MSMEG4199
ms4199
-
M. smegmatis · MC2-155
[AlphaFold] [Orthologs] [Phyre2] [UniProt] [MycoBrowser] [TnSeq DB] [SeqHub]
MC2-155 Coordinates: 4276933 – 4277454
Vulnerability Index (VI): 0.0110
M. tuberculosis homologs TB18.6, lppC
M. abscessus homologs MAB2103
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 MSMEG4194 MSMEG4195 MSMEG4196 MSMEG4197 pyrD MSMEG4199 MSMEG4200 MSMEG4201 MSMEG4202
Click the tabs above to view different types of data for this gene. The Vulnerability tab shows CRISPRi fitness data.
DNA and Protein Sequence help

DNA Sequence 

>ms4199_MSMEG4199_dna
TTCGACGGCGACCTGGTCGACGCGATGAACGCCAGCGTGCTGACACTGGATCCCGAGGCCCGCATCGTGCCGTACATGCTGTCGGCGGGCACCGATGCGAAGTCGTTCCAGCGCTTGGGTATTCGGTGCTTCGGCTTCGCGCCGCTGCGTCTGCCGCCGGATCTGGATTTCGCGGCGCTGTTCCACGGTGTGGACGAGCGGGTTCCGGTGGATGCGCTGCAATTCGGGGCGGGTGTTCTGGAACACTTCCTGCAGAACTGCTGACGCAATGCCGACCGAACGAACGAGGAAAGGGATCACATGACCAGTCCATACGACAACTTGCCGCAGCTGCCGAGTTTCACCCTCACGTCCGAGTCGGTCAGCGACGGGCAGCCGCTCGCCAACGATCAGGTCAGCGGCATCATGGGCGCAGGTGGCTCGGACATCTCGCCGCAGTTGAGCTGGTCGGGTTTCCCGGAGGAGACCAAGAGCTTCGCCGTCACGATCTACGACCCCGACGCGCCCACTGCATCGGGTTTCTGGCACTGGGCGGTCGCCGACCTGCCCGTCTCGGTCACCGAACTGCCCGCGGGTGCCGGTGACGGCAGCCCGCTGCCCGGCGGCGCCGTCACGCTCGCCAACGACGCGAGCGTCAAGCGCTACATCGGCGCCGCGCCGCCGGCCGGCCACGGACCGCACCGCTACTACATCGCGGTCCACGCCGTCGACGTCGAGAAGCTCGACCTGCCGGAGAACGCCACGCCGGCCTATCTGGGCTTCAATCTGTTCGGCCACGCGATCGCCCGCGCGGTCATCCACGGCACCTACGAACAGAAGTAG

Protein Sequence 

>Ms4199_MSMEG4199_protein
MTSPYDNLPQLPSFTLTSESVSDGQPLANDQVSGIMGAGGSDISPQLSWSGFPEETKSFAVTIYDPDAPTASGFWHWAVADLPVSVTELPAGAGDGSPLPGGAVTLANDASVKRYIGAAPPAGHGPHRYYIAVHAVDVEKLDLPENATPAYLGFNLFGHAIARAVIHGTYEQK

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)]
Vulnerability Assessment help
[Full list of passaging experiments]

Experiment (PMID: 34297925): 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) 0.0110 -0.0120
VI Lower Bound -1.8270 -1.9200
VI Upper Bound 2.0140 2.4390

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