Detailed view for LmjF.04.0580

Basic information

TDR Targets ID: 28723
Leishmania major, spermidine synthase

Source Database / ID:  TriTrypDB  GeneDB

pI: 5.012 | Length (AA): 300 | MW (Da): 32884 | Paralog Number: 0

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

Druggability Group : DG3

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

PF01564   Spermine/spermidine synthase domain
PF17284   Spermidine synthase tetramerisation domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003824   catalytic activity  

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
6 300 1uir (A) 1 287 31.00 0 1 1.35 -1.04
8 300 1xj5 (A) 44 330 46.00 0 1 1.58 -1.45
9 295 1zdz (A) 18 294 48.00 0 1 1.63 -1.45
1 299 5b1s (A) 1 293 68.00 0 1 1.88477 -1.38

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
Upper 80-100% 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_127074)

Species Accession Gene Product
Arabidopsis thaliana AT1G23820   spermidine synthase 1
Arabidopsis thaliana AT1G70310   Spermidine synthase 2
Arabidopsis thaliana AT5G19530   Thermospermine synthase ACAULIS5
Brugia malayi Bm1_44015   Spermidine synthase
Candida albicans CaO19.2250   spermidine synthase
Candida albicans CaO19.9790   spermidine synthase
Caenorhabditis elegans CELE_Y46G5A.19   Protein SPDS-1, isoform B
Dictyostelium discoideum DDB_G0268630   hypothetical protein
Drosophila melanogaster Dmel_CG8327   Spermidine Synthase
Escherichia coli b0121   spermidine synthase (putrescine aminopropyltransferase)
Echinococcus granulosus EgrG_000485300   spermidine synthase
Echinococcus multilocularis EmuJ_000485300   spermidine synthase
Homo sapiens ENSG00000116649   spermidine synthase
Leishmania braziliensis LbrM.04.0630   spermidine synthase, putative
Leishmania donovani LdBPK_040570.1   spermidine synthase, putative
Leishmania infantum LinJ.04.0570   spermidine synthase, putative
Leishmania major LmjF.04.0580   spermidine synthase
Leishmania mexicana LmxM.04.0580   spermidine synthase, putative
Loa Loa (eye worm) LOAG_01004   spermidine synthase
Mus musculus ENSMUSG00000006442   spermidine synthase
Mycobacterium tuberculosis Rv2601   Probable spermidine synthase SpeE (putrescine aminopropyltransferase) (aminopropyltransferase) (SPDSY)
Mycobacterium ulcerans MUL_1708   spermidine synthase
Oryza sativa 4328835   Os02g0237100
Oryza sativa 4342996   Os07g0408700
Plasmodium berghei PBANKA_0919300   spermidine synthase, putative
Plasmodium falciparum PF3D7_1129000   spermidine synthase
Plasmodium knowlesi PKNH_0927000   spermidine synthase, putative
Plasmodium vivax PVX_092065   spermidine synthase, putative
Plasmodium yoelii PY04977   spermidine synthase-related
Saccharomyces cerevisiae YLR146C   spermine synthase
Saccharomyces cerevisiae YPR069C   spermidine synthase
Schmidtea mediterranea mk4.005944.00   Spermidine synthase
Schmidtea mediterranea mk4.000519.03   Spermidine synthase
Schmidtea mediterranea mk4.010072.02   Spermidine synthase
Trypanosoma brucei gambiense Tbg972.9.4260   spermidine synthase, putative
Trypanosoma brucei Tb927.9.7770   spermidine synthase
Trypanosoma congolense TcIL3000_9_2680   spermidine synthase
Trypanosoma cruzi TcCLB.504033.130   spermidine synthase, putative
Trypanosoma cruzi TcCLB.510339.50   spermidine synthase, putative
Trypanosoma cruzi TcCLB.510337.40   spermidine synthase, putative
Trypanosoma cruzi TcCLB.503855.20   spermidine synthase, putative

Essentiality

LmjF.04.0580 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu2645 Mycobacterium tuberculosis non-essential nmpdr
Tb09.v1.0380 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.v1.0380 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.v1.0380 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.v1.0380 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0121 Escherichia coli non-essential goodall
PBANKA_0919300 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.

Phenotypes and Validation (curated)

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

Druggability index (range: 0 to 1): 0.8


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
Trypanosoma cruzi spermidine synthase, putative Compounds References
Homo sapiens spermidine synthase Compounds References
Rattus norvegicus Spermidine synthase Compounds References
Plasmodium falciparum spermidine synthase Compounds References
Sus scrofa Spermidine synthase 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
0.1194 0.6653 1
0.1138 0.3002 1
0.1164 0.6035 1
0.0679 0.2944 0.6725
0.0682 0.4958 0.7871
0.1127 0.7939 1
0.1193 0.2764 1
0.11 0.6365 1
0.052 0.4553 1
0.1071 0.6119 1
0.0687 0.3924 1
0.0679 0.2944 0.6725
0.1138 0.3002 1
0.1162 0.6652 1
0.0515 0.3525 1
0.0142 0.3075 0.3075
0.1058 0.789 1
0.1063 0.6227 1
0.1179 0.6749 1
0.0518 0.583 0.9049
0.0679 0.3925 1
0.0691 0.257 0.6679
0.0896 0.5302 1
0.0687 0.3924 1
0.104 0.587 0.9635
0.0518 0.912 0.912
0.0463 0.6051 1
0.114 0.6237 1
0.1045 0.615 1
0.0463 0.2847 1
0.0683 0.5029 1
0.0679 0.2944 0.6725
0.1138 0.3002 1
0.089 0.278 0.9329
0.1095 0.7795 1
0.0679 0.2944 0.6725
0.0463 0.6051 1
0.0463 0.2847 1
0.0736 0.2508 0.7218
0.114 0.6667 1
0.1106 0.6376 1
0.1124 0.7963 1
0.1089 0.7753 1
0.0463 0.2847 1
0.1097 0.7751 1
0.1098 0.7755 1
0.1133 0.6651 1
0.1131 0.3653 1
0.114 0.6237 1
0.0463 0.2847 1
0.1097 0.7751 1
0.1118 0.4845 1
0.0515 0.3161 1
0.1079 0.6088 1
0.0515 0.3704 0.5921
0.1202 0.6662 1
0.0324 0.2977 1
0.1101 0.6336 1
0.1055 0.7768 1
0.1115 0.66 1
0.1082 0.6337 1
0.0691 0.5022 0.9802
0.0523 0.2997 0.5613
0.1162 0.6113 1
0.0682 0.5016 0.6655
0.1132 0.6378 1
0.1138 0.3002 1
0.1081 0.6049 1
0.1156 0.6717 1
0.1149 0.672 1
0.0515 0.3704 0.5921
0.1088 0.602 1
0.0273 0.258 1
0.1193 0.2764 1
0.0699 0.3904 0.8161
0.1138 0.3002 1
0.0523 0.5876 0.5396
0.1064 0.6339 1
0.112 0.7815 1
0.11 0.6373 1
0.1208 0.6953 1
0.1045 0.6223 1
0.1202 0.6662 1
0.1107 0.7822 1
0.0851 0.2584 0.8659
0.1087 0.6059 1
0.0675 0.3912 1
0.0554 1 0.5
0.1067 0.7807 1
0.1154 0.6149 1
0.1095 0.7752 1
0.0675 0.3915 1
0.0201 0.3693 0.5275
0.114 0.6667 1
0.0687 0.3911 1
0.1219 0.6654 1
0.1097 0.7751 1
0.1134 0.6664 1
0.1141 0.6775 1
0.0463 0.6051 1
0.1138 0.5078 1
0.1061 0.4273 1
0.052 0.4553 1
0.0687 0.3924 1
0.109 0.6111 1
0.1079 0.6088 1
0.0434 1 0.5
0.0687 0.5033 0.7857
0.0201 0.3693 0.5275
0.1181 0.6668 1
0.0515 0.3124 1
0.1053 0.7669 1
0.1105 0.6083 1
0.1057 0.7735 1
0.0679 0.2944 0.6725
0.0434 1 0.5
0.1124 0.4235 1
0.1119 0.6295 1
0.1081 0.7754 1
0.0691 0.5029 0.664
0.1105 0.665 1
0.0463 0.2847 1
0.1118 0.4845 1
0.0851 0.2584 0.8659
0.0851 0.2584 0.8659
0.0463 0.2847 1
0.1138 0.3002 1
0.0736 0.2508 0.7218
0.0516 0.3778 1
0.114 0.6667 1
0.0679 0.2944 0.6725
0.1188 0.6667 1
0.1123 0.6665 1
0.0682 0.4827 0.7888
0.0463 0.2847 1
0.0515 0.3716 1
0.0888 0.4803 1
0.0672 0.6321 0.5963
0.0463 0.2847 1
0.1063 0.6227 1
0.1076 0.2766 1
0.0685 0.4946 0.7791
0.1071 0.784 1
0.1166 0.7092 1
0.114 0.6237 1
0.114 0.6237 1
0.1149 0.6776 1
0.0946 1 0.5
0.1076 0.6061 1
0.0434 1 0.5
0.1227 0.6654 1
0.1192 0.6655 1
0.1074 0.605 1
0.1153 0.6689 1
0.0705 0.5024 0.6637
0.1138 0.3002 1
0.1138 0.3002 1
0.1063 0.7732 1
0.0695 0.503 0.6639

Assayability

Assay information

No assay information for this target.

Reagent availability

  • Lmex007905AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Lmex007905; Recombinant protein: full-length; Source: L mexicana; Spermidine synthase ;

Bibliographic References

5 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier LmjF.04.0580 (Leishmania major), spermidine synthase
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