dnaZX Family assigned · medium auto-curated
H37Rv Rv3721c · MTBC0 mtbc0_003944 ·
578 aa · 4189116–4190852 (-) ·
RefSeq NP_218238.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA polymerase III subunit gamma/tau |
|---|---|
| MTBC0 PGAP re-annotation | DNA polymerase III subunits gamma/tau |
| Revised (this work) | DNA polymerase III subunits gamma/tau. Pfam: DNA_pol3_delta2 (PF13177.13), AAA (PF00004.36), AAA_22 (PF13401.13), DNAX_ATPase_lid (PF22608.3), DNA_pol3_gamma3 (PF12169.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNT9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA polymerase III subunit gamma/tau |
| EC (curated) |
EC 2.7.7.7
|
| Curated function | DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | dnaX |
| eggNOG description | DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity |
| Orthologous group | COG2812 |
| EC number |
EC 2.7.7.7
|
| KEGG orthology |
K02343
|
| KEGG pathways |
map00230, map00240, map01100, map03030, map03430, map03440
|
| KEGG modules |
M00260
|
| Gene Ontology (24) |
GO:0006139, GO:0006259, GO:0006260, GO:0006261, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009058, GO:0009059, GO:0009987, GO:0034641 +12 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 | 0.304 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 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 |
|---|---|---|---|---|
DNA_pol3_delta2 | PF13177.13 | 7.4e-38 | 18–175 | DNA polymerase III, delta subunit |
AAA | PF00004.36 | 1.2e-09 | 39–169 | ATPase family associated with various cellular activities (AAA) |
AAA_22 | PF13401.13 | 2.7e-06 | 39–154 | AAA domain |
DNAX_ATPase_lid | PF22608.3 | 3.8e-06 | 185–225 | DNA polymerase III clamp loader subunit, ATPase lid domain |
DNA_pol3_gamma3 | PF12169.14 | 1.7e-13 | 235–362 | DNA polymerase III subunits gamma and tau domain III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: adnA (ATP-dependent DNA helicase), medium confidence from genomic context alone (score 645 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2413c hyp |
hypothetical protein | 987 | 986 | experimental:829 database:900 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 983 | 982 | experimental:773 database:900 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 997 | 980 | experimental:773 database:900 textmining:881 |
Rv2191 hyp |
hypothetical protein | 963 | 949 | experimental:474 database:900 |
Rv3711c dnaQ |
DNA polymerase III subunit epsilon | 971 | 947 | experimental:474 database:900 textmining:494 |
Rv3644c |
DNA polymerase | 924 | 925 | database:900 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 804 | 786 | experimental:773 |
Rv2116 lppK |
lipoprotein LppK | 799 | 781 | experimental:773 |
Rv2478c hyp |
hypothetical protein | 809 | 780 | experimental:773 |
Rv0054 ssb |
single-strand DNA-binding protein | 809 | 780 | experimental:773 |
Rv3722c hyp |
hypothetical protein | 780 | 780 ctx | neighborhood:779 |
Rv3202c adnA |
ATP-dependent DNA helicase | 675 | 645 ctx | cooccurence:620 |
Rv3715c recR |
recombination protein RecR | 652 | 605 | coexpression:435 |
Rv0058 dnaB |
replicative DNA helicase | 693 | 573 | experimental:455 |
Rv3716c hyp |
hypothetical protein | 575 | 535 | coexpression:422 |
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 gamma/tau
- MTBC0 PGAP product: DNA polymerase III subunits gamma/tau
- Pfam (hmmscan --cut_ga): DNA_pol3_delta2 PF13177.13 (E=7e-38), AAA PF00004.36 (E=1e-09), AAA_22 PF13401.13 (E=3e-06), DNAX_ATPase_lid PF22608.3 (E=4e-06), DNA_pol3_gamma3 PF12169.14 (E=2e-13)
- (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_218238.1)
- Domains: Pfam-A via hmmscan --cut_ga — DNA_pol3_delta2 (PF13177.13), AAA (PF00004.36), AAA_22 (PF13401.13), DNAX_ATPase_lid (PF22608.3), DNA_pol3_gamma3 (PF12169.14)
- 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
COG2812 - Curated reference: UniProt P9WNT9 (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 —
39 functional partner(s); context anchor
adnA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003944|Rv3721c|dnaZX MALYRKYRPASFAEVVGQEHVTAPLSVALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTANPCGVCESCVSLAPNAPGSIDVVELDAASHGGVDDTRELRDRAFYAPVQSRYRVFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALLARICEQEGVVVDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAADTHVTYTRALGLLGVTDVALIDDAVDALAACDAAALFGAIESVIDGGHDPRRFATDLLERFRDLIVLQSVPDAASRGVVDAPEDALDRMREQAARIGRATLTRYAEVVQAGLGEMRGATAPRLLLEVVCARLLLPSASDAESALLQRVERIETRLDMSIPAPQAVPRPSAAAAEPKHQPAREPRPVLAPTPASSEPTVAAVRSMWPTVRDKVRLRSRTTEVMLAGATVRALEDNTLVLTHESAPLARRLSEQRNADVLAEALKDALGVNWRVRCETGEPAAAASPVGGGANVATAKAVNPAPTANSTQRDEEEHMLAEAGRGDPSPRRDPEEVALELLQNELGARRIDNA