Rv1443c Family assigned · low auto-curated · to review
H37Rv Rv1443c · MTBC0 - ·
161 aa · 1622207–1622692 (-) ·
RefSeq NP_215959.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 1z94-assembly1_A X-Ray Crystal Structure of Protein CV1439 from Chromobacterium (prob 1.00, TM 0.76). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06816
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ligand-binding SRPBCC domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Pfam Polyketide cyclase dehydrase and lipid transport |
| Orthologous group | COG4276 |
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 | 0.68 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
DUF8410 | PF28469.1 | 5.6e-61 | 14–158 | Domain of unknown function (DUF8410) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 88.0 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
1z94-assembly1_A |
1.00 | 0.76 | 5.2e-08 sig | 1z94-assembly1_A X-Ray Crystal Structure of Protein CV1439 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR12. |
7wa9-assembly1_A |
1.00 | 0.79 | 3.9e-07 sig | 7wa9-assembly1_A Crystal structure of MSMEG_5634 from Mycobacterium smegmatis |
5z8o-assembly1_A |
1.00 | 0.77 | 3.6e-07 sig | 5z8o-assembly1_A Structural of START superfamily protein MSMEG_0129 from Mycobacterium smegmatis |
2ns9-assembly1_B |
1.00 | 0.66 | 7.9e-08 sig | 2ns9-assembly1_B Crystal structure of protein APE2225 from Aeropyrum pernix K1, Pfam COXG |
8ho2-assembly1_B |
1.00 | 0.67 | 2.9e-07 sig | 8ho2-assembly1_B crystal structure of Norcoclaurine synthase from Chinese lotus (Nelumbo nucicera) |
1z94-assembly2_E-2 |
1.00 | 0.71 | 3.6e-07 sig | 1z94-assembly2_E-2 X-Ray Crystal Structure of Protein CV1439 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR12. |
4a8v-assembly1_A |
1.00 | 0.65 | 7.8e-07 sig | 4a8v-assembly1_A Crystal Structure of Birch Pollen Allergen Bet v 1 isoform j in complex with 8-Anilinonaphthalene-1-sulfonate (ANS) |
2vq5-assembly1_A-2 |
1.00 | 0.62 | 4.3e-07 sig | 2vq5-assembly1_A-2 X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppF (lipoprotein LppF), medium confidence from genomic context alone (score 674 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) |
|---|---|---|---|---|
Rv3594 hyp |
hypothetical protein | 675 | 675 ctx | cooccurence:675 |
Rv1921c lppF |
lipoprotein LppF | 674 | 674 ctx | cooccurence:674 |
Rv1754c hyp |
hypothetical protein | 510 | 510 ctx | cooccurence:510 |
Rv1541c lprI |
lipoprotein LprI | 504 | 504 ctx | cooccurence:504 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 481 | 481 ctx | cooccurence:481 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 468 | 468 ctx | cooccurence:468 |
Rv3875 esxA |
ESAT-6 protein EsxA | 453 | 453 ctx | cooccurence:450 |
Rv1978 hyp |
hypothetical protein | 450 | 450 ctx | cooccurence:450 |
Rv1288 hyp |
hypothetical protein | 429 | 430 ctx | cooccurence:428 |
Rv0097 |
oxidoreductase | 425 | 425 ctx | cooccurence:425 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 421 | 422 ctx | cooccurence:420 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF8410 PF28469.1 (E=6e-61)
- Foldseek best: 1z94-assembly1_A X-Ray Crystal Structure of Protein CV1439 from Chromobacterium (prob 1.00, E=5e-08, TM=0.76)
- (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_215959.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF8410 (PF28469.1)
- 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
COG4276 - Curated reference: UniProt O06816 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 88.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
11 functional partner(s); context anchor
lppF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1443c| MVGYAEPVLIERQSVVAAPAEQVWQRVVTPEGINDELRPWMTMSVPRGAKGMTVDTVPIGAPIGRAWLRLFGVLPFDYDRLSIAELEPGRRFREDSTMLSMRQWQHERTVTPEGDTKTIVRDRITFQTRAGLRFAAPLIAAGLRALFGHRHRRLQRHFAQG