Rv2714 Family assigned · medium auto-curated
H37Rv Rv2714 · MTBC0 mtbc0_002888 ·
324 aa · 3049480–3050454 (+) ·
RefSeq NP_217230.1
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 |
I6YA29
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved alanine and leucine rich 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 | 0.676 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 | 4.1e-63 | 43–261 | PAC2 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2715 (hydrolase), high confidence from genomic context alone (score 803 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) |
|---|---|---|---|---|
Rv2715 |
hydrolase | 803 | 803 ctx | neighborhood:802 |
Rv2716 hyp |
hypothetical protein | 754 | 754 ctx | neighborhood:753 |
Rv2713 sthA |
pyridine nucleotide transhydrogenase | 592 | 593 ctx | neighborhood:591 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 563 | 564 ctx | cooccurence:562 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 534 | 534 ctx | cooccurence:532 |
Rv3129 |
Rv3129, (MTCY164.40), len: 110 aa. Conserved hypothetical protein, with some similarity to various hypothetical proteins from Streptomyces c | 530 | 530 | coexpression:450 |
Rv1321 nucS |
endonuclease NucS | 524 | 524 ctx | cooccurence:521 |
Rv0004 hyp |
hypothetical protein | 483 | 483 ctx | cooccurence:483 |
Rv2901c hyp |
hypothetical protein | 477 | 478 ctx | cooccurence:476 |
Rv2712c hyp |
hypothetical protein | 457 | 457 ctx | neighborhood:457 |
Rv0080 hyp |
hypothetical protein | 447 | 447 | coexpression:447 |
Rv1875 hyp |
hypothetical protein | 447 | 447 | coexpression:447 |
Rv0121c hyp |
hypothetical protein | 447 | 447 | coexpression:447 |
Rv1331 clpS |
ATP-dependent Clp protease adapter protein ClpS | 428 | 429 ctx | cooccurence:427 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 428 | 429 ctx | cooccurence:415 |
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=4e-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_217230.1)
- 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 I6YA29 (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 —
23 functional partner(s); context anchor
Rv2715 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002888|Rv2714| MARDQGADEAREYEPGQPGMYELEFPAPQLSSSDGRGPVLVHALEGFSDAGHAIRLAAAHLKAALDTELVASFAIDELLDYRSRRPLMTFKTDHFTHSDDPELSLYALRDSIGTPFLLLAGLEPDLKWERFITAVRLLAERLGVRQTIGLGTVPMAVPHTRPITMTAHSNNRELISDFQPWISEIQVPGSASNLLEYRMAQHGHEVVGFTVHVPHYLTQTDYPAAAQALLEQVAKTGSLQLPLAALAEAAAEVQAKIDEQVQASAEVAQVVAALERQYDAFIDAQENRSLLTRDEDLPSGDELGAEFERFLAQQAEKKSDDDPT