Rv2563 Family assigned · medium auto-curated
H37Rv Rv2563 · MTBC0 mtbc0_002730 ·
349 aa · 2905834–2906883 (+) ·
RefSeq NP_217079.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamine ABC transporter permease |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter permease |
| Revised (this work) | ABC transporter permease. Pfam: MacB_PCD (PF12704.15), FtsX (PF02687.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG15
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized ABC transporter permease Rv2563 |
UniProt still lists this protein as Uncharacterized ABC transporter permease Rv2563; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | FtsX-like permease family |
| Orthologous group | COG0577 |
| KEGG orthology |
K02004
|
| KEGG modules |
M00258
|
| Gene Ontology (13) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0044425, GO:0044459, GO:0044464 +1 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) pseudogene candidate
| pN/pS | 0.318 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 5.89% of strains (8557) · 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 |
|---|---|---|---|---|
MacB_PCD | PF12704.15 | 1.9e-08 | 20–183 | MacB-like periplasmic core domain |
FtsX | PF02687.28 | 4.9e-13 | 233–342 | FtsX-like permease C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glnQ (glutamine ABC transporter ATP-binding protein), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 999 | 1000 ctx | neighborhood:882 cooccurence:408 coexpression:899 experimental:773 database:900 |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 931 | 925 ctx | cooccurence:410 coexpression:448 experimental:773 |
Rv0986 |
adhesion component ABC transporter ATP-binding protein | 882 | 875 | coexpression:442 experimental:773 |
Rv1157c hyp |
hypothetical protein | 646 | 646 ctx | cooccurence:628 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 500 | 500 ctx | cooccurence:497 |
Rv2562 |
Rv2562, (MTCY9C4.06c), len: 129 aa. Conserved hypothetical protein, highly similar, but shorter 83 aa, to downstream ORF AAK46951|RV2561|MT2 | 496 | 495 ctx | neighborhood:493 |
Rv3201c adnB |
ATP-dependent DNA helicase | 495 | 495 ctx | cooccurence:493 |
Rv2565 |
NTE family protein | 444 | 445 ctx | neighborhood:434 |
Rv2566 hyp |
hypothetical protein | 425 | 425 ctx | neighborhood:423 |
Rv2567 hyp |
hypothetical protein | 424 | 424 ctx | neighborhood:424 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 423 | 423 ctx | cooccurence:423 |
Rv2561 |
Rv2561, (MTCY9C4.07c), len: 97 aa. Conserved hypothetical protein, highly similar in part (and longer 33 aa) to upstream ORF AAK46951|RV2562 | 406 | 407 ctx | neighborhood:403 |
Rv0312 hyp |
hypothetical protein | 405 | 406 | |
Rv3365c hyp |
hypothetical protein | 428 | 404 | |
Rv1078 pra hyp |
hypothetical protein | 760 | 331 | textmining:657 |
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: glutamine ABC transporter permease
- MTBC0 PGAP product: ABC transporter permease
- Pfam (hmmscan --cut_ga): MacB_PCD PF12704.15 (E=2e-08), FtsX PF02687.28 (E=5e-13)
- (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_217079.1)
- Domains: Pfam-A via hmmscan --cut_ga — MacB_PCD (PF12704.15), FtsX (PF02687.28)
- 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
COG0577 - Curated reference: UniProt P9WG15 (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 —
19 functional partner(s); context anchor
glnQ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002730|Rv2563| MLFAALRDVQWRKRRLVIAIVSTGLVFAMTLVLTGLVNGFRVEAERTVDSMGVDAFVVKAGAAGPFLGSTPFAQIDLPQVARAPGVLAAAPLATAPSTIRQGTSARNVTAFGAPEHGPGMPRVSDGRAPSTPDEVAVSSTLGRNLGDDLQVGARTLRIVGIVPESTALAKIPNIFLTTEGLQQLAYNGQPTISSIGIDGMPRQLPDGYQTVNRADAVSDLMRPLKVAVDAITVVAVLLWIVAALIVGSVVYLSALERLRDFAVFKAIGVPTRSILAGLALQAVVVALLAAVVGGILSLLLAPLFPMTVVVPLSAFVALPAIATVIGLLASVAGLRRVVAIDPALAFGGP