helY Resolved · high auto-curated
H37Rv Rv2092c · MTBC0 mtbc0_002226 ·
906 aa · 2377958–2380678 (-) ·
RefSeq NP_216608.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP-dependent DNA helicase HelY |
|---|---|
| MTBC0 PGAP re-annotation | RNA helicase |
| Revised (this work) | RNA helicase. Pfam: ResIII (PF04851.22), DEAD (PF00270.36), Helicase_C (PF00271.38), SH3_HelY (PF26090.1), DSHCT (PF08148.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMR1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable helicase HelY |
| EC (curated) |
EC 3.6.4.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | helY |
| eggNOG description | dead DEAH box helicase |
| Orthologous group | COG4581 |
| KEGG orthology |
K03727
|
| Gene Ontology (56) |
GO:0003674, GO:0003724, GO:0003824, GO:0004004, GO:0004386, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +44 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 | 0.297 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 9 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 |
|---|---|---|---|---|
ResIII | PF04851.22 | 1.0e-09 | 17–166 | Type III restriction enzyme, res subunit |
DEAD | PF00270.36 | 4.1e-26 | 21–171 | DEAD/DEAH box helicase |
Helicase_C | PF00271.38 | 4.4e-06 | 341–416 | Helicase conserved C-terminal domain |
SH3_HelY | PF26090.1 | 1.1e-29 | 543–634 | HelY-like, SH3 domain |
DSHCT | PF08148.18 | 7.0e-39 | 728–901 | DSHCT (NUC185) domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tatC (Sec-independent protein translocase transmembrane protein TatC), high confidence from genomic context alone (score 822 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2093c tatC |
Sec-independent protein translocase transmembrane protein TatC | 821 | 822 ctx | neighborhood:815 |
Rv2095c pafC |
proteasome accessory factor C | 735 | 735 ctx | neighborhood:722 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 734 | 734 | coexpression:734 |
Rv2096c pafB |
proteasome accessory factor B | 732 | 732 ctx | neighborhood:687 |
Rv2364c era |
GTPase Era | 716 | 716 | coexpression:716 |
Rv2091c |
membrane protein | 690 | 690 ctx | neighborhood:688 |
Rv2094c tatA |
Sec-independent protein translocase membrane-bound protein TatA | 674 | 675 ctx | neighborhood:673 |
Rv2097c pafA |
proteasome accessory factor PafA | 651 | 651 ctx | neighborhood:561 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 624 | 624 ctx | cooccurence:624 |
Rv1830 |
HTH-type transcriptional regulator | 623 | 624 ctx | cooccurence:622 |
Rv1440 secG |
protein-export membrane protein SecG | 619 | 619 ctx | cooccurence:619 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 601 | 601 ctx | cooccurence:601 |
Rv2901c hyp |
hypothetical protein | 589 | 589 ctx | cooccurence:583 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 578 | 578 ctx | cooccurence:569 |
Rv1473 |
macrolide ABC transporter ATP-binding protein | 522 | 522 ctx | cooccurence:521 |
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 HelY
- MTBC0 PGAP product: RNA helicase
- Pfam (hmmscan --cut_ga): ResIII PF04851.22 (E=1e-09), DEAD PF00270.36 (E=4e-26), Helicase_C PF00271.38 (E=4e-06), SH3_HelY PF26090.1 (E=1e-29), DSHCT PF08148.18 (E=7e-39)
- (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_216608.1)
- Domains: Pfam-A via hmmscan --cut_ga — ResIII (PF04851.22), DEAD (PF00270.36), Helicase_C (PF00271.38), SH3_HelY (PF26090.1), DSHCT (PF08148.18)
- 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
COG4581 - Curated reference: UniProt P9WMR1 (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 —
34 functional partner(s); context anchor
tatC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002226|Rv2092c|helY MTELAELDRFTAELPFSLDDFQQRACSALERGHGVLVCAPTGAGKTVVGEFAVHLALAAGSKCFYTTPLKALSNQKHTDLTARYGRDQIGLLTGDLSVNGNAPVVVMTTEVLRNMLYADSPALQGLSYVVMDEVHFLADRMRGPVWEEVILQLPDDVRVVSLSATVSNAEEFGGWIQTVRGDTTVVVDEHRPVPLWQHVLVGKRMFDLFDYRIGEAEGQPQVNRELLRHIAHRREADRMADWQPRRRGSGRPGFYRPPGRPEVIAKLDAEGLLPAITFVFSRAGCDAAVTQCLRSPLRLTSEEERARIAEVIDHRCGDLADSDLAVLGYYEWREGLLRGLAAHHAGMLPAFRHTVEELFTAGLVKAVFATETLALGINMPARTVVLERLVKFNGEQHMPLTPGEYTQLTGRAGRRGIDVEGHAVVIWHPEIEPSEVAGLASTRTFPLRSSFAPSYNMTINLVHRMGPQQAHRLLEQSFAQYQADRSVVGLVRGIERGNRILGEIAAELGGSDAPILEYARLRARVSELERAQARASRLQRRQAATDALAALRRGDIITITHGRRGGLAVVLESARDRDDPRPLVLTEHRWAGRISSADYSGTTPVGSMTLPKRVEHRQPRVRRDLASALRSAAAGLVIPAARRVSEAGGFHDPELESSREQLRRHPVHTSPGLEDQIRQAERYLRIERDNAQLERKVAAATNSLARTFDRFVGLLTEREFIDGPATDPVVTDDGRLLARIYSESDLLVAECLRTGAWEGLKPAELAGVVSAVVYETRGGDGQGAPFGADVPTPRLRQALTQTSRLSTTLRADEQAHRITPSREPDDGFVRVIYRWSRTGDLAAALAAADVNGSGSPLLAGDFVRWCRQVLDLLDQVRNAAPNPELRATAKRAIGDIRRGVVAVDAG