Rv2557 Family assigned · medium auto-curated
H37Rv Rv2557 · MTBC0 - ·
224 aa · 2877072–2877746 (+) ·
RefSeq NP_217073.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains ABM (PF03992.23) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLA5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2557 |
UniProt still lists this protein as Uncharacterized protein Rv2557; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | cellular response to starvation |
| Orthologous group | COG1359 |
| Gene Ontology (15) |
GO:0006950, GO:0007154, GO:0008150, GO:0009267, GO:0009605, GO:0009987, GO:0009991, GO:0031667, GO:0031668, GO:0031669, GO:0033554, GO:0042594 +3 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 | 0.484 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
ABM | PF03992.23 | 9.1e-05 | 24–84 | Antibiotic biosynthesis monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3481c (integral membrane protein), medium confidence from genomic context alone (score 504 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) |
|---|---|---|---|---|
Rv2558 hyp |
hypothetical protein | 936 | 935 ctx | neighborhood:547 coexpression:860 |
Rv2556c hyp |
hypothetical protein | 596 | 596 ctx | neighborhood:594 |
Rv2302 hyp |
hypothetical protein | 567 | 568 ctx | cooccurence:539 |
Rv2721c hyp |
hypothetical protein | 550 | 551 ctx | cooccurence:548 |
Rv2160c |
Rv2160c, (MTCY270.08), len: 113 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator, similar to C-terminal | 512 | 513 | coexpression:427 |
Rv3481c |
integral membrane protein | 504 | 504 ctx | cooccurence:504 |
Rv2160A |
Rv2160A, len: 211 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator,similar to N-terminal half of AL51266 | 499 | 499 | |
Rv0569 hyp |
hypothetical protein | 496 | 496 ctx | cooccurence:462 |
Rv1411c lprG |
lipoprotein LprG | 493 | 494 ctx | cooccurence:487 |
Rv2553c mltG |
membrane protein | 480 | 480 ctx | neighborhood:466 |
Rv1888c |
Rv1888c, (MTCY180.30), len: 186 aa. Possible transmembrane protein. | 479 | 479 ctx | cooccurence:463 |
Rv2555c alaS |
alanine--tRNA ligase | 471 | 471 ctx | neighborhood:466 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 469 | 469 ctx | neighborhood:466 |
Rv2554c ruvX |
Holliday junction resolvase | 469 | 469 ctx | neighborhood:466 |
Rv2574 hyp |
hypothetical protein | 468 | 469 ctx | cooccurence:468 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): ABM PF03992.23 (E=9e-05)
- (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_217073.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABM (PF03992.23)
- 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
COG1359 - Curated reference: UniProt P9WLA5 (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 —
38 functional partner(s); context anchor
Rv3481c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2557| MTGGATGALPRTMKEGWIVYARSTTIQAQSECIDTGIAHVRDVVMPALQGMDGCIGVSLLVDRQSGRCIATSAWETAEAMHASREQVTPIRDRCAEMFGGTPAVEEWEIAAMHRDHRSAEGACVRATWVKVPADQVDQGIEYYKSSVLPQIEGLDGFCSASLLVDRTSGRAVSSATFDSFDAMERNRDQSNALKATSLREAGGEELDECEFELALAHLRVPELV