Rv1770 Family assigned · medium auto-curated
H37Rv Rv1770 · MTBC0 - ·
428 aa · 2003878–2005164 (+) ·
RefSeq NP_216286.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Peptidase_M28 (PF04389.23) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
O06803
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Peptidase family M28 |
| Orthologous group | COG2234 |
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 | 0.358 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (378) · 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 |
|---|---|---|---|---|
Peptidase_M28 | PF04389.23 | 1.3e-12 | 252–418 | Peptidase family M28 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1771 (L-gulono-1,4-lactone dehydrogenase), high confidence from genomic context alone (score 888 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) |
|---|---|---|---|---|
Rv1769 hyp |
hypothetical protein | 970 | 971 ctx | neighborhood:881 coexpression:734 |
Rv1771 |
L-gulono-1,4-lactone dehydrogenase | 887 | 888 ctx | neighborhood:881 |
Rv2045c lipT |
carboxylesterase LipT | 715 | 700 | database:587 |
Rv1104 |
Rv1104, (MTV017.57), len: 229 aa. Possible para-nitrobenzyl esterase (fragment; possibly first part). Similar to the N-terminal domain of ma | 713 | 698 | database:587 |
Rv1105 |
Rv1105, (MTV017.58), len: 171 aa. Possible para-nitrobenzyl esterase (fragment; possibly second part). Similar to C-terminal domain of many | 711 | 696 | database:587 |
Rv1990A |
Rv1990A, len: 111 aa. Possible dehydrogenase (fragment), similar to N-terminal part of several dehydrogenases and hypothetical proteins, e.g | 681 | 681 ctx | cooccurence:477 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 657 | 655 | database:584 |
Rv1004c |
membrane protein | 630 | 631 ctx | cooccurence:627 |
Rv3350c PPE56 |
PPE family protein PPE56 | 621 | 621 ctx | cooccurence:620 |
Rv0355c PPE8 |
PPE family protein PPE8 | 621 | 621 ctx | cooccurence:620 |
Rv3347c PPE55 |
PPE family protein PPE55 | 617 | 617 ctx | cooccurence:616 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 613 | 610 | database:584 |
Rv0304c PPE5 |
PPE family protein PPE5 | 608 | 609 ctx | cooccurence:607 |
Rv2337c hyp |
hypothetical protein | 599 | 600 ctx | cooccurence:529 |
Rv2124c metH |
methionine synthase | 618 | 588 | database:572 |
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): Peptidase_M28 PF04389.23 (E=1e-12)
- (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_216286.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M28 (PF04389.23)
- 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
COG2234 - Curated reference: UniProt O06803 (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 —
136 functional partner(s); context anchor
Rv1771 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1770| MDEAHPAHPADAGRPGGPIQGARRGAAMTPITALPTELAAMREVVETLAPIERAAGEPGEHKAAEWIVERLRTAGAQDARIEEEQYLDGYPRLHLKLSVIGVAAGVAGLLSRRLRIPAALAGVGAGLAIADDCANGPRIVRKRTETPRTTWNAVAEAGDPAGQLTVVVCAHHDAAHSGKFFEAHIEEVMVELFPGIVERIDTQLPNWWGPILAPALAGVGALRGSRPMMIAGTVGSALAAALFADIARSPVVPGANDNLSAVALLVALAERLRERPVKGVRVLLVSLGAEETLQGGIYGFLARHKPELDRDRTYFLNFDTIGSPELIMLEGEGPTVMEDYFYRPFRDLVIRAAERADAPLRRGIRSRNSTDAVLMSRAGYPTACFVSINRHKSVANYHLMSDTPENLCYETVSHAVTVAESVIRELAR