Rv0877 Still unknown · low auto-curated
H37Rv Rv0877 · MTBC0 mtbc0_000932 ·
262 aa · 979287–980075 (+) ·
RefSeq NP_215392.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3027 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3027. Function unknown. Foldseek best (non-significant) hit: 5kuy-assembly1_G Influenza hemagglutinin H3 A/Hong Kong/1/1968 in comp (prob 0.66, TM 0.50). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKR3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0877 |
UniProt still lists this protein as Uncharacterized protein Rv0877; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3027) |
| Orthologous group | 28NWB |
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 | 1.021 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3027 | PF11228.14 | 1.6e-82 | 45–234 | Protein of unknown function (DUF3027) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 91.5 (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 |
|---|---|---|---|---|
5kuy-assembly1_G |
0.66 | 0.50 | 2.4e-01 | 5kuy-assembly1_G Influenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with designed inhibitor protein HSB.2A |
4n6v-assembly7_4 |
0.44 | 0.56 | 1.2e+00 | 4n6v-assembly7_4 Partial rotational order disorder structure of human stefin B |
6i1m-assembly1_A |
0.20 | 0.48 | 7.4e-01 | 6i1m-assembly1_A Secreted type 1 cystatin from Fasciola hepatica |
6d63-assembly6_L |
0.16 | 0.43 | 1.2e+00 | 6d63-assembly6_L The structure of AtzH: a little known member of the atrazine breakdown pathway |
6d63-assembly6_K |
0.15 | 0.46 | 1.9e+00 | 6d63-assembly6_K The structure of AtzH: a little known member of the atrazine breakdown pathway |
6bju-assembly1_A |
0.14 | 0.40 | 1.3e+00 | 6bju-assembly1_A The structure of AtzH: a little known member of the atrazine breakdown pathway |
6bju-assembly2_C |
0.13 | 0.38 | 1.3e+00 | 6bju-assembly2_C The structure of AtzH: a little known member of the atrazine breakdown pathway |
1stf-assembly1_I |
0.12 | 0.51 | 5.4e+00 | 1stf-assembly1_I THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0876c (transmembrane protein), high confidence from genomic context alone (score 776 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) |
|---|---|---|---|---|
Rv0875c hyp |
hypothetical protein | 884 | 884 ctx | neighborhood:774 cooccurence:506 |
Rv0876c |
transmembrane protein | 776 | 776 ctx | neighborhood:774 |
Rv3662c hyp |
hypothetical protein | 635 | 636 ctx | cooccurence:631 |
Rv3202c adnA |
ATP-dependent DNA helicase | 609 | 609 ctx | cooccurence:608 |
Rv2699c hyp |
hypothetical protein | 603 | 604 ctx | cooccurence:598 |
Rv2239c hyp |
hypothetical protein | 599 | 600 ctx | cooccurence:596 |
Rv0048c |
membrane protein | 517 | 517 ctx | cooccurence:517 |
Rv1171 hyp |
hypothetical protein | 506 | 507 ctx | cooccurence:501 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 497 | 498 ctx | cooccurence:493 |
Rv0822c hyp |
hypothetical protein | 483 | 484 ctx | cooccurence:482 |
Rv1423 whiA |
transcriptional regulator WhiA | 475 | 476 ctx | cooccurence:471 |
Rv3847 hyp |
hypothetical protein | 455 | 455 ctx | cooccurence:449 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 453 | 453 ctx | cooccurence:445 |
Rv2891 hyp |
hypothetical protein | 453 | 453 ctx | cooccurence:451 |
Rv3597c lsr2 |
iron-regulated H-NS-like protein | 443 | 444 ctx | cooccurence:441 |
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: DUF3027 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3027 PF11228.14 (E=2e-82)
- Foldseek best: 5kuy-assembly1_G Influenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with d (prob 0.66, E=2e-01, TM=0.50)
- (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_215392.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3027 (PF11228.14)
- 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
28NWB - Curated reference: UniProt P9WKR3 (SwissProt, reviewed; 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 91.5, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
23 functional partner(s); context anchor
Rv0876c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000932|Rv0877| MTGPTEESAVATVADWPEGLAAVLRGAADQARAAVVEFSGPEAVGDYLGVSYEDGNAATHRFIAHLPGYQGWQWAVVVASYSGADHATISEVVLVPGPTALLAPDWVPWEQRVRPGDLSPGDLLAPAKDDPRLVPGYTASGDAQVDETAAEIGLGRRWVMSAWGRAQSAQRWHDGDYGPGSAMARSTKRVCRDCGFFLPLAGSLGAMFGVCGNELSADGHVVDRQYGCGAHSDTTAPAGGSTPIYEPYDDGVLDIIEKPAES