Rv0193c Family assigned · low
H37Rv Rv0193c · MTBC0 mtbc0_000207 ·
615 aa · 225073–226920 (-) ·
RefSeq NP_214707.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Putative 2-oxoglutarate / Fe(II)-dependent oxygenase. No Pfam domain above threshold, but Foldseek gives a significant match to a proline-hydroxylase (2OG-Fe(II) oxygenase) fold (prob 1.00, E=1e-4, TM=0.57). Structure-based hypothesis. |
Curated reference (UniProt)
| UniProt |
O07437
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EIH2 |
|---|
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 | 0.644 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 18 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 57.0 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
7e08-assembly1_A-2 |
1.00 | 0.57 | 1.0e-04 sig | 7e08-assembly1_A-2 Trans-3/4-proline-hydroxylase H11 with 4-Hydroxyl-proline |
7e01-assembly1_A-2 |
1.00 | 0.57 | 7.9e-05 sig | 7e01-assembly1_A-2 Trans-3/4-proline-hydroxylase H11 in the sixth reaction state |
8h7v-assembly2_B |
1.00 | 0.59 | 1.2e-04 sig | 8h7v-assembly2_B Trans-3/4-proline-hydroxylase H11 with AKG |
4nmi-assembly1_A-2 |
1.00 | 0.54 | 3.2e-05 sig | 4nmi-assembly1_A-2 Crystal Structure of the Apo ectoine hydroxylase ECTD from Salibacillus salexigens |
7dt0-assembly3_C |
1.00 | 0.61 | 1.9e-04 sig | 7dt0-assembly3_C Proline hydroxylase H11-N101I mutant |
8h7y-assembly1_A |
1.00 | 0.56 | 1.5e-04 sig | 8h7y-assembly1_A Trans-3/4-proline-hydroxylase H11 with AKG and L-proline |
8h7t-assembly1_A |
1.00 | 0.55 | 1.5e-04 sig | 8h7t-assembly1_A Trans-3/4-proline-hydroxylase H11 apo structure |
8h85-assembly1_A |
1.00 | 0.58 | 2.2e-04 sig | 8h85-assembly1_A Trans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0194 |
multidrug ABC transporter ATPase/permease | 955 | 877 | coexpression:804 textmining:653 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 783 | 783 | coexpression:783 |
Rv1190 hyp |
hypothetical protein | 774 | 774 | coexpression:774 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 761 | 761 | coexpression:761 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 740 | 740 | coexpression:740 |
Rv3114 hyp |
hypothetical protein | 734 | 734 | coexpression:734 |
Rv0195 |
two component transcriptional regulator | 903 | 732 | coexpression:731 textmining:655 |
Rv0603 hyp |
hypothetical protein | 731 | 731 | coexpression:731 |
Rv3111 moaC1 |
cyclic pyranopterin monophosphate synthase accessory protein | 731 | 731 | coexpression:731 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 730 | 730 | coexpression:730 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 493 | 494 | coexpression:494 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 431 | 431 | coexpression:431 |
Rv3113 |
phosphatase | 422 | 423 | coexpression:423 |
Rv3110 moaB1 |
pterin-4-alpha-carbinolamine dehydratase | 408 | 409 | coexpression:409 |
Rv3167c |
TetR family transcriptional regulator | 404 | 404 | coexpression:404 |
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
- MTBC0 PGAP product: 'hypothetical protein'
- Pfam: none above threshold
- Foldseek on the ESMFold model: significant match to a trans-proline-hydroxylase / 2OG-Fe(II) oxygenase fold (E=1e-4, TM=0.57)
ESM Atlas signal (exploratory)
Ancestral protein hash 196253476cc84faed042be27667dd710 ·
10 ESM-space neighbours (max similarity 0.823).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 2447 |
1.27 | DSBH Fe(II)/2OG oxygenase core |
| 2 | 2751 |
1.26 | Fe(II)/2OG oxygenase catalytic core |
| 3 | 13210 |
1.16 | 2OG oxygenase jelly-roll core |
| 4 | 13087 |
1.15 | DSBH 2OG oxygenase active-site lid |
| 5 | 15298 |
1.13 | 2OG oxygenase N-terminal activation |
| 6 | 5522 |
1.05 | 2OG oxygenase HxD/E core |
| 7 | 11797 |
1.04 | 2OG oxygenase N-terminal cap |
| 8 | 11638 |
1.02 | Fe/2OG oxygenase active site |
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_214707.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2EIH2 - Curated reference: UniProt O07437 (TrEMBL, unreviewed; Predicted)
- 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 57.0, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 19 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000207|Rv0193c| MIQISRDMSSLGQTATTQALPDNSDGIQLTKFAADDILPLEYAPPIGPELVSQDQLPAAWAYKRFRDLDDKESYRRKLLQELTDALAAQGSEAAEIATAALRDLIDQMAEQGAVVLADIVESDDFLELVKRYDELMAREGSRSFIHRFLDLRRSPGMLTDPAVNGALVHPLMIALISYAVGGPIRMIDARGKDAEPLSVLAQDNMLHIDNTPFNDEYKILITWRRGTAQGPAGQNFTFLPGTHKLARTCFVNEDGVPWSSENASIFTTPDSIRKVFDAQRQLGGQDHPTVIEVTDSERPLSSVFAAGSLVHHRFRTASGSARSCIILVFHRVADNPGRMVSDVEDSSDVSLSELLTRGVPDESYQQRFIATLCAAADEIAELLLKWKKTPQRPVSLPLQTKQIDGARFEEWISAATEAPEVREIRNRELTIPYGEVLSAEEFFDLIWRLMRFDKHGPLDLILYHDNREEPRKWARNLIREMSADRLYERLLGWLADIQQPRPADCLRPLQIHALISEVLKTLPLDEDQDPPADWHFDLLGMSHAEAARSVKHLLEDVAEALLRCEDMAAYLSTSLFAFWAVDAAYSLDGRRNLVVKDCARRLLRHYTMLSLTCFQ