Rv0875c Still unknown · low auto-curated
H37Rv Rv0875c · MTBC0 mtbc0_000930 ·
162 aa · 977018–977506 (-) ·
RefSeq NP_215390.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2771 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2771. Function unknown. Foldseek best (non-significant) hit: 6d0k-assembly1_D Crystal structure of a CLC-type fluoride/proton antip (prob 0.60, TM 0.45). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKR7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0875c |
UniProt still lists this protein as Uncharacterized protein Rv0875c; 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 (DUF2771) |
| Orthologous group | 2EMAJ |
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.091 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
DUF2771 | PF10969.14 | 8.9e-45 | 32–159 | Protein of unknown function (DUF2771) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 95.6 (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 |
|---|---|---|---|---|
6d0k-assembly1_D |
0.60 | 0.45 | 1.8e-01 | 6d0k-assembly1_D Crystal structure of a CLC-type fluoride/proton antiporter, E118Q mutant |
6fy3-assembly1_X |
0.54 | 0.37 | 1.3e-01 | 6fy3-assembly1_X Crystal structure of a V2-directed, RV144 vaccine-like antibody from HIV-1 infection, CAP228-3D, bound to a heterologous V2 peptide |
7t0r-assembly2_I |
0.38 | 0.41 | 4.2e-01 | 7t0r-assembly2_I Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the extracellular domains of CD4 and ibalizumab fAb |
5j7c-assembly1_C |
0.35 | 0.46 | 6.9e-01 | 5j7c-assembly1_C A picomolar affinity FN3 domain in complex with hen egg-white lysozyme |
7t0o-assembly1_Q |
0.33 | 0.34 | 1.9e-01 | 7t0o-assembly1_Q cryoEM reconstruction of the HIV gp140 in complex with the extracellular domains of CD4 and the adnectin domain of Combinectin. The gp140 and CD4 coordinates from entry 6EDU were rigid body fitted to the EM map along withe the crystal structure of CD4+adnectin |
6c83-assembly1_C |
0.28 | 0.39 | 3.6e-01 | 6c83-assembly1_C Structure of Aurora A (122-403) bound to inhibitory Monobody Mb2 and AMPPCP |
4lsd-assembly3_H |
0.21 | 0.39 | 5.5e-01 | 4lsd-assembly3_H Myokine structure |
9jqt-assembly1_A |
0.18 | 0.28 | 1.7e-01 | 9jqt-assembly1_A Structure of interleukin receptor common gamma chain (IL2Rgamma/CD132) in complex with 2D4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0876c (transmembrane protein), high confidence from genomic context alone (score 968 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) |
|---|---|---|---|---|
Rv0876c |
transmembrane protein | 968 | 968 ctx | neighborhood:882 coexpression:740 |
Rv0877 hyp |
hypothetical protein | 884 | 884 ctx | neighborhood:774 cooccurence:506 |
Rv1171 hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:770 |
Rv0048c |
membrane protein | 756 | 756 ctx | cooccurence:756 |
Rv3779 |
transmembrane protein | 745 | 745 ctx | cooccurence:743 |
Rv0902c prrB |
two component sensor histidine kinase PrrB | 740 | 740 | coexpression:740 |
Rv1353c |
HTH-type transcriptional regulator | 730 | 731 ctx | cooccurence:729 |
Rv2079 hyp |
hypothetical protein | 705 | 706 ctx | cooccurence:705 |
Rv0275c |
transcriptional regulator | 703 | 703 ctx | cooccurence:701 |
Rv3202c adnA |
ATP-dependent DNA helicase | 700 | 701 ctx | cooccurence:699 |
Rv3166c hyp |
hypothetical protein | 689 | 690 ctx | cooccurence:688 |
Rv1635c |
mannosyltransferase | 654 | 654 ctx | cooccurence:649 |
Rv0822c hyp |
hypothetical protein | 633 | 633 ctx | cooccurence:628 |
Rv2423 hyp |
hypothetical protein | 629 | 629 ctx | cooccurence:629 |
Rv1363c |
membrane protein | 628 | 628 ctx | cooccurence:627 |
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: DUF2771 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2771 PF10969.14 (E=9e-45)
- Foldseek best: 6d0k-assembly1_D Crystal structure of a CLC-type fluoride/proton antiporter, E11 (prob 0.60, E=2e-01, TM=0.45)
- (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_215390.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2771 (PF10969.14)
- 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
2EMAJ - Curated reference: UniProt P9WKR7 (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 95.6, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
63 functional partner(s); context anchor
Rv0876c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000930|Rv0875c| MKRGVATLPVILVILLSVAAGAGAWLLVRGHGPQQPEISAYSHGHLTRVGPYLYCNVVDLDDCQTPQAQGELPVSERYPVQLSVPEVISRAPWRLLQVYQDPANTTSTLFRPDTRLAVTIPTVDPQRGRLTGIVVQLLTLVVDHSGELRDVPHAEWSVRLIF