MSMEG4388 (MSMEG4388)

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 MSMEG4385 MSMEG4386 MSMEG4387 MSMEG4388 MSMEG4389 MSMEG4390 MSMEG4391 MSMEG4392
Species: M. smegmatis
Strain: MC2-155
PATRIC Annotation: -
Synonyms:
M. tuberculosis homologs oppD, dppD, cysA1, RVBD1687c, modC, [+ 20 remaining orthologs]
M. abscessus homologs MAB0429, MAB0722, MAB2803c, MAB2435, MAB1226, [+ 21 remaining orthologs]
Gene Start: 4479425
Gene End: 4481053
Vulnerability Index (VI): 0.4720
VI Lower Bound: 0.0560
VI Upper Bound: 1.0750
[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

GGACATTCGCGCGGCCAGATCATCCGGCGGCACGTGTTCCCCAACGCCATGCGCCCACTGGTGGTGCTCGGCACCATGGGCATCGGCCAGTCCATCGTGTGGGCGTCCTCGCTGAGCTTTCTGGGTCTCGGCGTCGCACCGCCTGCCCCGGAGTGGGGCGCGATGCTCAACGCCGGCCGCGACTTCGTCTCCACCGCATGGTGGCTGGAACTGTTCCCGGGCCTGGCCATCGTCGGCTGCACACTGGCCGTCACGGTGGTCGGCCGCTACCTGCAGCAGCGCCTCGAAGGAAGACTGTCATGAGTGAGTTGTTGCTGAACGTGGCGGACCTCACGGTCGGCTTCGGCGACCATGAGGTGGTGCGCGGCCTGTCCTTCCATGTCGCGCCGGGCGAATGCTTCGCGATCGTCGGCGAATCCGGTTCGGGCAAGAGCGTCACCGCCCGCACCATCCTCGGCCTGGCCGGGCCCACCGCACGGGTCGGTGCCACCCGTCTGGAACTCAACGGAAAATCCCTGCTGGGCAACAAAGACCGGGATTGGCGACGCATCCGGGGCCGCGAGGTCGGTTTCGTGCTCCAGGACGCGCTGGTGTCGCTGGACCCGCTGCGCAAGGTGGGCGACGAGATCGCCGAGACACTGCGCCTGCACAGGTTCGGCAACAAGGCCGCCCGCCGCAGGCACGTCCTGGAACTGCTCGAGGCCGTCGGTGTTCCCGAACCCGAACTCAAGGCCCGGCAACTGCCCGGCGAACTGTCCGGCGGGCAGCGCCAGCGTGCCCTGATCGCCTCGGCCATCGCGCTCGACCCGCCGCTGGTGATCGCCGACGAGCCCACCACGGCCCTGGACGTCACAGTGCAGGCCCAGATCCTGGATCTGCTGGCCGCGATGAAAAACAAGGGCACGGGCCTGGTGTTGATCAGCCACGACCTCGCGGTGGTGGGCCGGTTGGCTGATCGGGTCGCGGTCATGCGCAACGGTGTTCTGGTCGAGCAGGGTCCGGTCGCAGAGGTGCTGGCCGCGCCGTCACACCCCTACACCCAGACCCTGCTGGACGCGGTCCCGGCCGCGCACCGCAAGGGCACCCGCCTGTCGCACCAACCCGCGCGCACGATGCACGGCACGCGGCAGACCGACGACGGTGTGCTGCTGGCGGCCCGCAACCTGGTCAAGCGGTTTCGCGGACCCGACGGCGTGGAGCGCACGGCGGTCAACGACGTGTCGTTCGAGATCGGCGTCGGCGAAACCCTCGGCATCGTCGGGGAATCCGGTTCGGGTAAGACCACCACGGCCCGCATGGCGCTCGCGCTCACCGAGCCCGACGAGGGCACGGTGCACCTGCTCGGCCAGCCGTGGAGTGAGCTCACCGAGAAGGAGCGCCGCAGCCGGCGCCGCCGCATCTCGGTGGTGTACCAGGATCCGCTGAGCTCGTTCGACCCACGCTGGACCGTGCGGCGCATCCTCGCCGATGCGCTCCCCGCCGAGCGCTACCCGGATGCCAAGGCCCGCGACGCGCGGGTGCGTGAACTGCTCGACGATGTCGGTCTGAGCTCCGAGCAACTCGATCGCCGACCGTTACTGCTCTCCGGTGGGCAGCGTCAGCGCGTGGCGATCGCGCGTGCCCTGGCCCCGGAGCCGTCGCTGATCGTGTGTGACGAACCGGTGTCCGCGCTCGACGTCACGATTCAGGCGCAGGTGCTGGACCTGCTGACCGATCTGCAGGAGCAACTCGGGCTGAGCTATTTGTTCATCTCGCACGACCTGGGGGTCATCCACCACGTGGCCGATCGCGTGCTGGTGATGCGGGAGGGCCGGGTGGTCGAATCCGGATCGGCCGCACAGATCTTCGACGCCCCGCAGGACCCGTACACCCAGCAGTTGCTGGCCAGTCTTCCCGCCGCCGAACCGATGTCAGGAGCCGTACTGTGA

Protein Sequence

MSELLLNVADLTVGFGDHEVVRGLSFHVAPGECFAIVGESGSGKSVTARTILGLAGPTARVGATRLELNGKSLLGNKDRDWRRIRGREVGFVLQDALVSLDPLRKVGDEIAETLRLHRFGNKAARRRHVLELLEAVGVPEPELKARQLPGELSGGQRQRALIASAIALDPPLVIADEPTTALDVTVQAQILDLLAAMKNKGTGLVLISHDLAVVGRLADRVAVMRNGVLVEQGPVAEVLAAPSHPYTQTLLDAVPAAHRKGTRLSHQPARTMHGTRQTDDGVLLAARNLVKRFRGPDGVERTAVNDVSFEIGVGETLGIVGESGSGKTTTARMALALTEPDEGTVHLLGQPWSELTEKERRSRRRRISVVYQDPLSSFDPRWTVRRILADALPAERYPDAKARDARVRELLDDVGLSSEQLDRRPLLLSGGQRQRVAIARALAPEPSLIVCDEPVSALDVTIQAQVLDLLTDLQEQLGLSYLFISHDLGVIHHVADRVLVMREGRVVESGSAAQIFDAPQDPYTQQLLASLPAAEPMSGAVL
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) 0.4720 1.3620
VI Lower Bound 0.0560 -0.3140
VI Upper Bound 1.0750 4.0010

Specific References

General References