Rv1065 Family assigned · medium auto-curated
H37Rv Rv1065 · MTBC0 mtbc0_001145 ·
188 aa · 1194774–1195340 (+) ·
RefSeq NP_215581.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | cysteine dioxygenase family protein |
| Revised (this work) | Cysteine dioxygenase family protein. Pfam: CDO_I (PF05995.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53413
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cysteine dioxygenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | cdoA |
| eggNOG description | cysteine dioxygenase |
| Orthologous group | COG1917 |
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 | 0.36 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 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 |
|---|---|---|---|---|
CDO_I | PF05995.19 | 2.9e-08 | 56–117 | Cysteine dioxygenase type I |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3249c (TetR family transcriptional regulator), medium confidence from genomic context alone (score 686 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) |
|---|---|---|---|---|
Rv1066 hyp |
hypothetical protein | 996 | 996 ctx | neighborhood:836 fusion:615 cooccurence:631 coexpression:860 |
Rv3249c |
TetR family transcriptional regulator | 685 | 686 ctx | cooccurence:683 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 573 | 574 ctx | cooccurence:571 |
Rv1064c lpqV |
lipoprotein LpqV | 572 | 572 ctx | neighborhood:568 |
Rv0128 |
transmembrane protein | 547 | 547 ctx | cooccurence:547 |
Rv0184 hyp |
hypothetical protein | 542 | 543 ctx | cooccurence:540 |
Rv0485 |
transcriptional regulator | 521 | 521 | |
Rv3118 sseC1 hyp |
hypothetical protein | 496 | 497 ctx | cooccurence:480 |
Rv0814c sseC2 hyp |
hypothetical protein | 486 | 487 ctx | cooccurence:480 |
Rv1845c blaR |
sensor-transducer protein BlaR | 450 | 450 ctx | cooccurence:444 |
Rv1639c hyp |
hypothetical protein | 432 | 432 ctx | cooccurence:424 |
Rv3035 hyp |
hypothetical protein | 426 | 427 ctx | cooccurence:423 |
Rv1063c |
NTE family protein | 423 | 423 ctx | neighborhood:421 |
Rv3818 hyp |
hypothetical protein | 400 | 401 | |
Rv3820c papA2 |
trehalose-2-sulfate acyltransferase | 400 | 400 ctx | cooccurence:400 |
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: cysteine dioxygenase family protein
- Pfam (hmmscan --cut_ga): CDO_I PF05995.19 (E=3e-08)
- (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_215581.1)
- Domains: Pfam-A via hmmscan --cut_ga — CDO_I (PF05995.19)
- 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
COG1917 - Curated reference: UniProt O53413 (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 —
15 functional partner(s); context anchor
Rv3249c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001145|Rv1065| MVMPLVTPTTAVPSPGPTRLRVADLLRATDQAADDVLGGRCDHLLPDGGVPQTQRWYTRIHGDEELDIWLISWVPGQPTELHDHGGSLGALTVLSGSLNEYRWDGRRLRRRRLDAGDQAGFPLGWVHDVVWAPRPIGGPDAAGMAVAPTLSVHAYSPPLTAMSYYEITERNTLRRQRTELTDQPEGSG