Rv0923c Family assigned · medium auto-curated
H37Rv Rv0923c · MTBC0 mtbc0_000981 ·
354 aa · 1032730–1033794 (-) ·
RefSeq NP_215438.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | poly-gamma-glutamate hydrolase family protein |
| Revised (this work) | Poly-gamma-glutamate hydrolase family protein. Pfam: GGACT (PF06094.18), AIG2_2 (PF13772.12), Gamma_PGA_hydro (PF05908.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XWK6
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phage-related replication protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | Replication protein |
| Orthologous group | COG2105 |
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 | 2.928 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 8 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 |
|---|---|---|---|---|
GGACT | PF06094.18 | 1.1e-12 | 8–104 | Gamma-glutamyl cyclotransferase, AIG2-like |
AIG2_2 | PF13772.12 | 5.5e-14 | 57–137 | AIG2-like family |
Gamma_PGA_hydro | PF05908.17 | 2.1e-37 | 170–322 | Poly-gamma-glutamate hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mntH (divalent metal cation transporter MntH), high confidence from genomic context alone (score 887 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) |
|---|---|---|---|---|
Rv0924c mntH |
divalent metal cation transporter MntH | 887 | 887 ctx | neighborhood:882 |
Rv0925c hyp |
hypothetical protein | 710 | 710 ctx | neighborhood:708 |
Rv2079 hyp |
hypothetical protein | 608 | 609 ctx | cooccurence:605 |
Rv2423 hyp |
hypothetical protein | 596 | 596 ctx | cooccurence:596 |
Rv1347c mbtK |
lysine N-acetyltransferase MbtK | 575 | 575 ctx | cooccurence:575 |
Rv3899c hyp |
hypothetical protein | 565 | 565 ctx | cooccurence:560 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 554 | 554 ctx | cooccurence:554 |
Rv1904 hyp |
hypothetical protein | 543 | 543 ctx | cooccurence:542 |
Rv0926c hyp |
hypothetical protein | 516 | 517 ctx | neighborhood:514 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 503 | 504 ctx | cooccurence:496 |
Rv1796 mycP5 |
membrane-anchored mycosin MycP | 493 | 494 ctx | cooccurence:491 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 493 | 494 ctx | cooccurence:488 |
Rv2067c hyp |
hypothetical protein | 478 | 479 ctx | cooccurence:476 |
Rv0875c hyp |
hypothetical protein | 463 | 463 ctx | cooccurence:458 |
Rv0497 |
transmembrane protein | 434 | 434 ctx | cooccurence:426 |
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: poly-gamma-glutamate hydrolase family protein
- Pfam (hmmscan --cut_ga): GGACT PF06094.18 (E=1e-12), AIG2_2 PF13772.12 (E=5e-14), Gamma_PGA_hydro PF05908.17 (E=2e-37)
- (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_215438.1)
- Domains: Pfam-A via hmmscan --cut_ga — GGACT (PF06094.18), AIG2_2 (PF13772.12), Gamma_PGA_hydro (PF05908.17)
- 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
COG2105 - Curated reference: UniProt I6XWK6 (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 —
22 functional partner(s); context anchor
mntH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000981|Rv0923c| MPDRRHPYFAYGSNLCAHQMASRCPDAGAPRPAVLSDHNWLINQRGVATVEPFAGNKVHGVLWQLSERDLVRLDSAEGVPVRYRRERLTVHTDDTALPAWVYIDHRVMPGRPRPGYLPRVIDGARHHGLPQRWIDYLHRWDPARWPLPVLPSSRSGPAPQSLSELLSQPGVIETSQLRSRFGFLAIHGGGLEQVTDLIAERSAEAAGASVYLLRHPDNYPHHLPSARFDPAESARLAEFLDHVDVAVSLHGYDRIGRSTQLLAGGRNRALAAHLARHIQLPGYRVVTDLAAIPEELRGLHPDNPVNRVRDGGTQLELSIRVRGLGPRSTLPGVGGMSPVTATLVQGLVTAARSW