Rv1171 Family assigned · low
H37Rv Rv1171 · MTBC0 mtbc0_001260 ·
146 aa · 1309748–1310188 (+) ·
RefSeq NP_215687.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Polytopic integral membrane protein with 4 predicted transmembrane helices (DeepTMHMM). RefSeq leaves it 'hypothetical protein'. A topological feature consistent with a membrane transporter/permease or membrane-embedded enzyme; the transported substrate and molecular function are undetermined. |
Curated reference (UniProt)
| UniProt |
O50427
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 | 2AY9H |
|---|
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 | 1.618 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 90.2 (very high). A confident model makes the fold comparison meaningful.
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 |
|---|---|---|---|---|
3n1e-assembly2_B |
0.28 | 0.40 | 2.1e+00 | 3n1e-assembly2_B Vps54 C-terminal domain |
3axj-assembly1_B |
0.25 | 0.39 | 2.1e+00 | 3axj-assembly1_B High resolution crystal structure of C3PO |
8ub8-assembly1_F |
0.18 | 0.41 | 2.7e+00 | 8ub8-assembly1_F Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Pre-active State 1a |
8ub8-assembly1_D |
0.14 | 0.37 | 3.0e+00 | 8ub8-assembly1_D Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Pre-active State 1a |
8f5h-assembly1_A |
0.11 | 0.44 | 6.8e+00 | 8f5h-assembly1_A SARS-CoV-2 S2 helix epitope scaffold |
8ube-assembly1_B |
0.10 | 0.30 | 3.2e+00 | 8ube-assembly1_B Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Resting State 1a |
6dg6-assembly4_D |
0.08 | 0.33 | 3.9e+00 | 6dg6-assembly4_D Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic |
7pp1-assembly1_AAA |
0.08 | 0.38 | 6.8e+00 | 7pp1-assembly1_AAA Crystal structure of the P2Y12 receptor in complex with the inverse agonist selatogrel. |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mshB (1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase), high confidence from genomic context alone (score 778 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) |
|---|---|---|---|---|
Rv1170 mshB |
1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase | 778 | 778 ctx | neighborhood:777 |
Rv0875c hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:770 |
Rv0048c |
membrane protein | 767 | 767 ctx | cooccurence:767 |
Rv0822c hyp |
hypothetical protein | 711 | 712 ctx | cooccurence:709 |
Rv3202c adnA |
ATP-dependent DNA helicase | 708 | 709 ctx | cooccurence:708 |
Rv1776c |
transcriptional regulator | 707 | 707 ctx | cooccurence:702 |
Rv1635c |
mannosyltransferase | 698 | 699 ctx | cooccurence:698 |
Rv0188 |
transmembrane protein | 693 | 694 ctx | cooccurence:691 |
Rv3847 hyp |
hypothetical protein | 693 | 694 ctx | cooccurence:692 |
Rv1610 |
membrane protein | 671 | 672 ctx | cooccurence:668 |
Rv3166c hyp |
hypothetical protein | 632 | 632 ctx | cooccurence:630 |
Rv1249c |
membrane protein | 609 | 609 ctx | cooccurence:605 |
Rv3481c |
integral membrane protein | 605 | 605 ctx | cooccurence:604 |
Rv1353c |
HTH-type transcriptional regulator | 594 | 594 ctx | cooccurence:585 |
Rv3899c hyp |
hypothetical protein | 593 | 593 ctx | cooccurence:592 |
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
- DeepTMHMM: 4 transmembrane helices (type TM)
- Integral membrane topology (localisation feature, not a function)
- DeepTMHMM topology prediction (project 'Still unknown gene function', phase8, 2026-06-10). A topological feature, not a demonstrated molecular function.
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_215687.2)
- 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
2AY9H - Curated reference: UniProt O50427 (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 90.2, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
68 functional partner(s); context anchor
mshB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001260|Rv1171| MGHRVDTLSDRQRANLTTGATDRAIRLVVLALLTVDGVVSALAGALLMPWYIGSAPFPISALISGLVNAALVWAAARWTTSSRVAALPLWAWLLTVAAMSFGGPGDDVILGGQGLLVYGALVFVVAGAVPPAWVLWRRRVQADGSG