MSMEG4113 (MSMEG4113)

background  +5   0  -5 -10 -15 sgRNA L2FC (+ATc/–ATc) TnSeq Gene Essentiality Predictions (1, 2) Essential Growth Defect Non-Essential Growth Advantage Unknown Operon Legend (3) Operon (1) PMID: 28096490 (2) PMID: 31388080 (3) PMID: 26536359 MSMEG4110 MSMEG4111 MSMEG4112 MSMEG4113 menB MSMEG4115 MSMEG4116 MSMEG4117
Species: M. smegmatis
Strain: MC2-155
PATRIC Annotation: -
Synonyms:
M. tuberculosis homologs fadE9, fadE25, fadE35
M. abscessus homologs MAB2085, MAB1863, MAB3618c, MAB1188c, MAB2395
Gene Start: 4193473
Gene End: 4194528
Vulnerability Index (VI): 0.0760
VI Lower Bound: -0.2010
VI Upper Bound: 0.3510
[AlphaFold] [Orthologs] [Phyre2] [UniProt] [MycoBrowser] [TnSeq DB] [SeqHub]

Essentiality:

Call Condition Type Source Notes
Non Essential in vitro CRISPRi [Bosch & DeJesus et al. (2021)]
Non Essential in vitro TnSeq [Dragset et al. (2019)]


DNA and Protein Sequence help

DNA Sequence

GTACCTCAACGGCAAATTCACCGCGGCCAAAGCCGAGGCCATGGGTCTGGTCAACGAGGTCGTCGAACCCAATAAACTCATGAACCGGGCCACCGAGATCGCCCGCGAGATCTCGACCCGCAGCCCGCTCGCGATCGGTGCGCTCAAGGGCGCGTTCTCGGCGCGCCACAACGGCGTATCCGGCCAGGCCCGAATGGCGCACGATCAACAGCTCACGCTGTACCTGCAGACACAGGAAGCACACGAGGTCAGCGCCTCGTTCGGCGAGCGCAGGCAGCCCAACACCGAGAGCTTCTGGTCGTGAGCGCTTCACCCCAGTGGTGGGGGCCCGCCCTCGACGACGACGGGCGCAGCCTGCGAGATGTGCTCGACGAGTTCATCGACGCGCACGAACCAACTCTCACCGACGACGTCACCGCGGTCACCGCGCTCGTCAGGGAGCTTGCCGGACTGGGCATCTGGACACTCGGCACCGCGGAGACAGCCGGAGGCGGCGGCGCCGATCGCACACTGACCACAGTAGCGTTCGAACGGCTCGGGCGGGCCTGGCCCGCATTGGGCTGGGCCGCGGTGCAGGCGCACACGGCCATCGACGTGCTGGCGGGCGACGACCGGTTCGCCGATTTGGTCACCGCGCTGCATGTCGGGAATGCCGCCGTGGCGGTGGCCGACGCTCAATCGCTGCACGTCCGCCTGCAGCGCGACGGCGCCGCGATCACCGGCACGGTGGACCGCGTCGACGCCGCCGCCGAGGAGCCCCACCTGCTGGTGCTTTTCGACGGCGGCACGGCGGCGCTGATCGAACCGGCCGCGCTCACCCGGGACCCGGTGCACCGCACGGGCTTGGGCGGTGCCCTGACACGATCCCTCGACATCGACGCGCGGGCTGCCCACGTGGTCGACGGTGTGGACGTCGACGCCGCGCGGGTCCGGCTAAGGCTGGGCGCGGCAGCGGTCGCGGCCGGTATCGCGGGAGCCGCAGCAGACGCCGCGGTGTCCTACGCCGCTGAGCGCAGGCAGTTCGGTGACACACTGACCGCGATCCCCACTGTCCGCAAGTCTCTTATGGAGCAGACCTCGCGTGCCGTGCTCATCCTCGGCGCGGTTCTCGGCGCCGCCGAGGACCCCATCCAAGCGGCCGCGGTCGCACTGCACGCACTCGACGGAGCGATCGACGTGGCCGCGGATGCATTGCAATCCCACGGCGGCTACGGCTATCTCGTCGAGTACGACGCCGAGCGGCGGCTCCGTGACGCGGTGTCACTGCGCGCCGCGGCAGACGTGAGGGGACAGGCCACGACAACAGCACGAACACTGGTGGGCGTGGGGCCCGCCGGGATCTCCGCAAAGGACTGA

Protein Sequence

VSASPQWWGPALDDDGRSLRDVLDEFIDAHEPTLTDDVTAVTALVRELAGLGIWTLGTAETAGGGGADRTLTTVAFERLGRAWPALGWAAVQAHTAIDVLAGDDRFADLVTALHVGNAAVAVADAQSLHVRLQRDGAAITGTVDRVDAAAEEPHLLVLFDGGTAALIEPAALTRDPVHRTGLGGALTRSLDIDARAAHVVDGVDVDAARVRLRLGAAAVAAGIAGAAADAAVSYAAERRQFGDTLTAIPTVRKSLMEQTSRAVLILGAVLGAAEDPIQAAAVALHALDGAIDVAADALQSHGGYGYLVEYDAERRLRDAVSLRAAADVRGQATTTARTLVGVGPAGISAKD
Vulnerability Assesment help
[Full list of passaging experiments]

Experiment: We designed an M. tuberculosis CRISPRi library (RLC12) to target all annotated Mtb genes with single guide RNAs (sgRNAs) of varying predicted knockdown efficiencies. In parallel, we constructed a M. smegmatis CRISPRi library (RLC11) to target all annotated Msmeg genes, similar to the Mtb sgRNA library. RLC12 was transformed into M. tuberculosis H37Rv; RLC11 into M. smegmatis mc2-155. We passaged both CRISPRi libraries for nearly 30 generations in the presence or absence of the CRISPRi-inducer anhydrotetracycline (ATc). At the indicated timepoints, genomic DNA was harvested and the representation of individual sgRNAs was counted using Illumina sequencing. Here, we show sgRNA log2 fold-change values (L2FC) (plus versus minus ATc) over consecutive generations for sgRNAs targeting the gene you selected. sgRNAs are color-coded based on their predicted strength from blue (strength=0; weak) to red (strength=1; strong).

In order to quantify gene vulnerability, data were subsequently analyzed with a hierarchical model at the sgRNA level (two-line model) and gene level (Hill curve). The vulnerability quantification is shown below. [More information]

M. smegmatis Reference Fitness Experiment M. tuberculosis H37Rv Reference Fitness Experiment M. tuberculosis HN878 Reference Fitness Experiment
 
 
M. smegmatis Gene-Level Logistic Regression M. tuberculosis H37Rv Gene-Level Logistic Regression (Most similar ortholog) M. tuberculosis HN878 Gene-Level Logistic Regression (Most similar ortholog)
 
Vulnerability Index (VI) 0.0760 0.6680
VI Lower Bound -0.2010 -1.1580
VI Upper Bound 0.3510 3.5460

Specific References

General References