Rv1680 Family assigned · medium auto-curated
H37Rv Rv1680 · MTBC0 mtbc0_001788 ·
274 aa · 1916444–1917268 (+) ·
RefSeq NP_216196.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | phosphate/phosphite/phosphonate ABC transporter substrate-binding protein |
| Revised (this work) | Phosphate/phosphite/phosphonate ABC transporter substrate-binding protein. Pfam: Phosphonate-bd (PF12974.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33182
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphate ABC transporter substrate-binding protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | ABC transporter, phosphonate, periplasmic substrate-binding protein |
| Orthologous group | COG3221 |
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 | 0.403 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Phosphonate-bd | PF12974.13 | 2.1e-34 | 35–258 | ABC transporter, phosphonate, periplasmic substrate-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE16 (acyl-CoA dehydrogenase FadE16), high confidence from genomic context alone (score 989 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 989 | 989 ctx | neighborhood:879 cooccurence:415 coexpression:860 |
Rv1681 moeX |
molybdopterin biosynthesis protein MoeX | 988 | 988 ctx | neighborhood:882 coexpression:863 |
Rv1678 |
integral membrane protein | 976 | 977 ctx | neighborhood:879 coexpression:815 |
Rv0273c |
transcriptional regulator | 733 | 733 | coexpression:733 |
Rv2760c vapB42 |
antitoxin VapB42 | 733 | 733 | coexpression:733 |
Rv3727 |
oxidoreductase | 669 | 670 | coexpression:615 |
Rv1676 hyp |
hypothetical protein | 637 | 637 ctx | neighborhood:566 |
Rv1682 hyp |
hypothetical protein | 628 | 615 ctx | neighborhood:497 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 596 | 586 | |
Rv1677 dsbF |
lipoprotein DsbF | 544 | 544 ctx | neighborhood:529 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 461 | 428 | coexpression:428 |
Rv0911 hyp |
hypothetical protein | 422 | 423 | coexpression:423 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 404 | 404 | coexpression:404 |
Rv2759c vapC42 |
ribonuclease VapC42 | 404 | 404 | coexpression:404 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 455 | 397 |
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: hypothetical protein
- MTBC0 PGAP product: phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): Phosphonate-bd PF12974.13 (E=2e-34)
- (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_216196.1)
- Domains: Pfam-A via hmmscan --cut_ga — Phosphonate-bd (PF12974.13)
- 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
COG3221 - Curated reference: UniProt O33182 (TrEMBL, unreviewed; 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 —
16 functional partner(s); context anchor
fadE16 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001788|Rv1680| MSTEPLVVGAVAYTPNVVPIWEGIRGYFQDSESPDTQMDFVLYSNYARLVDSLIAGHIDIAWNTNLAYVRTVLQTGGRCTPLAQRDTDVDYTTVFVAHAGSDLHGAKDIAGKRLALGSADSAHAAILPLYYLRRAGIAESDLQVIRFDTDIGKHGDTGRSELDAVDAVLAGEADVAAIGSSTWAAMGAAELMGESLTEVWRTDGYCHCMFTALDTLPAERYQPWLDRLLAMSWDDSEHRKILELEGLRRWVPPHLDGYKPLFEAVQEQGIDPRW