Rv1190 Resolved · high auto-curated
H37Rv Rv1190 · MTBC0 mtbc0_001278 ·
292 aa · 1341422–1342300 (+) ·
RefSeq NP_215706.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta fold hydrolase |
| Revised (this work) | Alpha/beta fold hydrolase. Pfam: Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86348
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | AB hydrolase-1 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | dhmA2 |
| eggNOG description | Haloalkane dehalogenase |
| Orthologous group | COG0596 |
| EC number |
EC 3.8.1.5
|
| KEGG orthology |
K01563
|
| KEGG pathways |
map00361, map00625, map01100, map01120
|
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 | 0.119 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 2 missense, 0 nonsense, 7 frameshift |
| Disruption | 7 distinct premature-stop/frameshift site(s); most common in 1.53% of strains (2220) · convergent |
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 |
|---|---|---|---|---|
Abhydrolase_1 | PF00561.27 | 3.8e-14 | 43–140 | alpha/beta hydrolase fold |
Abhydrolase_6 | PF12697.14 | 8.5e-15 | 45–282 | Alpha/beta hydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigI (ECF RNA polymerase sigma factor SigI), high confidence from genomic context alone (score 972 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) |
|---|---|---|---|---|
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 971 | 972 ctx | neighborhood:741 coexpression:860 |
Rv1931c |
transcriptional regulator | 863 | 864 | coexpression:841 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 858 | 858 | coexpression:839 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 851 | 851 | coexpression:850 |
Rv2488c |
LuxR family transcriptional regulator | 847 | 846 | coexpression:845 |
Rv3167c |
TetR family transcriptional regulator | 842 | 842 | coexpression:837 |
Rv1267c embR |
transcriptional regulator EmbR | 838 | 838 | coexpression:838 |
Rv0887c hyp |
hypothetical protein | 835 | 836 | coexpression:799 |
Rv3736 |
AraC/XylS family transcriptional regulator | 830 | 830 | coexpression:804 |
Rv1725c hyp |
hypothetical protein | 829 | 829 | coexpression:803 |
Rv3840 |
transcriptional regulator | 824 | 824 | coexpression:824 |
Rv1674c |
transcriptional regulator | 815 | 815 | coexpression:815 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 815 | 815 | coexpression:815 |
Rv1395 |
HTH-type transcriptional regulator | 814 | 814 | coexpression:783 |
Rv0603 hyp |
hypothetical protein | 810 | 810 | coexpression:810 |
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: alpha/beta fold hydrolase
- Pfam (hmmscan --cut_ga): Abhydrolase_1 PF00561.27 (E=4e-14), Abhydrolase_6 PF12697.14 (E=9e-15)
- (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_215706.1)
- Domains: Pfam-A via hmmscan --cut_ga — Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14)
- 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
COG0596 - Curated reference: UniProt O86348 (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 —
76 functional partner(s); context anchor
sigI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001278|Rv1190| MTMKSLAALDRPSWLSSSAWPWQPYLLSHHQGGIAVTDIGDGPAVLFVHVGSWSFVWRDVLLRLANDFRCVAIDAPGCGLSDRLSTPPTLAQAADAITSVIDALQLRDLTLVAHDLGGPAGFLAAARRGDRVAALAAVNCFAWRPTGPLFRGMLAAMGSAPVRELDAAINALARATSTRFGAGRHWSRADRAAFRAGIDAPARRAWHAYFRDARRAHALYTDVDAALRGGLADRPLLTIFGQFNDPLRFQPRWKELFPTARQLQVRRGNHFPMCDDPDLVAGALTSFVQRST