Rv1891 Still unknown · low auto-curated
H37Rv Rv1891 · MTBC0 mtbc0_002005 ·
135 aa · 2157805–2158212 (+) ·
RefSeq NP_216407.1
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: 6xl5-assembly1_D Cryo-EM structure of EcmrR-RNAP-promoter open complex (prob 0.04, TM 0.37). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07741
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)
| Orthologous group | 2ASSI |
|---|
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 | 1.345 · 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 84.3 (confident). 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 |
|---|---|---|---|---|
6xl5-assembly1_D |
0.04 | 0.37 | 4.3e+00 | 6xl5-assembly1_D Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo) |
7ade-assembly1_Y |
0.03 | 0.36 | 6.1e+00 | 7ade-assembly1_Y Transcription termination complex IVa |
6vhh-assembly1_A |
0.03 | 0.23 | 2.1e+00 | 6vhh-assembly1_A Human Teneurin-2 and human Latrophilin-3 binary complex |
1rwi-assembly1_B |
0.02 | 0.23 | 2.0e+00 | 1rwi-assembly1_B Extracellular domain of Mycobacterium tuberculosis PknD |
1rwl-assembly1_A |
0.02 | 0.20 | 2.7e+00 | 1rwl-assembly1_A Extracellular domain of Mycobacterium tuberculosis PknD |
4s20-assembly1_D |
0.01 | 0.29 | 9.2e+00 | 4s20-assembly1_D Structural basis for transcription reactivation by RapA |
7pgm-assembly1_C |
0.01 | 0.29 | 9.7e+00 | 7pgm-assembly1_C HHIP-C in complex with heparin |
7bam-assembly1_B |
0.01 | 0.15 | 4.6e+00 | 7bam-assembly1_B human Teneurin4 WT C2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1892 (membrane protein), high confidence from genomic context alone (score 962 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) |
|---|---|---|---|---|
Rv1892 |
membrane protein | 962 | 962 ctx | neighborhood:861 coexpression:740 |
Rv1893 hyp |
hypothetical protein | 893 | 893 ctx | neighborhood:856 |
Rv1890c hyp |
hypothetical protein | 574 | 573 ctx | neighborhood:573 |
Rv1889c |
Rv1889c, (MTCY180.29), len: 118 aa. Conserved hypothetical protein. Part of large family of Mycobacterium tuberculosis proteins with conserv | 443 | 443 ctx | neighborhood:443 |
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: 6xl5-assembly1_D Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RP (prob 0.04, E=4e+00, TM=0.37)
- (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_216407.1)
- 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
2ASSI - Curated reference: UniProt O07741 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 84.3, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
4 functional partner(s); context anchor
Rv1892 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002005|Rv1891| MIRELVTTAAITGAAIGGAPVAGADPQRYDGDVPGMNYDASLGAPCSSWERFIFGRGPSGQAEACHFPPPNQFPPAETGYWVISYPLYGVQQVGAPCPKPQAAAQSPDGLPMLCLGARGWQPGWFTGAGFFPPEP