Rv2613c Resolved · high auto-curated
H37Rv Rv2613c · MTBC0 mtbc0_002781 ·
195 aa · 2964162–2964749 (-) ·
RefSeq NP_217129.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | AP-4-A phosphorylase |
|---|---|
| MTBC0 PGAP re-annotation | ATP adenylyltransferase |
| Revised (this work) | ATP adenylyltransferase. Pfam: DcpS_C (PF11969.14), HIT (PF01230.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMK9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | AP-4-A phosphorylase |
| EC (curated) |
EC 2.7.7.53
|
| Curated function | Catabolizes diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) into ADP and ATP. It does not catalyze the reverse phosphorolysis reaction. The optimum substrates are dinucleoside polyphosphates containing four or five phosphate residues. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolismG Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | COG0537 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases |
| Orthologous group | COG0537 |
| EC number |
EC 2.7.7.53
|
| KEGG orthology |
K19710
|
| KEGG pathways |
map00230
|
| Gene Ontology (64) |
GO:0003674, GO:0003824, GO:0003877, GO:0004551, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006725, GO:0006753, GO:0006793, GO:0006796 +52 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 | 0.339 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
DcpS_C | PF11969.14 | 1.6e-06 | 68–157 | Scavenger mRNA decapping enzyme C-term binding |
HIT | PF01230.30 | 5.1e-16 | 70–159 | HIT domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pgsA1 (CDP-diacylglycerol--inositol 3-phosphatidyltransferase), high confidence from genomic context alone (score 922 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 964 | 922 ctx | neighborhood:882 textmining:565 |
Rv2611c |
phosphatidylinositol mannoside acyltransferase | 964 | 906 ctx | neighborhood:882 textmining:638 |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 945 | 905 ctx | neighborhood:879 textmining:456 |
Rv1286 cysC |
adenylyl-sulfate kinase | 903 | 904 | database:900 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 902 | 903 | database:900 |
Rv2614c thrS |
threonine--tRNA ligase | 955 | 900 ctx | neighborhood:881 textmining:569 |
Rv2609c |
membrane protein | 934 | 831 ctx | neighborhood:798 textmining:631 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 711 | 711 | database:585 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 658 | 646 | database:592 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 611 | 612 | database:595 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 617 | 610 | database:538 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 611 | 604 | database:538 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 610 | 604 | database:586 |
Rv0861c ercc3 |
DNA helicase Ercc3 | 574 | 575 | database:543 |
Rv2605c tesB2 |
acyl-CoA thioesterase II | 572 | 572 ctx | neighborhood:544 |
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: AP-4-A phosphorylase
- MTBC0 PGAP product: ATP adenylyltransferase
- Pfam (hmmscan --cut_ga): DcpS_C PF11969.14 (E=2e-06), HIT PF01230.30 (E=5e-16)
- (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_217129.1)
- Domains: Pfam-A via hmmscan --cut_ga — DcpS_C (PF11969.14), HIT (PF01230.30)
- 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
COG0537 - Curated reference: UniProt P9WMK9 (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 —
38 functional partner(s); context anchor
pgsA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002781|Rv2613c| MSDEDRTDRATEDHTIFDRGVGQRDQLQRLWTPYRMNYLAEAPVKRDPNSSASPAQPFTEIPQLSDEEGLVVARGKLVYAVLNLYPYNPGHLMVVPYRRVSELEDLTDLESAELMAFTQKAIRVIKNVSRPHGFNVGLNLGTSAGGSLAEHLHVHVVPRWGGDANFITIIGGSKVIPQLLRDTRRLLATEWARQP