Rv0084 Formate hydrogenlyase subunit 4

Summary

Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0084 hycD Formate hydrogenlyase subunit 4 CDS 92328 93278 + 951 316 FALSE

Rv0084 (Formate hydrogenlyase subunit 4) is predicted to be co-regulated in modules bicluster_0143 with residual 0.53 and bicluster_0235 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 130.00 for bicluster_0143 and 0.00 and 240.00 for bicluster_0235 respectively.

These modules are enriched for following go terms: cellular respiration, energy derivation by oxidation of organi..., generation of precursor metabolites and ..., oxidation-reduction process, NADH dehydrogenase activity, oxidoreductase activity, acting on NAD(P..., oxidoreductase activity, acting on NAD(P... .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Re-Annotated Start Tuberculist Annotated Start
-0.019 500 92828 -509 92319 92328
Last update: 10/16/2017 - 17:54
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-17915 MT0091 550
Product (LegacyBRC) Product (RefSeq)
POSSIBLE FORMATE HYDROGENLYASE HYCD [FHL] formate hydrogenlyase HYCD
Operon # Operon
56 - - - - - - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607226 NP_214598.1 Run
No TFOE experiment results were found

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
0.290000 0.92

How essentiality calculations were done?

The relative representation of each mutant was determined by calculating the fold change (sequence reads/insertion in cholesterol divided by sequence reads/insertion in glycerol) for each gene. Statistical significance was determined by t-test. Each insertion site in each replicate sample was treated as a separate data point. The hyperbola used for defining genes specifically required for growth in cholesterol was defined by the formula, y = 3.8/x+0.7. Genes above this line are annotated as required for growth on cholesterol.

TRIP log2 fold abundance change

reports the log2 abundance fold change of each TFI strain, relative to no induction, in absence or presence of drug, averaged across experimental replicates. Also reported are the accompanying z-scores and two-sided t-test p-values for each TFI strain under each condition. Please refer to Ma et al., 2020, Nature Microbiology for more information.

p-value Untreated:
p-value INH: