Rv0828c Resolved · high auto-curated
H37Rv Rv0828c · MTBC0 - ·
140 aa · 921191–921613 (-) ·
RefSeq NP_215343.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | deaminase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Deaminase. Pfam: dCMP_cyt_deam_1 (PF00383.30), MafB19-deam (PF14437.13). |
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 |
O53839
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible deaminase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolismJ Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | guaD |
| eggNOG description | MafB19-like deaminase |
| Orthologous group | COG0590 |
| EC number |
EC 3.5.4.3
|
| KEGG orthology |
K01487
|
| KEGG pathways |
map00230, map01100
|
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 | 0.315 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
dCMP_cyt_deam_1 | PF00383.30 | 7.7e-12 | 7–68 | Cytidine and deoxycytidylate deaminase zinc-binding region |
MafB19-deam | PF14437.13 | 3.3e-08 | 13–69 | MafB19-like deaminase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0830 (S-adenosylmethionine-dependent methyltransferase), high confidence from genomic context alone (score 700 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0830 |
S-adenosylmethionine-dependent methyltransferase | 700 | 700 ctx | neighborhood:699 |
Rv0827c kmtR |
HTH-type transcriptional regulator KmtR | 675 | 675 ctx | neighborhood:675 |
Rv2122c hisE |
phosphoribosyl-ATP pyrophosphatase | 640 | 627 | coexpression:627 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 642 | 622 | database:610 |
Rv0829 |
Rv0829, (MTV043.21), len: 96 aa. Possible transposase for IS1605' (fragment), similar to C-terminal end of many mycobacterial transposases a | 583 | 582 ctx | neighborhood:581 |
Rv0120c fusA2 |
elongation factor G | 551 | 551 | database:550 |
Rv0684 fusA1 |
elongation factor G | 550 | 551 | database:550 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 453 | 454 | coexpression:435 |
Rv3086 adhD |
alcohol dehydrogenase D | 428 | 428 | coexpression:410 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 427 | 427 | coexpression:409 |
Rv0761c adhB |
alcohol dehydrogenase B | 426 | 427 | coexpression:408 |
Rv2259 mscR |
S-nitrosomycothiol reductase MscR | 426 | 427 | coexpression:408 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 425 | 425 | coexpression:406 |
Rv3421c tsaB hyp |
hypothetical protein | 471 | 424 | coexpression:404 |
Rv2641 cadI |
cadmium inducible protein CadI | 432 | 418 | coexpression:418 |
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): deaminase
- Pfam (hmmscan --cut_ga): dCMP_cyt_deam_1 PF00383.30 (E=8e-12), MafB19-deam PF14437.13 (E=3e-08)
- (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_215343.1)
- Domains: Pfam-A via hmmscan --cut_ga — dCMP_cyt_deam_1 (PF00383.30), MafB19-deam (PF14437.13)
- 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
COG0590 - Curated reference: UniProt O53839 (TrEMBL, unreviewed; Predicted)
- 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 —
32 functional partner(s); context anchor
Rv0830 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0828c| MPAGMAGFRRWAQTNDPTAHAESLAIRAACTKLGTEHLVGTTLNVLAHPCPMCYGSLYYCSPDEVVFLTSRDAYEPHYVDDRRYFEPATFYDEFAKEWQDRRLPMRQEHRPDIRAGAVDVYRFRQEPNGGERSAIAAPTG