Rv2295 Family assigned · low auto-curated
H37Rv Rv2295 · MTBC0 mtbc0_002435 ·
212 aa · 2591521–2592159 (+) ·
RefSeq NP_216811.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | CbrC family protein |
| Revised (this work) | CbrC family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFL7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0167 protein Rv2295 |
| Curated function | Probably plays a role in host phagosome maturation arrest. |
UniProt still lists this protein as UPF0167 protein Rv2295; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterised protein family (UPF0167) |
| Orthologous group | COG3196 |
| KEGG orthology |
K09925
|
| Gene Ontology (48) |
GO:0002682, GO:0002683, GO:0008150, GO:0009605, GO:0009607, GO:0031347, GO:0031348, GO:0035821, GO:0043207, GO:0044003, GO:0044403, GO:0044413 +36 more
|
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 | 0.507 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 missense, 2 nonsense, 0 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.29% of strains (422) · clonal |
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 |
|---|---|---|---|---|
UPF0167 | PF03691.19 | 8.4e-67 | 37–211 | Uncharacterised protein family (UPF0167) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE8 (PPE family protein PPE8), medium confidence from genomic context alone (score 676 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) |
|---|---|---|---|---|
Rv0355c PPE8 |
PPE family protein PPE8 | 675 | 676 ctx | cooccurence:674 |
Rv2209 |
integral membrane protein | 673 | 674 ctx | cooccurence:669 |
Rv3350c PPE56 |
PPE family protein PPE56 | 667 | 667 ctx | cooccurence:667 |
Rv3347c PPE55 |
PPE family protein PPE55 | 667 | 667 ctx | cooccurence:665 |
Rv3343c PPE54 |
PPE family protein PPE54 | 649 | 649 ctx | cooccurence:647 |
Rv0304c PPE5 |
PPE family protein PPE5 | 648 | 648 ctx | cooccurence:646 |
Rv1917c PPE34 |
PPE family protein PPE34 | 646 | 647 ctx | cooccurence:644 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 645 | 645 ctx | cooccurence:645 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 643 | 643 ctx | cooccurence:643 |
Rv1004c |
membrane protein | 643 | 643 ctx | cooccurence:642 |
Rv0330c hyp |
hypothetical protein | 621 | 622 ctx | cooccurence:620 |
Rv0442c PPE10 |
PPE family protein PPE10 | 611 | 611 ctx | cooccurence:609 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 606 | 606 ctx | cooccurence:606 |
Rv2082 hyp |
hypothetical protein | 603 | 603 ctx | cooccurence:601 |
Rv0305c PPE6 |
PPE family protein PPE6 | 598 | 599 ctx | cooccurence:597 |
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: CbrC family protein
- Pfam (hmmscan --cut_ga): UPF0167 PF03691.19 (E=8e-67)
- (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_216811.1)
- Domains: Pfam-A via hmmscan --cut_ga — UPF0167 (PF03691.19)
- 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
COG3196 - Curated reference: UniProt P9WFL7 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
59 functional partner(s); context anchor
PPE8 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002435|Rv2295| MDQSANHACLPTPLASTTGRGQDHEMPVEETSTPQKLPQFRYHPDPVGTGSIVADEVSCVSCEQRRPYTYTGPVYAEEELNEAICPWCIADGSAASRFDATFTDAMWAVPDDVPEDVTEEVLCRTPGFTGWLQEEWLHHCGDAAAFLGPVGASEVADLPDALDALRNEYRGYDWPADKIEEFILTLDRNGLATAYLFRCLSCGVHLAYADFA