRARLVLLIFTTMPVLALATWQFRRASNWTYRRARHRLGTVTATLREYAAGLRIAQAFRAEYRGLQSYFAHSDDYRRLGVRGQRLLALYYPFVALLCSLATTLVLLDGAREVRAGVISVGALVTYLLYIELLYTPIGELAQMFDDYQRAAVAAGRIRSLLSTRTPSSPAARPVGTLRGEVVFDAVHYSYRTREVPALAGINLRIPAGQTVVFVGSTGSGKSTLIKLVARFYDPTHGTVRVDGCDLREFDVDGYRNRLGIVTQEQYVFAGTVRDAIAYGRPDATDAQVERAAREVGAHPMITALDNGYLHQVTAGGRNLSAGQLQLLALARARLVDPDILLLDEATVALDPATEAVVQRATLTLAARRTTLIVAHGLAIAEHADRIVVLEHGTVVEDGAHTELLAAGGHYSRLWAAHTRLCSPEITQLQCIDA
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