Rv1320c Family assigned · medium auto-curated
H37Rv Rv1320c · MTBC0 mtbc0_001416 ·
567 aa · 1493216–1494919 (-) ·
RefSeq NP_215836.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | adenylate cyclase |
|---|---|
| MTBC0 PGAP re-annotation | adenylate/guanylate cyclase domain-containing protein |
| Revised (this work) | Adenylate/guanylate cyclase domain-containing protein. 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.
Curated reference (UniProt)
| UniProt |
P9WQ29
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1320c |
UniProt still lists this protein as Uncharacterized protein Rv1320c; 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 | HAMP domain |
| Orthologous group | COG2114 |
| EC number |
EC 4.6.1.1
|
| KEGG orthology |
K01768
|
| KEGG pathways |
map00230, map02025, map04113, map04213
|
| KEGG modules |
M00695
|
| Gene Ontology (19) |
GO:0003674, GO:0003824, GO:0004016, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0009975, GO:0016020 +7 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) pseudogene candidate
| pN/pS | 0.925 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 13 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 2.51% of strains (3641) · 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 | 1.0e-09 | 275–326 | HAMP domain |
Guanylate_cyc | PF00211.26 | 3.3e-13 | 358–503 | Adenylate and Guanylate cyclase catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1319c (adenylate cyclase), high confidence from genomic context alone (score 764 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2445c ndkA |
nucleoside diphosphate kinase | 914 | 912 | database:900 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 908 | 905 | database:900 |
Rv1617 pykA |
pyruvate kinase | 907 | 902 | database:900 |
Rv0805 cpdA |
3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA | 924 | 900 | database:900 |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 810 | 811 | database:800 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 810 | 811 | database:800 |
Rv0869c moaA2 |
molybdenum cofactor biosynthesis protein MoaA | 806 | 807 | database:800 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 806 | 807 | database:800 |
Rv3609c folE |
GTP cyclohydrolase I | 801 | 801 | database:800 |
Rv1319c |
adenylate cyclase | 774 | 764 ctx | neighborhood:760 |
Rv2434c |
transmembrane protein | 700 | 681 ctx | neighborhood:496 |
Rv1647 |
adenylate cyclase | 690 | 679 ctx | cooccurence:675 |
Rv2212 |
adenylyl cyclase | 683 | 672 ctx | cooccurence:668 |
Rv1364c |
sigma factor regulatory protein | 654 | 602 ctx | neighborhood:544 |
Rv1321 nucS |
endonuclease NucS | 598 | 598 ctx | neighborhood:598 |
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: adenylate cyclase
- MTBC0 PGAP product: adenylate/guanylate cyclase domain-containing protein
- Pfam (hmmscan --cut_ga): HAMP PF00672.31 (E=1e-09), Guanylate_cyc PF00211.26 (E=3e-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_215836.1)
- 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 P9WQ29 (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 —
49 functional partner(s); context anchor
Rv1319c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001416|Rv1320c| MPSEKATTRHLPGAVETLSPRTGRRPETPAYGSWLLGRVSESPRMRRVRIQGMLTVAILVTNVIGLIVGAMLLTVAFPKPSVILDAPHWVSFGIVPGYCVLAFILGTYWLTRQTARALRWAIEERTPSHDEARSAFLVPLRVALAVLFLWGAAAALWTIIYGLANRLFIPRFLFSMGVIGVVAATSCYLLTEFALRPMAAQALEVGATPRSLVRGIVGRTMLVWLLCSGVPNVGVALTAIFDDTFWELSNDQFMITVLILWAPLLIFGFILMWILAWLTATPVRVVREALNRVEQGDLSGDLVVFDGTELGELQRGFNRMVEGLRERERVRDLFGRHVGREVAAAAERERPKLGGEERHVAVVFVDIVGSTQLVTSRPAAEVVMLLNRFFTVIVDEVNHHRGLVNKFQGDASLAVFGAPNRLSHPEDAALATARAIADRLASEMPECQAGIGVAAGQVVAGNVGAHERFEYTVIGEPVNEAARLCELAKSYPSRLLASSQTLRGASENECARWSLGETVTLRGHDQPIRLASPVQQLQMPAQSADIVGGALGDHQTHTIYRGAHPTD