Rv1319c Resolved · high auto-curated
H37Rv Rv1319c · MTBC0 - ·
535 aa · 1480894–1482501 (-) ·
RefSeq NP_215835.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | adenylate cyclase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Adenylate cyclase. Pfam: HAMP (PF00672.31), Guanylate_cyc (PF00211.26). |
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 |
P9WQ31
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1319c |
UniProt still lists this protein as Uncharacterized protein Rv1319c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | Thought to play a role in regulation of cellular metabolism by catalysing the synthesis of a second messenger, camp catalytic activity ATP 3',5'-cyclic AMP pyrophosphate |
| Orthologous group | COG2114 |
| EC number |
EC 4.6.1.1
|
| KEGG orthology |
K01768
|
| KEGG pathways |
map00230, map02025, map04113, map04213
|
| KEGG modules |
M00695
|
| Gene Ontology (57) |
GO:0003674, GO:0003824, GO:0004016, GO:0005575, GO:0005576, GO:0006139, GO:0006163, GO:0006164, GO:0006171, GO:0006725, GO:0006753, GO:0006793 +45 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 | 0.416 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (292) · clonal |
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 |
|---|---|---|---|---|
HAMP | PF00672.31 | 7.8e-09 | 276–327 | HAMP domain |
Guanylate_cyc | PF00211.26 | 1.8e-13 | 361–524 | Adenylate and Guanylate cyclase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1320c (adenylate cyclase), high confidence from genomic context alone (score 764 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1617 pykA |
pyruvate kinase | 905 | 902 | database:900 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 905 | 902 | database:900 |
Rv0805 cpdA |
3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA | 922 | 900 | database:900 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 900 | 900 | database:900 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 806 | 807 | database:800 |
Rv0869c moaA2 |
molybdenum cofactor biosynthesis protein MoaA | 806 | 807 | database:800 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 802 | 803 | database:800 |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 802 | 803 | database:800 |
Rv3609c folE |
GTP cyclohydrolase I | 800 | 800 | database:800 |
Rv1320c |
adenylate cyclase | 774 | 764 ctx | neighborhood:760 |
Rv2212 |
adenylyl cyclase | 687 | 667 ctx | cooccurence:667 |
Rv1647 |
adenylate cyclase | 678 | 660 ctx | cooccurence:660 |
Rv1318c |
adenylate cyclase | 657 | 655 ctx | neighborhood:650 |
Rv1321 nucS |
endonuclease NucS | 565 | 565 ctx | neighborhood:565 |
Rv1636 TB15.3 |
iron-regulated universal stress protein | 544 | 541 ctx | cooccurence:541 |
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): adenylate cyclase
- Pfam (hmmscan --cut_ga): HAMP PF00672.31 (E=8e-09), Guanylate_cyc PF00211.26 (E=2e-13)
- (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_215835.1)
- Domains: Pfam-A via hmmscan --cut_ga — HAMP (PF00672.31), Guanylate_cyc (PF00211.26)
- 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
COG2114 - Curated reference: UniProt P9WQ31 (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 —
41 functional partner(s); context anchor
Rv1320c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1319c| MPAKKTMAQRLGQALETMTRQCGQLPETPAYGSWLLGRVSESPSRRWVRIKRIVTVYIMTANLTGIVVALLVVTFAFPVPSIYTDAPWWVTFGVAPAYATLALAIGTYWITTRIVRASIRWAIEERAPSQADGRNTLLLPFRVAAVHLILWDIGGALLATLYGLANRVFVTIILFSVTICGVLVATNCYLFTEFALRPVAAKALEAGRPPRRFAPGIMGRTMTVWSLGSGVPVTGIATTALYVLLVHNLTETQLASAVLILSITTLIFGFLVMWILAWLTAAPVRVVRAALKRVEQGDLRGDLVVFDGTELGELQRGFNAMVNGLRERERVRDLFGRHVGREVAAAAERERPQLGGEDRHAAVVFVDIVGSTQLVDNQPAAHVVKLLNRFFAIVVNEVDRHHGLINKFAGDAALAIFGAPNRLDRPEDAALAAARAIADRLANEMPEVQAGIGVAAGQIVAGNVGAKQRFEYTVVGKPVNQAARLCELAKSHPARLLASSDTLHAASETERAHWSLGETVTLRGHEQPTRLAVPT