helZ Resolved · high auto-curated
H37Rv Rv2101 · MTBC0 mtbc0_002234 ·
1013 aa · 2388862–2391903 (+) ·
RefSeq NP_216617.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | helicase HelZ |
|---|---|
| MTBC0 PGAP re-annotation | DEAD/DEAH box helicase |
| Revised (this work) | DEAD/DEAH box helicase. Pfam: DUF3670 (PF12419.14), SNF2-rel_dom (PF00176.30), Helicase_C (PF00271.38). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YCF3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable helicase HelZ |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionL Replication, recombination and repair
|
|---|---|
| Preferred name | helZ |
| eggNOG description | SNF2 family N-terminal domain |
| Orthologous group | COG0553 |
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 | 0.433 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 15 synonymous, 17 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 0.60% of strains (867) · convergent |
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 |
|---|---|---|---|---|
DUF3670 | PF12419.14 | 1.3e-41 | 352–486 | SNF2 Helicase protein |
SNF2-rel_dom | PF00176.30 | 2.3e-67 | 536–819 | SNF2-related domain |
Helicase_C | PF00271.38 | 1.0e-20 | 840–950 | Helicase conserved C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2102 hyp |
hypothetical protein | 996 | 996 ctx | neighborhood:767 fusion:899 cooccurence:771 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 986 | 986 | experimental:910 database:843 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 986 | 985 | experimental:905 database:841 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 983 | 982 | experimental:912 database:806 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 952 | 951 | experimental:879 database:596 |
Rv2133c hyp |
hypothetical protein | 922 | 915 | experimental:832 database:485 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 920 | 912 | experimental:769 database:614 |
Rv2116 lppK |
lipoprotein LppK | 919 | 911 | experimental:769 database:614 |
Rv3170 aofH |
flavin-containing monoamine oxidase | 918 | 910 | experimental:442 database:844 |
Rv1329c dinG |
ATP-dependent helicase DinG | 942 | 869 | database:812 textmining:578 |
Rv1629 polA |
DNA polymerase I | 930 | 863 | experimental:538 database:660 textmining:513 |
Rv2737c recA |
recombinase A | 944 | 852 | experimental:841 textmining:638 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 844 | 824 | experimental:434 database:621 |
Rv2090 |
5'-3' exonuclease | 830 | 810 | experimental:447 database:660 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 894 | 804 | experimental:434 database:621 textmining:481 |
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: helicase HelZ
- MTBC0 PGAP product: DEAD/DEAH box helicase
- Pfam (hmmscan --cut_ga): DUF3670 PF12419.14 (E=1e-41), SNF2-rel_dom PF00176.30 (E=2e-67), Helicase_C PF00271.38 (E=1e-20)
- (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_216617.2)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3670 (PF12419.14), SNF2-rel_dom (PF00176.30), Helicase_C (PF00271.38)
- 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
COG0553 - Curated reference: UniProt I6YCF3 (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 — 111 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002234|Rv2101|helZ MLVLHGFWSNSGGMRLWAEDSDLLVKSPSQALRSARPHPFAAPADLIAGIHPGKPATAVLLLPSLRSAPLDSPELIRLAPRPAARTDPMLLAWTVPVVDLDPTAALAAFDQPAPDVRYGASVDYLAELAVFARELVERGRVLPQLRRDTHGAAACWRPVLQGRDVVAMTSLVSAMPPVCRAEVGGHDPHELATSALDAMVDAAVRAALSPMDLLPPRRGRSKRHRAVEAWLTALTCPDGRFDAEPDELDALAEALRPWDDVGIGTVGPARATFRLSEVETENEETPAGSLWRLEFLLQSTQDPSLLVPAEQAWNDDGSLRRWLDRPQELLLTELGRASRIFPELVPALRTACPSGLELDADGAYRFLSGTAAVLDEAGFGVLLPSWWDRRRKLGLVLSAYTPVDGVVGKASKFGREQLVEFRWELAVGDDPLSEEEIAALTETKSPLIRLRGQWVALDTEQLRRGLEFLERKPTGRKTTAEILALAASHPDDVDTPLEVTAVRADGWLGDLLAGAAAASLQPLDPPDGFTATLRPYQQRGLAWLAFLSSLGLGSCLADDMGLGKTVQLLALETLESVQRHQDRGVGPTLLLCPMSLVGNWQQEAARFAPNLRVYAHHGGARLHGEALRDHLERTDLVVSTYTTATRDIDELAEYEWNRVVLDEAQAVKNSLSRAAKAVRRLRAAHRVALTGTPMENRLAELWSIMDFLNPGLLGSSERFRTRYAIPIERHGHTEPAERLRASTRPYILRRLKTDPAIIDDLPEKIEIKQYCQLTTEQASLYQAVVADMMEKIENTEGIERRGNVLAAMAKLKQVCNHPAQLLHDRSPVGRRSGKVIRLEEILEEILAEGDRVLCFTQFTEFAELLVPHLAARFGRAARDIAYLHGGTPRKRRDEMVARFQSGDGPPIFLLSLKAGGTGLNLTAANHVVHLDRWWNPAVENQATDRAFRIGQRRTVQVRKFICTGTLEEKIDEMIEEKKALADLVVTDGEGWLTELSTRDLREVFALSEGAVGE