Rv3114 Resolved · high auto-curated
H37Rv Rv3114 · MTBC0 mtbc0_003310 ·
176 aa · 3502124–3502654 (+) ·
RefSeq NP_217630.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | nucleoside deaminase |
| Revised (this work) | Nucleoside 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.
Curated reference (UniProt)
| UniProt |
O05791
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | CMP/dCMP-type deaminase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolismJ Translation, ribosomal structure and biogenesis
|
|---|---|
| eggNOG description | MafB19-like deaminase |
| Orthologous group | COG0590 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (213) · 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 |
|---|---|---|---|---|
dCMP_cyt_deam_1 | PF00383.30 | 4.8e-18 | 21–114 | Cytidine and deoxycytidylate deaminase zinc-binding region |
MafB19-deam | PF14437.13 | 2.9e-07 | 63–118 | MafB19-like deaminase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3113 (phosphatase), high confidence from genomic context alone (score 971 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3113 |
phosphatase | 971 | 971 ctx | neighborhood:770 coexpression:865 |
Rv3112 moaD1 |
molybdenum cofactor biosynthesis protein MoaD | 925 | 925 ctx | neighborhood:489 coexpression:860 |
Rv3110 moaB1 |
pterin-4-alpha-carbinolamine dehydratase | 920 | 920 ctx | neighborhood:453 coexpression:860 |
Rv3111 moaC1 |
cyclic pyranopterin monophosphate synthase accessory protein | 920 | 920 ctx | neighborhood:453 coexpression:860 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 913 | 913 | coexpression:868 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 797 | 797 | coexpression:797 |
Rv1358 |
transcriptional regulator | 765 | 765 | coexpression:765 |
Rv2492 hyp |
hypothetical protein | 754 | 739 | coexpression:730 |
Rv0193c hyp |
hypothetical protein | 734 | 734 | coexpression:734 |
Rv2122c hisE |
phosphoribosyl-ATP pyrophosphatase | 638 | 625 | coexpression:625 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 641 | 622 | database:610 |
Rv0120c fusA2 |
elongation factor G | 553 | 554 | database:550 |
Rv0684 fusA1 |
elongation factor G | 552 | 552 | database:550 |
Rv3115 |
transposase | 467 | 467 ctx | neighborhood:467 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 457 | 457 | coexpression:438 |
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: hypothetical protein
- MTBC0 PGAP product: nucleoside deaminase
- Pfam (hmmscan --cut_ga): dCMP_cyt_deam_1 PF00383.30 (E=5e-18), MafB19-deam PF14437.13 (E=3e-07)
- (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_217630.1)
- 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 O05791 (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 —
42 functional partner(s); context anchor
Rv3113 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003310|Rv3114| MVAARLPFGWPADSGVTADIIEAAMELAIDTARHATAPFGAALLDVTTLRAFSGGNTYFESGDRFAHAETNVLRAAMSTLPELSNHVLISTAEPCPMCAAASVLSGVRAIIFGTSIETLIQCGWFQIRISASDVVAASTRPTRPSVYSGFLSHKTDLLYRNSENRRAMNPWTDPSH