dnaQ Family assigned · medium auto-curated
H37Rv Rv3711c · MTBC0 mtbc0_003934 ·
329 aa · 4179802–4180791 (-) ·
RefSeq NP_218228.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA polymerase III subunit epsilon |
|---|---|
| MTBC0 PGAP re-annotation | DEDDh family exonuclease |
| Revised (this work) | DEDDh family exonuclease. Pfam: RNase_T (PF00929.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69678
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable DNA polymerase III |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | dnaQ |
| eggNOG description | DNA polymerase III |
| Orthologous group | COG0847 |
| EC number |
EC 2.7.7.7
|
| KEGG orthology |
K02342
|
| KEGG pathways |
map00230, map00240, map01100, map03030, map03430, map03440
|
| KEGG modules |
M00260
|
| Gene Ontology (54) |
GO:0003674, GO:0003824, GO:0004518, GO:0004527, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006259, GO:0006260 +42 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 | 3.58 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.22% of strains (321) · 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 |
|---|---|---|---|---|
RNase_T | PF00929.32 | 7.8e-21 | 18–170 | Exonuclease |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobQ2 (cobyric acid synthase CobQ), high confidence from genomic context alone (score 742 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 956 | 952 | experimental:510 database:900 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 979 | 950 | experimental:481 database:900 textmining:600 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 971 | 947 | experimental:474 database:900 textmining:494 |
Rv3644c |
DNA polymerase | 951 | 947 | experimental:474 database:900 |
Rv2413c hyp |
hypothetical protein | 948 | 942 | experimental:442 database:900 |
Rv2191 hyp |
hypothetical protein | 932 | 902 | database:900 |
Rv3713 cobQ2 |
cobyric acid synthase CobQ | 885 | 742 ctx | neighborhood:739 textmining:574 |
Rv3712 |
ligase | 903 | 741 ctx | neighborhood:739 textmining:641 |
Rv0722 rpmD |
50S ribosomal protein L30 | 728 | 718 | database:583 |
Rv0651 rplJ |
50S ribosomal protein L10 | 681 | 682 | database:588 |
Rv0704 rplB |
50S ribosomal protein L2 | 708 | 646 | database:578 |
Rv0701 rplC |
50S ribosomal protein L3 | 702 | 644 | database:579 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 665 | 644 | database:540 |
Rv3443c rplM |
50S ribosomal protein L13 | 655 | 643 | database:580 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 662 | 641 | database:540 |
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: DNA polymerase III subunit epsilon
- MTBC0 PGAP product: DEDDh family exonuclease
- Pfam (hmmscan --cut_ga): RNase_T PF00929.32 (E=8e-21)
- (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_218228.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNase_T (PF00929.32)
- 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
COG0847 - Curated reference: UniProt O69678 (TrEMBL, unreviewed; 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 —
63 functional partner(s); context anchor
cobQ2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003934|Rv3711c|dnaQ MSHTWGRPASHQDRGWAVIDVETSGFRPGQARIISLAVLGLDAAGRLEQSVVSLLNPKVDPGPTHVHGLTAAMLDDQPQFADIAGEVVDVLRGRTLVAHNVAFDYAFLAAEAEIAEAELPVDFVMCTVELARRLQLGVDNLRLETLAAHWGVPQQRPHDAFDDARVLTGILAAALESARELDVWLPVHPVTRRRWPNGRVTHDELRPLKALAARMACPYLNPGRYVQGRPLVQGMRVGLAAEVKRTHEELVERILHAGLAYSDVVDRDTSLVVCNATAPEHGKGYHALQLGVPVMPEARFMECIGAVVGGASVEDFTDVAPVEKQLALF