add Resolved · high auto-curated
H37Rv Rv3313c · MTBC0 mtbc0_003523 ·
365 aa · 3723225–3724322 (-) ·
RefSeq NP_217830.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | adenosine deaminase |
|---|---|
| MTBC0 PGAP re-annotation | adenosine deaminase |
| Revised (this work) | Adenosine deaminase. Pfam: A_deaminase (PF00962.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P63907
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Adenosine deaminase |
| EC (curated) |
EC 3.5.4.4
|
| Curated function | Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | add |
| eggNOG description | adenosine deaminase |
| Orthologous group | COG1816 |
| EC number |
EC 3.5.4.4
|
| KEGG orthology |
K01488
|
| KEGG pathways |
map00230, map01100, map05340
|
| Gene Ontology (91) |
GO:0003674, GO:0003824, GO:0004000, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006144, GO:0006152, GO:0006154 +79 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 | 0.168 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
A_deaminase | PF00962.29 | 1.9e-131 | 14–354 | Adenosine deaminase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deoA (thymidine phosphorylase), high confidence from genomic context alone (score 920 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3307 deoD |
purine nucleoside phosphorylase | 953 | 938 | database:922 |
Rv3314c deoA |
thymidine phosphorylase | 989 | 920 ctx | neighborhood:882 textmining:870 |
Rv3315c cdd |
cytidine deaminase | 976 | 915 ctx | neighborhood:881 textmining:731 |
Rv2202c adoK |
adenosine kinase | 991 | 914 | database:900 textmining:901 |
Rv3393 iunH |
nucleoside hydrolase | 918 | 910 | database:900 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 779 | 779 ctx | neighborhood:746 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 749 | 749 ctx | neighborhood:746 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 691 | 691 ctx | neighborhood:677 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 688 | 688 ctx | neighborhood:677 |
Rv3312A mtp |
pilin | 628 | 629 ctx | neighborhood:624 |
Rv2584c apt |
adenine phosphoribosyltransferase | 767 | 539 | experimental:405 textmining:517 |
Rv3000 |
transmembrane protein | 521 | 522 ctx | neighborhood:520 |
Rv3396c guaA |
GMP synthase | 732 | 468 | textmining:518 |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 463 | 463 | coexpression:462 |
Rv1021 mazG |
nucleoside triphosphate pyrophosphohydrolase | 430 | 430 |
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: adenosine deaminase
- MTBC0 PGAP product: adenosine deaminase
- Pfam (hmmscan --cut_ga): A_deaminase PF00962.29 (E=2e-131)
- (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_217830.1)
- Domains: Pfam-A via hmmscan --cut_ga — A_deaminase (PF00962.29)
- 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
COG1816 - Curated reference: UniProt P63907 (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 —
37 functional partner(s); context anchor
deoA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003523|Rv3313c|add MTAAPTLQTIRLAPKALLHDHLDGGLRPATVLDIAGQVGYDDLPATDVDALASWFRTQSHSGSLERYLEPFSHTVAVMQTPEALYRVAFECAQDLAADSVVYAEVRFAPELHISCGLSFDDVVDTVLTGFAAGEKACAADGQPITVRCLVTAMRHAAMSREIAELAIRFRDKGVVGFDIAGAEAGHPPTRHLDAFEYMRDHNARFTIHAGEAFGLPSIHEAIAFCGADRLGHGVRIVDDIDVDADGGFQLGRLAAILRDKRIPLELCPSSNVQTGAVASIAEHPFDLLARARFRVTVNTDNRLMSDTSMSLEMHRLVEAFGYGWSDLARFTVNAMKSAFIPFDQRLAIIDEVIKPRFAALMGHSE