dnaG Resolved · high auto-curated
H37Rv Rv2343c · MTBC0 mtbc0_002495 ·
639 aa · 2645283–2647202 (-) ·
RefSeq NP_216859.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA primase |
|---|---|
| MTBC0 PGAP re-annotation | DNA primase |
| Revised (this work) | DNA primase. Pfam: Zn_ribbon_DnaG (PF01807.26), DNAG_N (PF08275.18), Toprim_4 (PF13662.13), Toprim (PF01751.29), Toprim_2 (PF13155.13), DnaB_bind (PF10410.15), DnaG_DnaB_bind (PF08278.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNW1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA primase |
| EC (curated) |
EC 2.7.7.101
|
| Curated function | RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | dnaG |
| eggNOG description | RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication |
| Orthologous group | COG0358 |
| KEGG orthology |
K02316
|
| KEGG pathways |
map03030
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.28 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 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 |
|---|---|---|---|---|
Zn_ribbon_DnaG | PF01807.26 | 2.0e-34 | 6–100 | CHC2 zinc finger |
DNAG_N | PF08275.18 | 2.1e-36 | 127–255 | DNA primase catalytic core, N-terminal domain |
Toprim_4 | PF13662.13 | 1.3e-12 | 263–333 | Toprim domain |
Toprim | PF01751.29 | 5.7e-08 | 264–332 | Toprim domain |
Toprim_2 | PF13155.13 | 7.9e-11 | 265–355 | Toprim-like |
DnaB_bind | PF10410.15 | 1.9e-19 | 376–429 | DnaB-helicase binding domain of primase |
DnaG_DnaB_bind | PF08278.17 | 2.3e-34 | 487–614 | DNA primase DnaG DnaB-binding |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dgt (deoxyguanosine triphosphate triphosphohydrolase), high confidence from genomic context alone (score 899 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0058 dnaB |
replicative DNA helicase | 995 | 983 | experimental:916 database:540 textmining:735 |
Rv2344c dgt |
deoxyguanosine triphosphate triphosphohydrolase | 938 | 899 ctx | neighborhood:881 textmining:411 |
Rv1713 engA |
GTPase Der | 873 | 866 | coexpression:863 |
Rv1340 rphA |
ribonuclease PH | 852 | 824 | experimental:821 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 833 | 811 ctx | cooccurence:426 coexpression:646 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 817 | 793 | coexpression:644 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 750 | 739 ctx | cooccurence:555 coexpression:405 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 864 | 694 ctx | cooccurence:610 textmining:576 |
Rv2345 |
transmembrane protein | 676 | 676 ctx | neighborhood:673 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 753 | 647 ctx | cooccurence:563 |
Rv3201c adnB |
ATP-dependent DNA helicase | 653 | 622 | |
Rv3644c |
DNA polymerase | 661 | 616 ctx | cooccurence:595 |
Rv1629 polA |
DNA polymerase I | 897 | 611 | textmining:748 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 680 | 603 ctx | cooccurence:590 |
Rv2906c trmD |
tRNA (guanine-N1)-methyltransferase | 596 | 570 ctx | cooccurence:497 |
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 primase
- MTBC0 PGAP product: DNA primase
- Pfam (hmmscan --cut_ga): Zn_ribbon_DnaG PF01807.26 (E=2e-34), DNAG_N PF08275.18 (E=2e-36), Toprim_4 PF13662.13 (E=1e-12), Toprim PF01751.29 (E=6e-08), Toprim_2 PF13155.13 (E=8e-11), DnaB_bind PF10410.15 (E=2e-19), DnaG_DnaB_bind PF08278.17 (E=2e-34)
- (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_216859.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zn_ribbon_DnaG (PF01807.26), DNAG_N (PF08275.18), Toprim_4 (PF13662.13), Toprim (PF01751.29), Toprim_2 (PF13155.13), DnaB_bind (PF10410.15), DnaG_DnaB_bind (PF08278.17)
- 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
COG0358 - Curated reference: UniProt P9WNW1 (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 —
126 functional partner(s); context anchor
dgt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002495|Rv2343c|dnaG MSGRISDRDIAAIREGARIEDVVGDYVQLRRAGADSLKGLCPFHNEKSPSFHVRPNHGHFHCFGCGEGGDVYAFIQKIEHVSFVEAVELLADRIGHTISYTGAATSVQRDRGSRSRLLAANAAAAAFYAQALQSDEAAPARQYLTERSFDAAAARKFGCGFAPSGWDSLTKHLQRKGFEFEELEAAGLSRQGRHGPMDRFHRRLLWPIRTSAGEVVGFGARRLFDDDAMEAKYVNTPETLLYKKSSVMFGIDLAKRDIAKGHQAVVVEGYTDVMAMHLAGVTTAVASCGTAFGGEHLAMLRRLMMDDSFFRGELIYVFDGDEAGRAAALKAFDGEQKLAGQSFVAVAPDGMDPCDLRLKCGDAALRDLVARRTPLFEFAIRAAIAEMDLDSAEGRVAALRRCVPMVGQIKDPTLRDEYARQLAGWVGWADVAQVIGRVRGEAKRTKHPRLGRLGSTTIARAAQRPTAGPPTELAVRPDPRDPTLWPQREALKSALQYPALAGPVFDALTVEGFTHPEYAAVRAAIDTAGGTSAGLSGAQWLDMVRQQTTSTVTSALISELGVEAIQVDDDKLPRYIAGVLARLQEVWLGRQIAEVKSKLQRMSPIEQGDEYHALFGDLVAMEAYRRSLLEQASGDDLTA