Rv3113 Family assigned · medium auto-curated
H37Rv Rv3113 · MTBC0 mtbc0_003309 ·
222 aa · 3501439–3502107 (+) ·
RefSeq NP_217629.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphatase |
|---|---|
| MTBC0 PGAP re-annotation | HAD family hydrolase |
| Revised (this work) | HAD family hydrolase. Pfam: Hydrolase (PF00702.33), HAD_2 (PF13419.13), Hydrolase_like (PF13242.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05790
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible phosphatase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | HAD-hyrolase-like |
| Orthologous group | COG0546 |
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 | 3.23 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.49% of strains (712) · 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 |
|---|---|---|---|---|
Hydrolase | PF00702.33 | 2.3e-10 | 8–180 | haloacid dehalogenase-like hydrolase |
HAD_2 | PF13419.13 | 3.4e-16 | 9–185 | Haloacid dehalogenase-like hydrolase |
Hydrolase_like | PF13242.13 | 3.7e-06 | 146–212 | HAD-hyrolase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moaB1 (pterin-4-alpha-carbinolamine dehydratase), high confidence from genomic context alone (score 938 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3114 hyp |
hypothetical protein | 971 | 971 ctx | neighborhood:770 coexpression:865 |
Rv3110 moaB1 |
pterin-4-alpha-carbinolamine dehydratase | 940 | 938 ctx | neighborhood:489 coexpression:866 |
Rv3112 moaD1 |
molybdenum cofactor biosynthesis protein MoaD | 931 | 932 ctx | neighborhood:535 coexpression:859 |
Rv3111 moaC1 |
cyclic pyranopterin monophosphate synthase accessory protein | 925 | 925 ctx | neighborhood:489 coexpression:860 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 913 | 914 ctx | neighborhood:408 coexpression:860 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 836 | 836 | coexpression:802 |
Rv1358 |
transcriptional regulator | 772 | 772 | coexpression:736 |
Rv0894 |
transcriptional regulator | 556 | 557 | coexpression:494 |
Rv0842 |
integral membrane protein | 456 | 457 ctx | cooccurence:454 |
Rv1307 atpH |
ATP synthase subunit b/delta | 467 | 450 | coexpression:418 |
Rv3115 |
transposase | 443 | 443 ctx | neighborhood:443 |
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 503 | 436 | coexpression:404 |
Rv0193c hyp |
hypothetical protein | 422 | 423 | coexpression:423 |
Rv3197 |
ABC transporter ATP-binding protein | 411 | 412 | coexpression:402 |
Rv0647c hyp |
hypothetical protein | 408 | 408 |
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: phosphatase
- MTBC0 PGAP product: HAD family hydrolase
- Pfam (hmmscan --cut_ga): Hydrolase PF00702.33 (E=2e-10), HAD_2 PF13419.13 (E=3e-16), Hydrolase_like PF13242.13 (E=4e-06)
- (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_217629.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase (PF00702.33), HAD_2 (PF13419.13), Hydrolase_like (PF13242.13)
- 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
COG0546 - Curated reference: UniProt O05790 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
17 functional partner(s); context anchor
moaB1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003309|Rv3113| MTSRDGFTIVWDWNGTLCDDRTILLDAVGQTLVNEGFEPLSQQQLIQRFARPLRTFFENACGRDLLTSEWERVQSTFRRIYRSREAEVTLVEDAYDVLAQGNRSAAGQFLLSLAPHDELMHFVQKYGIAKWFNEIRGRTRPDQEKPMMLAELIMQRSLNPTRVVHIGDSLEDAAAASAVGAISVLVTGASLQPPDRVMLKQLQPFVASSLKQALQYAGGDGD