glnQ Family assigned · medium auto-curated
H37Rv Rv2564 · MTBC0 mtbc0_002731 ·
330 aa · 2906886–2907878 (+) ·
RefSeq NP_217080.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamine ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | ATP-binding cassette domain-containing protein |
| Revised (this work) | ATP-binding cassette domain-containing protein. Pfam: ABC_tran (PF00005.34), cNMP_binding (PF00027.36). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQI5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized ABC transporter ATP-binding protein Rv2564 |
UniProt still lists this protein as Uncharacterized ABC transporter ATP-binding protein Rv2564; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | ABC transporter |
| Orthologous group | COG0664 |
| KEGG orthology |
K02003
|
| KEGG modules |
M00258
|
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 | 1.798 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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 | 9.1e-34 | 24–172 | ABC transporter |
cNMP_binding | PF00027.36 | 7.0e-19 | 229–311 | Cyclic nucleotide-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2563 (glutamine ABC transporter permease), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2563 |
glutamine ABC transporter permease | 999 | 1000 ctx | neighborhood:882 cooccurence:408 coexpression:899 experimental:773 database:900 |
Rv0072 |
glutamine ABC transporter permease | 933 | 928 ctx | cooccurence:430 coexpression:447 experimental:773 |
Rv2562 |
Rv2562, (MTCY9C4.06c), len: 129 aa. Conserved hypothetical protein, highly similar, but shorter 83 aa, to downstream ORF AAK46951|RV2561|MT2 | 692 | 681 ctx | neighborhood:498 |
Rv0393 hyp |
hypothetical protein | 663 | 631 | |
Rv2561 |
Rv2561, (MTCY9C4.07c), len: 97 aa. Conserved hypothetical protein, highly similar in part (and longer 33 aa) to upstream ORF AAK46951|RV2562 | 639 | 626 ctx | neighborhood:408 |
Rv3580c cysS1 |
cysteine--tRNA ligase | 632 | 619 ctx | cooccurence:498 |
Rv3419c gcp |
O-sialoglycoprotein endopeptidase | 610 | 610 ctx | cooccurence:567 |
Rv0386 |
transcriptional regulator | 643 | 601 | experimental:447 |
Rv1358 |
transcriptional regulator | 643 | 600 | experimental:447 |
Rv2488c |
LuxR family transcriptional regulator | 643 | 600 | experimental:447 |
Rv3000 |
transmembrane protein | 597 | 598 ctx | cooccurence:525 |
Rv2048c pks12 |
polyketide synthase | 691 | 587 | database:431 |
Rv1527c pks5 |
polyketide synthase | 689 | 584 | database:431 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 689 | 584 | database:431 |
Rv0397 hyp |
hypothetical protein | 619 | 584 |
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 ATP-binding protein
- MTBC0 PGAP product: ATP-binding cassette domain-containing protein
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=9e-34), cNMP_binding PF00027.36 (E=7e-19)
- (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_217080.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), cNMP_binding (PF00027.36)
- 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
COG0664 - Curated reference: UniProt P9WQI5 (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 —
124 functional partner(s); context anchor
Rv2563 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002731|Rv2564|glnQ MGGLTISDLVVEYSSGGYAVRPIDGLSLDVAPGSLVILLGPSGCGKTTLLSCLGGILRPKSGSIKFDDVDITTLEGAALAKYRRDKVGIVFQAFNLVSSLTALENVMVPLRAAGVSRAAARKRAEDLLIRVNLGERMKHRPGDMSGGQQQRVAVARAIALDPQLILADEPTAHLDFIQVEEVLRLIRSLAQGDRVVVVATHDSRMLPLADRVLELMPAQVSPNQPPETVHVKAGEVLFEQSTMGDLIYVVSEGEFEIVRELADGGEELVKTAAPGDYFGEIGVLFHLPRSATVRARSDATAVGYTAQAFRERLGVTRVADLIEHRELASE