MTBC Gene Atlas

rhlE Resolved · high auto-curated

H37Rv Rv3211 · MTBC0 mtbc0_003417 · 527 aa · 3609939–3611522 (+) · RefSeq NP_217727.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)ATP-dependent RNA helicase RhlE
MTBC0 PGAP re-annotationDEAD/DEAH box helicase
Revised (this work)DEAD/DEAH box helicase. Pfam: DEAD (PF00270.36), 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 O05855 TrEMBL · unreviewed · Evidence at protein level
UniProt nameRNA helicase
EC (curated) EC 3.6.4.13

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category L Replication, recombination and repair
Preferred namerhlE
eggNOG descriptionBelongs to the DEAD box helicase family
Orthologous groupCOG0513
EC number EC 3.6.4.13
KEGG orthology K05592, K11927
KEGG pathways map03018

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 0.641 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 4 synonymous, 7 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)

PfamAccessioni-EvalueResiduesDescription
DEADPF00270.36 6.4e-4235–216 DEAD/DEAH box helicase
Helicase_CPF00271.38 7.1e-31257–365 Helicase conserved C-terminal domain

Functional interaction network (STRING v12, guilt-by-association)

PartnerProductScoreNo text-miningChannels (≥400)
Rv2783c gpsI bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase 985 957 coexpression:866 experimental:676 textmining:679
Rv3433c nnr bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase 934 927 experimental:781 database:659
Rv0702 rplD 50S ribosomal protein L4 944 916 coexpression:434 experimental:722 database:508
Rv3443c rplM 50S ribosomal protein L13 924 893 experimental:798
Rv0701 rplC 50S ribosomal protein L3 897 884 coexpression:455 experimental:796
Rv3212 hyp hypothetical protein 879 880 ctx neighborhood:869
Rv0009 ppiA iron-regulated peptidyl-prolyl cis-trans isomerase PpiA 880 873 experimental:473 database:626
Rv0684 fusA1 elongation factor G 908 867 experimental:597 database:626
Rv3458c rpsD 30S ribosomal protein S4 879 866 database:662
Rv0120c fusA2 elongation factor G 873 862 experimental:597 database:626
Rv2582 ppiB peptidyl-prolyl cis-trans isomerase B 861 853 experimental:473 database:626
Rv0715 rplX 50S ribosomal protein L24 845 826 experimental:814
Rv0721 rpsE 30S ribosomal protein S5 836 821 database:662
Rv1630 rpsA 30S ribosomal protein S1 837 818 experimental:411 database:662
Rv0714 rplN 50S ribosomal protein L14 854 813 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 RhlE
  • MTBC0 PGAP product: DEAD/DEAH box helicase
  • Pfam (hmmscan --cut_ga): DEAD PF00270.36 (E=6e-42), Helicase_C PF00271.38 (E=7e-31)
  • (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_217727.1)
  • Domains: Pfam-A via hmmscan --cut_ga — DEAD (PF00270.36), 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 COG0513
  • Curated reference: UniProt O05855 (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 — 187 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_003417|Rv3211|rhlE
MTAVKHTTESTFAKLGVRDEIVRALGEEGIKRPFAIQELTLPLALDGEDVIGQARTGMGKTFAFGVPLLQRITSGDGTRPLTGAPRALVVVPTRELCLQVTDDLATAGKYLTAGPDTDDAAAVRRRLSVVSIYGGRPYEPQIEALRAGADVVVGTPGRLLDLCQQGHLQLGGLSVLVLDEADEMLDLGFLPDIERILRQIPADRQSMLFSATMPDPIITLARTFMVRPTHIRAEAPHSSAVHDATEQFVYRAHALDKVELVSRVLQARDRGATMIFTRTKRTAQKVADELTERGFAVGAVHGDLGQLAREKALKAFRTGGIDVLVATDVAARGIDIDDVTHVINYQCPEDEKMYVHRIGRTGRAGRTGVAVTLVDWDELPRWSMIDQALGLGSPDPAETYSNSPHLYAELAIPATAGGTVGPARKSQGRRRDTDCDGQKTAQHARNTPRRRRTRGGKPVTGHPGTNPISSPIVGGDATSEPGSGTASDSGSDVVSGSRSGNGEAARRRRRRRRRPTHAQDGFAARAN