dnaA Resolved · high auto-curated
H37Rv Rv0001 · MTBC0 mtbc0_000001 ·
507 aa · 1–1524 (+) ·
RefSeq NP_214515.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | chromosomal replication initiator protein DnaA |
|---|---|
| MTBC0 PGAP re-annotation | chromosomal replication initiator protein DnaA |
| Revised (this work) | Chromosomal replication initiator protein DnaA. Pfam: Bac_DnaA (PF00308.25), IstB_IS21 (PF01695.24), AAA (PF00004.36), Bac_DnaA_C (PF08299.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNW3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Chromosomal replication initiator protein DnaA |
| EC (curated) |
EC 3.6.4.-
|
| Curated function | Plays an essential role in the initiation and regulation of chromosomal replication. ATP-DnaA binds to the origin of replication (oriC) to initiate formation of the DNA replication initiation complex once per cell cycle. Binds the DnaA box (a 9 base pair repeat at the origin) and separates the double-stranded (ds)DNA. Forms a right-handed helical filament on oriC DNA; dsDNA binds to the exterior of the filament while single-stranded (ss)DNA is stabiized in the filament's interior. The ATP-DnaA-oriC complex binds and stabilizes one strand of the AT-rich DNA unwinding element (DUE), permitting l. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | dnaA |
| eggNOG description | it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box) 5'-TTATC CA A CA A-3'. DnaA binds to ATP and to acidic phospholipids |
| Orthologous group | COG0593 |
| KEGG orthology |
K02313
|
| KEGG pathways |
map02020, map04112
|
| Gene Ontology (114) |
GO:0000166, GO:0003674, GO:0003676, GO:0003677, GO:0003688, GO:0003690, GO:0003824, GO:0005488, GO:0005524, GO:0005575, GO:0005618, GO:0005622 +102 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 | 0.634 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 14 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 |
|---|---|---|---|---|
Bac_DnaA | PF00308.25 | 9.8e-78 | 168–329 | Bacterial DnaA ATPAse domain |
IstB_IS21 | PF01695.24 | 6.2e-07 | 204–307 | IstB-like ATP binding protein |
AAA | PF00004.36 | 1.1e-04 | 205–323 | ATPase family associated with various cellular activities (AAA) |
Bac_DnaA_C | PF08299.18 | 4.6e-27 | 415–480 | Bacterial dnaA protein helix-turn-helix |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaN (DNA polymerase III subunit beta), high confidence from genomic context alone (score 966 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0002 dnaN |
DNA polymerase III subunit beta | 998 | 966 ctx | cooccurence:520 coexpression:711 experimental:737 textmining:965 |
Rv2116 lppK |
lipoprotein LppK | 932 | 924 | coexpression:707 experimental:737 |
Rv0058 dnaB |
replicative DNA helicase | 959 | 796 | experimental:785 textmining:812 |
Rv0003 recF |
DNA replication/repair protein RecF | 958 | 712 | coexpression:520 textmining:862 |
Rv3918c parA |
chromosome partitioning protein ParA | 725 | 606 | |
Rv3213c |
SOJ/ParA-like protein | 693 | 571 | |
Rv1708 |
initiation inhibitor protein | 774 | 555 | textmining:515 |
Rv3923c rnpA |
ribonuclease P protein component | 834 | 552 | coexpression:477 textmining:645 |
Rv3921c yidC |
membrane protein insertase YidC | 770 | 539 | textmining:522 |
Rv0113 gmhA |
phosphoheptose isomerase | 554 | 495 | experimental:469 |
Rv3116 moeB2 |
molybdenum cofactor biosynthesis protein MoeB | 479 | 480 | coexpression:415 |
Rv3206c moeB1 |
adenylyltransferase/sulfurtransferase MoeZ | 475 | 476 | coexpression:410 |
Rv1298 rpmE |
50S ribosomal protein L31 | 446 | 447 | coexpression:428 |
Rv2986c hupB |
DNA-binding protein HU | 636 | 429 | experimental:417 |
Rv1674c |
transcriptional regulator | 460 | 429 | coexpression:410 |
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: chromosomal replication initiator protein DnaA
- MTBC0 PGAP product: chromosomal replication initiator protein DnaA
- Pfam (hmmscan --cut_ga): Bac_DnaA PF00308.25 (E=1e-77), IstB_IS21 PF01695.24 (E=6e-07), AAA PF00004.36 (E=1e-04), Bac_DnaA_C PF08299.18 (E=5e-27)
- (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_214515.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_DnaA (PF00308.25), IstB_IS21 (PF01695.24), AAA (PF00004.36), Bac_DnaA_C (PF08299.18)
- 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
COG0593 - Curated reference: UniProt P9WNW3 (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 —
97 functional partner(s); context anchor
dnaN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000001|Rv0001|dnaA MTDDPGSGFTTVWNAVVSELNGDPKVDDGPSSDANLSAPLTPQQRAWLNLVQPLTIVEGFALLSVPSSFVQNEIERHLRAPITDALSRRLGHQIQLGVRIAPPATDEADDTTVPPSENPATTSPDTTTDNDEIDDSAAARGDNQHSWPSYFTERPHNTDSATAGVTSLNRRYTFDTFVIGASNRFAHAAALAIAEAPARAYNPLFIWGESGLGKTHLLHAAGNYAQRLFPGMRVKYVSTEEFTNDFINSLRDDRKVAFKRSYRDVDVLLVDDIQFIEGKEGIQEEFFHTFNTLHNANKQIVISSDRPPKQLATLEDRLRTRFEWGLITDVQPPELETRIAILRKKAQMERLAVPDDVLELIASSIERNIRELEGALIRVTAFASLNKTPIDKALAEIVLRDLIADANTMQISAATIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAERREVFDHVKELTTRIRQRSKR