Rv1961 Still unknown · low auto-curated
H37Rv Rv1961 · MTBC0 mtbc0_002076 ·
164 aa · 2223328–2223822 (+) ·
RefSeq NP_216477.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 5umr-assembly1_A Crystal structure of N-terminal domain of human FACT (prob 0.33, TM 0.74). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95253
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)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | helicase |
| Orthologous group | COG1061 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 45.0 (very 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 |
|---|---|---|---|---|
5umr-assembly1_A |
0.33 | 0.74 | 2.3e+00 | 5umr-assembly1_A Crystal structure of N-terminal domain of human FACT complex subunit SSRP1 |
3nvx-assembly1_A |
0.18 | 0.77 | 5.1e+00 | 3nvx-assembly1_A Molecular mechanism of guidance cue recognition |
3cwy-assembly1_A-2 |
0.15 | 0.46 | 2.1e+00 | 3cwy-assembly1_A-2 Structure of CagD from H. pylori pathogenicity island crystallized in the presence of Cu(II) ions |
3f0w-assembly1_A |
0.15 | 0.50 | 2.2e+00 | 3f0w-assembly1_A Human NUMB-like protein, phosphotyrosine interaction domain |
4wj7-assembly3_C |
0.13 | 0.32 | 7.3e-01 | 4wj7-assembly3_C CCM2 PTB domain in complex with KRIT1 NPxY/F3 |
5njk-assembly3_C |
0.13 | 0.55 | 3.4e+00 | 5njk-assembly3_C PTB domain of human Numb isoform-1 |
3nvx-assembly2_B |
0.13 | 0.76 | 7.4e+00 | 3nvx-assembly2_B Molecular mechanism of guidance cue recognition |
6vxk-assembly1_C |
0.13 | 0.78 | 7.9e+00 | 6vxk-assembly1_C Cryo-EM Structure of the full-length A39R/PlexinC1 complex |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1329c dinG |
ATP-dependent helicase DinG | 888 | 879 | experimental:685 database:622 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 853 | 854 | experimental:627 database:621 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 856 | 853 | experimental:578 database:621 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 847 | 848 | experimental:613 database:621 |
Rv1629 polA |
DNA polymerase I | 787 | 768 | experimental:430 database:580 |
Rv2090 |
5'-3' exonuclease | 766 | 752 | experimental:430 database:580 |
Rv2101 helZ |
helicase HelZ | 711 | 689 | database:615 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 688 | 688 | database:620 |
Rv2529 hyp |
hypothetical protein | 706 | 687 | database:610 |
Rv1947 hyp |
hypothetical protein | 636 | 636 ctx | fusion:633 |
Rv1334 mec |
[CysO | 630 | 630 | database:613 |
Rv3036c TB22.2 hyp |
hypothetical protein | 620 | 620 | database:563 |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 620 | 620 | database:563 |
Rv2328 PE23 |
PE family protein PE23 | 620 | 620 | database:563 |
Rv0832 PE_PGRS12 |
PE-PGRS family protein PE_PGRS12 | 620 | 620 | database:563 |
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: hypothetical protein
- Foldseek best: 5umr-assembly1_A Crystal structure of N-terminal domain of human FACT complex su (prob 0.33, E=2e+00, TM=0.74)
- (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_216477.1)
- 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
COG1061 - Curated reference: UniProt P95253 (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 45.0, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 36 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002076|Rv1961| MFLPTNAQYQLLVVGVSPWDTPSPSGRISWGSAWPHQARRAQTCQRVRRHWMIDTTEAAYRLTYQPDGTSITVRENLVDILARELLGPIRGPQEVLPFSPRSQYLVGHLAPVKLTGAALIDDNAVQARANAEALAEGGGVPAYAADETTPTPTTTPKTAHPSRA