Rv2125 Family assigned · medium auto-curated
H37Rv Rv2125 · MTBC0 mtbc0_002257 ·
292 aa · 2413556–2414434 (+) ·
RefSeq NP_216641.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PAC2 family protein |
| Revised (this work) | PAC2 family protein. Pfam: PAC2 (PF09754.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33260
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PAC2 family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PAC2 family |
| Orthologous group | COG2047 |
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 | 0.067 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
PAC2 | PF09754.16 | 2.2e-63 | 21–238 | PAC2 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: metH (methionine synthase), high confidence from genomic context alone (score 753 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) |
|---|---|---|---|---|
Rv2124c metH |
methionine synthase | 882 | 753 ctx | neighborhood:750 textmining:543 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 633 | 634 ctx | cooccurence:627 |
Rv1456c |
antibiotic ABC transporter permease | 554 | 554 ctx | cooccurence:554 |
Rv0121c hyp |
hypothetical protein | 511 | 511 | coexpression:447 |
Rv1828 |
HTH-type transcriptional regulator | 501 | 501 ctx | cooccurence:498 |
Rv1321 nucS |
endonuclease NucS | 480 | 481 ctx | cooccurence:473 |
Rv0504c hyp |
hypothetical protein | 479 | 480 ctx | cooccurence:477 |
Rv2110c prcB |
proteasome subunit beta | 496 | 466 | |
Rv3129 |
Rv3129, (MTCY164.40), len: 110 aa. Conserved hypothetical protein, with some similarity to various hypothetical proteins from Streptomyces c | 450 | 450 | coexpression:450 |
Rv0080 hyp |
hypothetical protein | 449 | 450 | coexpression:450 |
Rv2109c prcA |
proteasome subunit alpha | 479 | 449 | |
Rv1875 hyp |
hypothetical protein | 449 | 449 | coexpression:449 |
Rv0884c serC |
phosphoserine aminotransferase | 447 | 447 ctx | cooccurence:439 |
Rv2242 hyp |
hypothetical protein | 439 | 440 ctx | cooccurence:436 |
Rv1457c |
antibiotic ABC transporter permease | 438 | 439 ctx | cooccurence:435 |
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: PAC2 family protein
- Pfam (hmmscan --cut_ga): PAC2 PF09754.16 (E=2e-63)
- (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_216641.1)
- Domains: Pfam-A via hmmscan --cut_ga — PAC2 (PF09754.16)
- 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
COG2047 - Curated reference: UniProt O33260 (TrEMBL, unreviewed; 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 —
26 functional partner(s); context anchor
metH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002257|Rv2125| MTPSEGNAPLPELHNTVVVAAFEGWNDAGDAASDAVAHLAASWQALPIVEIDDEAYYDYQVNRPVIRQVDGVTRELQWPAMRISHCRPPGSDRDVVLMCGVEPNMRWRTFCDELLAVIDKLNVDTVVILGALLADTPHTRPVPVSGAAYSAASARQFGLQETRYEGPTGIAGVFQSACVGAGIPAVTFWAAVPHYVSHPPNPKATIALLRRVEDVLDVEVPLADLPAQAEAWEREITETIAEDHELAEYVQTLEQHGDAAVDMNEALGNIDGDALAAEFERYLRRRRPGFGR