deaD Resolved · high auto-curated
H37Rv Rv1253 · MTBC0 mtbc0_001342 ·
563 aa · 1408414–1410105 (+) ·
RefSeq NP_215769.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP-dependent RNA helicase DeaD |
|---|---|
| MTBC0 PGAP re-annotation | DEAD/DEAH box helicase |
| Revised (this work) | DEAD/DEAH box helicase. Pfam: DEAD (PF00270.36), Helicase_C (PF00271.38), DeaD_dimer (PF25399.2), DbpA (PF03880.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH05
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP-dependent RNA helicase DeaD |
| EC (curated) |
EC 3.6.4.13
|
| Curated function | DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesisK TranscriptionL Replication, recombination and repair
|
|---|---|
| Preferred name | deaD |
| eggNOG description | DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation |
| Orthologous group | COG0513 |
| EC number |
EC 3.6.4.13
|
| KEGG orthology |
K05592, K11927
|
| KEGG pathways |
map03018
|
| Gene Ontology (43) |
GO:0003674, GO:0003724, GO:0003824, GO:0004004, GO:0004386, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139 +31 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 | 1.181 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 10 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 |
|---|---|---|---|---|
DEAD | PF00270.36 | 1.1e-47 | 37–202 | DEAD/DEAH box helicase |
Helicase_C | PF00271.38 | 1.5e-30 | 237–345 | Helicase conserved C-terminal domain |
DeaD_dimer | PF25399.2 | 1.7e-22 | 379–444 | RNA helicase DeaD dimerization domain |
DbpA | PF03880.22 | 9.6e-21 | 471–540 | DbpA RNA binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1254 (acyltransferase), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 933 | 926 | experimental:781 database:659 |
Rv0702 rplD |
50S ribosomal protein L4 | 920 | 912 | coexpression:404 experimental:722 database:508 |
Rv3443c rplM |
50S ribosomal protein L13 | 897 | 889 | experimental:798 |
Rv1254 |
acyltransferase | 884 | 884 ctx | neighborhood:881 |
Rv0701 rplC |
50S ribosomal protein L3 | 891 | 877 | coexpression:423 experimental:796 |
Rv0120c fusA2 |
elongation factor G | 872 | 861 | experimental:597 database:626 |
Rv0684 fusA1 |
elongation factor G | 872 | 861 | experimental:597 database:626 |
Rv3458c rpsD |
30S ribosomal protein S4 | 874 | 859 | database:662 |
Rv0009 ppiA |
iron-regulated peptidyl-prolyl cis-trans isomerase PpiA | 861 | 853 | experimental:473 database:626 |
Rv2582 ppiB |
peptidyl-prolyl cis-trans isomerase B | 856 | 848 | experimental:473 database:626 |
Rv2101 helZ |
helicase HelZ | 844 | 824 | experimental:434 database:621 |
Rv0715 rplX |
50S ribosomal protein L24 | 843 | 824 | experimental:814 |
Rv0721 rpsE |
30S ribosomal protein S5 | 829 | 812 | database:662 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 881 | 810 | coexpression:405 experimental:676 textmining:403 |
Rv0714 rplN |
50S ribosomal protein L14 | 810 | 810 | experimental:783 |
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 RNA helicase DeaD
- MTBC0 PGAP product: DEAD/DEAH box helicase
- Pfam (hmmscan --cut_ga): DEAD PF00270.36 (E=1e-47), Helicase_C PF00271.38 (E=1e-30), DeaD_dimer PF25399.2 (E=2e-22), DbpA PF03880.22 (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_215769.1)
- Domains: Pfam-A via hmmscan --cut_ga — DEAD (PF00270.36), Helicase_C (PF00271.38), DeaD_dimer (PF25399.2), DbpA (PF03880.22)
- 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
COG0513 - Curated reference: UniProt P9WH05 (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 —
166 functional partner(s); context anchor
Rv1254 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001342|Rv1253|deaD MAFPEYSPAASAATFADLQIHPRVLRAIGDVGYESPTAIQAATIPALMAGSDVVGLAQTGTGKTAAFAIPMLSKIDITSKVPQALVLVPTRELALQVAEAFGRYGAYLSQLNVLPIYGGSSYAVQLAGLRRGAQVVVGTPGRVIDHLERATLDLSRVDFLVLDEADEMLTMGFADDVERILSETPEYKQVALFSATMPPAIRKLSAKYLHDPFEVTCKAKTAVAENISQSYIQVARKMDALTRVLEVEPFEAMIVFVRTKQATEEIAEKLRARGFSAAAISGDVPQAQRERTITALRDGDIDILVATDVAARGLDVERISHVLNYDIPHDTESYVHRIGRTGRAGRSGAALIFVSPRELHLLKAIEKATRQTLTEAQLPTVEDVNTQRVAKFADSITNALGGPGIELFRRLVEEYEREHDVPMADIAAALAVQCRGGEAFLMAPDPPLSRRNRDQRRDRPQRPKRRPDLTTYRVAVGKRHKIGPGAIVGAIANEGGLHRSDFGQIRIGPDFSLVELPAKLPRATLKKLAQTRISGVLIDLRPYRPPDAARRHNGGKPRRKHVG