Rv3000 Family assigned · medium auto-curated
H37Rv Rv3000 · MTBC0 mtbc0_003189 ·
219 aa · 3379921–3380580 (+) ·
RefSeq NP_217516.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter permease |
| Revised (this work) | ABC transporter permease. Pfam: ABC_tran (PF00005.34), UPF0014 (PF03649.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X5Z8
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Possible conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | transport system permease |
| Orthologous group | COG0390 |
| KEGG orthology |
K02069
|
| KEGG modules |
M00211
|
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 | 0.821 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (249) · 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_tran | PF00005.34 | 2.9e-14 | 21–122 | ABC transporter |
UPF0014 | PF03649.19 | 1.2e-31 | 112–203 | Uncharacterised protein family (UPF0014) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppY (lipoprotein LppY), medium confidence from genomic context alone (score 681 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2999 lppY |
lipoprotein LppY | 681 | 681 ctx | neighborhood:634 |
Rv0986 |
adhesion component ABC transporter ATP-binding protein | 615 | 616 ctx | cooccurence:572 |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 597 | 598 ctx | cooccurence:525 |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 542 | 542 ctx | cooccurence:463 |
Rv3314c deoA |
thymidine phosphorylase | 522 | 523 ctx | neighborhood:520 |
Rv3313c add |
adenosine deaminase | 521 | 522 ctx | neighborhood:520 |
Rv3315c cdd |
cytidine deaminase | 520 | 520 ctx | neighborhood:520 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 483 | 483 ctx | cooccurence:483 |
Rv2998A |
Rv2998A, len: 67 aa. Probable conserved hypothetical protein, (possibly gene fragment), highly similar to central part of two-component sens | 450 | 450 ctx | neighborhood:443 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 449 | 450 ctx | cooccurence:448 |
Rv0350 dnaK |
chaperone protein DnaK | 449 | 450 ctx | cooccurence:448 |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 448 | 449 ctx | cooccurence:447 |
Rv1349 irtB |
iron ABC transporter ATP-binding protein/permease IrtB | 468 | 448 ctx | cooccurence:436 |
Rv0304c PPE5 |
PPE family protein PPE5 | 442 | 442 ctx | cooccurence:442 |
Rv0355c PPE8 |
PPE family protein PPE8 | 438 | 438 ctx | cooccurence:438 |
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: transmembrane protein
- MTBC0 PGAP product: ABC transporter permease
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=3e-14), UPF0014 PF03649.19 (E=1e-31)
- (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_217516.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), UPF0014 (PF03649.19)
- 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
COG0390 - Curated reference: UniProt I6X5Z8 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
29 functional partner(s); context anchor
lppY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003189|Rv3000| MAVHGFLLERVSVVRDEATVLRQVSAHFPAGRCSAVRGASGSGKTTLLRLLNRLIDPTSGKVWLDGVPLTDLDVLVLRRRVGLVAQAPVVLTDAVLNEVRVGRPDLPEGRVTELLARLCLGQSAREAFLPHQRSALRTALIPAIDSTKVVGLISLPGAMSGLILAGVDPLTAIRYQIVVMYLLLAATAVAALTCARLAERALFDRAHRLVSLPAATRRA