Rv2407 Family assigned · medium auto-curated
H37Rv Rv2407 · MTBC0 mtbc0_002563 ·
280 aa · 2728944–2729786 (+) ·
RefSeq NP_216923.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease Z |
|---|---|
| MTBC0 PGAP re-annotation | Rv2407 family type 3 sulfatase |
| Revised (this work) | Rv2407 family type 3 sulfatase. Pfam: Anti-Pycsar_Apyc1 (PF23023.2), Lactamase_B (PF00753.34), Lactamase_B_2 (PF12706.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGZ5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Ribonuclease Z |
| EC (curated) |
EC 3.1.26.11
|
| Curated function | Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | rnz |
| eggNOG description | Zinc phosphodiesterase, which displays some tRNA 3'- processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA |
| Orthologous group | COG1234 |
| EC number |
EC 3.1.26.11
|
| KEGG orthology |
K00784
|
| KEGG pathways |
map03013
|
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 | 1.081 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Anti-Pycsar_Apyc1 | PF23023.2 | 4.6e-13 | 3–204 | Anti-Pycsar protein Apyc1 |
Lactamase_B | PF00753.34 | 1.1e-12 | 18–179 | Metallo-beta-lactamase superfamily |
Lactamase_B_2 | PF12706.14 | 2.3e-19 | 32–241 | Beta-lactamase superfamily domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3829c (dehydrogenase), medium confidence from genomic context alone (score 546 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2406c hyp |
hypothetical protein | 548 | 548 ctx | neighborhood:548 |
Rv3829c |
dehydrogenase | 548 | 546 ctx | cooccurence:541 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 465 | 465 | |
Rv0045c |
hydrolase | 429 | 429 ctx | cooccurence:428 |
Rv0712 hyp |
hypothetical protein | 891 | 200 | textmining:870 |
Rv3762c |
hydrolase | 888 | 166 | textmining:872 |
Rv1730c |
penicillin-binding protein | 673 | 80 | textmining:660 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 881 | 72 | textmining:878 |
Rv3849 espR |
ESX-1 transcriptional regulator EspR | 436 | 47 | textmining:433 |
Rv3205c hyp |
hypothetical protein | 870 | 41 | textmining:870 |
Rv0484c |
short-chain type oxidoreductase | 870 | 41 | textmining:870 |
Rv2511 orn |
oligoribonuclease | 410 | 41 | textmining:411 |
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: ribonuclease Z
- MTBC0 PGAP product: Rv2407 family type 3 sulfatase
- Pfam (hmmscan --cut_ga): Anti-Pycsar_Apyc1 PF23023.2 (E=5e-13), Lactamase_B PF00753.34 (E=1e-12), Lactamase_B_2 PF12706.14 (E=2e-19)
- (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_216923.1)
- Domains: Pfam-A via hmmscan --cut_ga — Anti-Pycsar_Apyc1 (PF23023.2), Lactamase_B (PF00753.34), Lactamase_B_2 (PF12706.14)
- 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
COG1234 - Curated reference: UniProt P9WGZ5 (SwissProt, reviewed; Inferred from homology)
- 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 —
12 functional partner(s); context anchor
Rv3829c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002563|Rv2407| MLEITLLGTGSPIPDPDRAGPSTLVRAGAQAFLVDCGRGVLQRAAAVGVGAAGLSAVLLTHLHSDHIAELGDVLITSWVTNFAADPAPLPIIGPPGTAEVVEATLKAFGHDIGYRIAHHADLTTPPPIEVHEYTAGPAWDRDGVTIRVAPTDHRPVTPTIGFRIESDGASVVLAGDTVPCDSLDQLAAGADALVHTVIRKDIVTQIPQQRVKDICDYHSSVQEAAATANRAGVGTLVMTHYVPAIGPGQEEQWRALAATEFSGRIEVGNDLHRVEVHPRR