Rv2597 Still unknown · low auto-curated
H37Rv Rv2597 · MTBC0 mtbc0_002764 ·
206 aa · 2949908–2950528 (+) ·
RefSeq NP_217113.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF4178 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF4178. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL73
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2597 |
UniProt still lists this protein as Uncharacterized protein Rv2597; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4178) |
| Orthologous group | 2A0M8 |
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 | 0.347 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF4178 | PF13785.12 | 6.0e-33 | 54–191 | Domain of unknown function (DUF4178) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2600 (integral membrane protein), high confidence from genomic context alone (score 946 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2598 hyp |
hypothetical protein | 976 | 977 ctx | neighborhood:874 cooccurence:773 |
Rv2600 |
integral membrane protein | 946 | 946 ctx | neighborhood:778 cooccurence:763 |
Rv2601 speE |
spermidine synthase | 905 | 906 ctx | neighborhood:629 cooccurence:753 |
Rv2599 |
membrane protein | 875 | 876 ctx | neighborhood:874 |
Rv1006 hyp |
hypothetical protein | 702 | 703 ctx | cooccurence:701 |
Rv1868 hyp |
hypothetical protein | 685 | 685 ctx | cooccurence:685 |
Rv1435c hyp |
hypothetical protein | 640 | 640 ctx | cooccurence:640 |
Rv2047c hyp |
hypothetical protein | 597 | 597 ctx | cooccurence:597 |
Rv2596 vapC40 |
ribonuclease VapC40 | 590 | 590 ctx | neighborhood:590 |
Rv2595 vapB40 |
antitoxin VapB40 | 590 | 590 ctx | neighborhood:590 |
Rv3033 hyp |
hypothetical protein | 558 | 559 ctx | cooccurence:558 |
Rv2571c |
transmembrane protein | 446 | 447 ctx | cooccurence:444 |
Rv3134c |
universal stress protein | 446 | 446 ctx | cooccurence:446 |
Rv3060c |
GntR family transcriptional regulator | 443 | 443 ctx | cooccurence:443 |
Rv0180c |
transmembrane protein | 440 | 441 ctx | cooccurence:405 |
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: membrane protein
- MTBC0 PGAP product: DUF4178 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF4178 PF13785.12 (E=6e-33)
- (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_217113.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4178 (PF13785.12)
- 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
2A0M8 - Curated reference: UniProt P9WL73 (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 —
21 functional partner(s); context anchor
Rv2600 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002764|Rv2597| MGNLLVVIAVALFIAAIVVLVVAIRRPKTPATPGGRRDPLAFDAMPQFGPRQLGPGAIVSHGGIDYVVRGSVTFREGPFVWWEHLLEGGDTPTWLSVQEDDGRLELAMWVKRTDLGLQPGGQHVIDGVTFQETERGHAGYTTEGTTGLPAGGEMDYVDCASAGQGADESMLLSFERWAPDMGWEIATGKSVLAGELTVYPAPPVSA