Detailed view for LmjF.25.1200

Basic information

TDR Targets ID: 28418
Leishmania major, modification methylase-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.8976 | Length (AA): 840 | MW (Da): 89386 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG2

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00145   C-5 cytosine-specific DNA methylase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008168   methyltransferase activity  
GO:0003677   DNA binding  
GO:0006306   DNA methylation  

Metabolic Pathways

Cysteine and methionine metabolism (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 4 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
425 557 1dct (A) 43 162 36.00 0.0000000000047 1 0.55 -0.64
317 557 3lx6 (A) 87 285 38.00 0 0.93 0.387605 0.6
431 557 1svu (A) 59 172 32.00 0.00064 1 0.15989 0.49
438 526 5cqc (A) 80 197 42.00 0.061 0.34 0.137652 1.3

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile amastigotes, metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_138689)

Species Accession Gene Product
Escherichia coli b1961   DNA cytosine methyltransferase
Leishmania braziliensis LbrM.25.1170   modification methylase-like protein
Leishmania donovani LdBPK_251230.1   modification methylase-like protein
Leishmania infantum LinJ.25.1230   modification methylase-like protein
Leishmania major LmjF.25.1200   modification methylase-like protein
Leishmania mexicana LmxM.25.1200   modification methylase-like protein
Trypanosoma brucei gambiense Tbg972.3.1110   cytosine-specific DNA methylase, putative
Trypanosoma brucei Tb927.3.1360   cytosine-specific DNA methylase, putative
Trypanosoma congolense TcIL3000_3_570   cytosine-specific DNA methylase, putative

Essentiality

LmjF.25.1200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.1360 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.1360 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.1360 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.1360 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1961 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Spiroplasma monobiae CpG DNA methylase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0068 0.4497 0.5
0.0072 0.4497 0.5
0.0434 0.3112 1
0.0271 0.3778 0.88
0.0247 0.2515 0.4387
0.0976 0.2979 1
0.0937 0.4859 1
0.0441 0.3578 0.9393
0.0499 0.2874 0.4526
0.0518 0.2772 0.4141
0.0545 0.3072 0.4823
0.0157 0.8656 0.5
0.0246 0.5263 1
0.0059 0.3579 0.5
0.0249 0.2515 0.4387
0.0483 0.2625 0.4302
0.0866 0.6943 1
0.0048 0.4497 0.5
0.0276 0.3778 0.88
0.0468 0.358 0.9391
0.0617 0.3335 0.4999
0.0273 0.3469 1
0.0059 0.366 0.5
0.0262 0.2507 0.4387
0.0241 0.2942 0.8037
0.051 0.369 0.4677
0.0072 0.4497 0.5
0.0252 0.558 1
0.0253 0.2507 0.4387
0.0511 0.2912 0.4349
0.0898 0.4876 1
0.0262 0.3781 0.88
0.0581 0.3331 0.5335
0.0157 0.2575 1
0.0269 0.3778 0.8807
0.0256 0.2515 0.4387
0.0064 0.2961 1
0.0547 0.3057 0.4794
0.0976 0.2979 1
0.0157 0.2524 0.6488
0.0251 0.3495 0.5
0.087 0.294 0.8508
0.0253 0.2507 0.4387
0.0242 0.8286 0.5
0.0058 0.3563 0.5
0.0528 0.2882 0.4756
0.0268 0.3778 0.88
0.0627 0.3652 0.6882
0.0064 0.2961 1
0.026 0.3778 0.88
0.0475 0.3182 0.3998
0.054 0.3687 0.4644
0.00431057 0.5 0.5
0.0956 0.2945 1
0.0663 0.3541 0.5659
0.0253 0.2572 0.5
0.0287 0.2507 0.3186
0.0341 0.3073 0.5
0.0436 0.5275 1
0.0157 0.8655 0.5
0.0864 0.2949 0.8508
0.0279 0.3777 0.8796
0.0248 0.2507 0.4387
0.0072 0.4497 0.5
0.0557 0.4052 1
0.0274 0.3971 1
0.0901 0.3272 1
0.0913 0.2936 0.8508
0.0062 0.4497 0.5
0.0267 0.2659 1
0.0058 0.4497 0.5
0.0558 0.6597 1
0.0585 0.3337 0.5259
0.087 0.2936 0.8508
0.006 0.4497 0.5
0.0514 0.283 0.4159
0.026 0.2507 0.4387
0.024 0.2503 0.438
0.0048 0.7364 0.7364
0.0864 0.296 0.8522
0.0057 0.4497 0.5
0.0118 0.3963 0.5
0.0433 0.2757 0.5
0.0059 0.4497 0.5
0.0157 0.3941 0
0.0342 0.4442 1
0.0276 0.3778 0.88
0.0663 0.3541 0.5659
0.0267 0.2659 1
0.088 0.4804 0.7894
0.0404 0.4405 1
0.0663 0.3541 0.5659
0.0913 0.2936 0.8508
0.0546 0.3077 0.4822
0.0901 0.4859 1
0.0625 0.3621 0.5301
0.0059 0.4497 0.5
0.0558 0.3087 0.4599
0.006 0.4497 0.5
0.0241 0.3004 1
0.028 0.2661 1
0.0256 0.3382 1
0.024 0.2507 0.4386
0.0908 0.5336 1
0.0247 0.2906 1
0.0288 0.3368 1
0.0059 0.4497 0.5
0.0242 0.4348 0.5
0.0705 0.3682 0.5988
0.0447 0.3212 1
0.0913 0.2936 0.8508
0.0241 0.2942 0.8037
0.0547 0.3047 0.4807
0.0064 0.4497 0.5
0.026 0.3788 0.8807
0.0096 0.6636 0.5
0.0558 0.3044 0.4835
0.0619 0.3259 0.4876
0.023 0.4243 0.5
0.085 0.459 0.9547
0.0625 0.3313 0.4958
0.0287 0.2507 0.3186
0.0273 0.3469 1
0.0247 0.2511 0.4387
0.0281 0.295 0.5
0.0839 0.4753 0.7765
0.0952 0.5727 0.7878
0.0486 0.3386 1
0.025 0.2515 0.4387
0.0546 0.5367 0.9395
0.0913 0.2936 0.8508
0.0358 0.2591 1
0.0976 0.2979 1
0.0246 0.5263 1
0.0441 0.3578 0.9393
0.0057 0.4497 0.5
0.0497 0.2864 0.4603
0.0158 0.8655 0.5
0.0061 0.4497 0.5
0.0617 0.3335 0.4999
0.0585 0.3149 0.5231
0.0158 0.8654 0.5
0.0581 0.3331 0.5335
0.0942 0.486 1
0.0253 0.2515 0.4387
0.0279 0.3777 0.8796
0.0286 0.5274 1
0.0479 0.3336 1
0.0663 0.3541 0.5659
0.0091 0.3769 0.5
0.0913 0.2936 0.8508
0.0286 0.2507 0.4387
0.0951 0.4896 0.811
0.0126 0.2647 1
0.0225 0.4785 1
0.0262 0.2507 0.4387
0.0951 0.2977 1
0.0864 0.2949 0.8508
0.048 0.256 0.3808
0.0483 0.2625 0.4302
0.0864 0.296 0.8522
0.0752 0.3883 0.634
0.0582 0.3156 0.5209
0.029 0.2598 0.5
0.0465 0.3259 1
0.0477 0.2556 0.3804
0.007 0.4497 0.5
0.0151 0.3224 1
0.0258 0.2518 0.4401
0.0245 0.2515 0.4387
0.0246 0.3242 1
0.0529 0.3132 1
0.0206 0.3269 1
0.0224 0.4393 1
0.0245 0.5254 1
0.028 0.3774 0.5471
0.0956 0.2945 1
0.0265 0.3778 0.881
0.0251 0.2515 0.4387
0.0255 0.4359 1
0.0245 0.2515 0.4387
0.0242 0.2507 0.4386
0.0495 0.3595 0.3857
0.0268 0.3778 0.8807
0.0599 0.2531 0.522
0.087 0.2936 0.8508
0.0157 0.2524 0.6488
0.0937 0.4859 1
0.087 0.2936 0.8508
0.0251 0.5557 1
0.087 0.294 0.8508
0.0262 0.2507 0.4387
0.0599 0.2531 0.522
0.0911 0.5333 0.867
0.0305 0.5022 1
0.0157 0.8656 0.5
0.0072 0.4497 0.5
0.0245 0.2507 0.4387
0.0253 0.2515 0.4387
0.0225 0.4785 1
0.0262 0.3781 0.88
0.0253 0.2503 0.4401
0.0242 0.8286 0.5
0.0558 0.3185 0.4652
0.0286 0.4018 1
0.0061 0.4497 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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Gene identifier LmjF.25.1200 (Leishmania major), modification methylase-like protein
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