adnB Resolved · high auto-curated
H37Rv Rv3201c · MTBC0 mtbc0_003405 ·
1101 aa · 3595873–3599178 (-) ·
RefSeq NP_217717.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP-dependent DNA helicase |
|---|---|
| MTBC0 PGAP re-annotation | ATP-dependent DNA helicase AdnB |
| Revised (this work) | ATP-dependent DNA helicase AdnB. Pfam: UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), UvrD_C (PF13361.13), PDDEXK_1 (PF12705.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53347
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | DNA 3'-5' helicase |
| EC (curated) |
EC 5.6.2.4
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | uvrD2 |
| eggNOG description | Belongs to the helicase family. UvrD subfamily |
| Orthologous group | COG0210 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K03657
|
| KEGG pathways |
map03420, map03430
|
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 | 0.375 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 11 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 |
|---|---|---|---|---|
UvrD-helicase | PF00580.28 | 2.3e-45 | 26–337 | UvrD/REP helicase N-terminal domain |
AAA_19 | PF13245.13 | 9.0e-12 | 29–320 | AAA domain |
UvrD_C | PF13361.13 | 1.1e-16 | 654–770 | UvrD-like helicase C-terminal domain |
PDDEXK_1 | PF12705.14 | 8.1e-16 | 903–1071 | PD-(D/E)XK nuclease superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: adnA (ATP-dependent DNA helicase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3202c adnA |
ATP-dependent DNA helicase | 999 | 1000 ctx | neighborhood:881 experimental:997 database:540 |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 959 | 959 | database:900 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 951 | 952 | database:900 |
Rv3200c |
transmembrane cation transporter | 812 | 804 ctx | neighborhood:801 |
Rv3199c nudC |
NADH pyrophosphatase | 746 | 747 ctx | neighborhood:747 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 739 | 739 ctx | neighborhood:544 |
Rv2737c recA |
recombinase A | 805 | 731 | experimental:632 |
Rv1157c hyp |
hypothetical protein | 885 | 703 ctx | cooccurence:698 textmining:631 |
Rv1629 polA |
DNA polymerase I | 801 | 695 ctx | neighborhood:544 |
Rv0058 dnaB |
replicative DNA helicase | 753 | 670 | coexpression:406 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 694 | 636 | experimental:456 |
Rv1402 priA |
primosomal protein N' | 647 | 631 ctx | cooccurence:590 |
Rv2343c dnaG |
DNA primase | 653 | 622 | |
Rv1633 uvrB |
excinuclease ABC subunit UvrB | 625 | 590 | experimental:564 |
Rv3365c hyp |
hypothetical protein | 568 | 569 ctx | cooccurence:555 |
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: ATP-dependent DNA helicase
- MTBC0 PGAP product: ATP-dependent DNA helicase AdnB
- Pfam (hmmscan --cut_ga): UvrD-helicase PF00580.28 (E=2e-45), AAA_19 PF13245.13 (E=9e-12), UvrD_C PF13361.13 (E=1e-16), PDDEXK_1 PF12705.14 (E=8e-16)
- (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_217717.1)
- Domains: Pfam-A via hmmscan --cut_ga — UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), UvrD_C (PF13361.13), PDDEXK_1 (PF12705.14)
- 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
COG0210 - Curated reference: UniProt O53347 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
86 functional partner(s); context anchor
adnA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003405|Rv3201c|adnB MTQTAAPARYSPAELACALGLFPPTAEQAAVIAAPPGPLVVIAGAGAGKTETMAARVVWLVANGYAEPGQVLGLTFTRKAAGQLLRRVRSRLARLAGIGLGCGDPAACAPVVSTYHAFAGSLLRDYGLLLPLEPDTRLLSETELWQLAFDVVSGYDGVLCTDKSPAAVTSIVVRLWGQLGEHLVDTRALRDTHVELERLVHALPAGRYQRDRGPSQWLLRMLATQTQRAELVPLLDALGERMHAGKVMDFAMQMASAARLAATSPQVGQDLRRRYRVVLLDEYQDTGHAQRVVLSSLFGGGVDDGLALTAVGDPIQSIYGWRGASATNLPRFTTDFPLSDGTPAPVLELLTSWRNPPQALRVANGISAEARRRSVAVRALRPRPDAPPGAVRCALLPDVQAEREWIADHLRMRYQRAEADGVKPPTAAVLVRRNADAAAIADTLRARGIPAEVVGLAGLLSIPEVAEVVAMLRLVADPTAGAAAMRVLTGPRWRLGARDLAALWRRALTLSGESPSTASPESIAMAASADADNPCLADAISDPGSAEGYSVAGYGRIGALAGELSALRGRLGHSLPDLVAEVRRVLGVDCEVRASAPVSGGWAGPEHLDAFADVVAGYAERASARSSEASVAGLLAYLDVAEVVENGLPPAELTVACDRVQVLTVHAAKGLEWQVVAVAHLSRGVFPSTVSRSSWLTDPAELPPLLRGDRASAGAHGIPVLDTSAVADRKQLSDKISEHRRLLDRRRVDEERRLLYVAVTRAEDTLLVSGHHWGPTGTKPRGPSEFLCELKDIIDRSAAAGDPCGVVEQWASAPAGDERNPLCDNAIEAVWPADPLAARRGDVERGAALVAAAMSADLPGSTTDIDHPPRPGDAPWSTDVDALLAERAHAARGAPARGLPNHLSVSSLVELVGDPVGARQRLMCRLPKRPDPHAWLGDAFHAWVQQFYGAELLFDLGDLPGAADREVGDPEELAALQRAFTASSWAARTPAAVEVPFEMPIGDTVVRGRIDAVFVDPDGGATVVDWKTGKPPHGPAAMRQAAVQLAVYRLAWAALRGCPTSSVRTAFYYVRSGITVVPDELPAPGELAMLLTDCAGRRSDT