Detailed view for PF3D7_0817900

Basic information

TDR Targets ID: 771
Plasmodium falciparum, high mobility group protein B2
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.6562 | Length (AA): 99 | MW (Da): 11535 | Paralog Number: 1

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

PF00505   HMG (high mobility group) box

Gene Ontology

Mouse over links to read term descriptions.
GO:0006359   regulation of transcription from RNA polymerase III promoter  
GO:0005634   nucleus  
GO:0003677   DNA binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
1 96 2gzk (A) 64 159 41.00 0 1 1.41 0.22
24 91 2cs1 (A) 8 73 33.00 0.000000000059 0.81 1.16 -1
9 99 2mrc (A) 2 92 91.00 0 1 1.93359 -0.54
60 90 2hdz (A) 38 68 29.00 0.073 0.17 0.709931 -0.98

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:

PDB tag
  • 2MRC:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Show/Hide expression data references
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_126740)

Species Accession Gene Product
Arabidopsis thaliana AT1G20696   high mobility group B3 protein
Arabidopsis thaliana AT3G51880   high mobility group protein B1
Arabidopsis thaliana AT1G20693   high mobility group B2 protein
Babesia bovis BBOV_IV001910   high mobility group protein-like protein NHP1
Brugia malayi Bm1_28675   HMG box family protein
Brugia malayi Bm1_25620   high mobility group protein
Brugia malayi Bm1_45200   High mobility group protein 1.2
Caenorhabditis elegans CELE_F47D12.4   Protein HMG-1.2, isoform A
Cryptosporidium hominis Chro.20230   high mobility group protein
Cryptosporidium hominis Chro.20322   high mobility group box 1
Cryptosporidium parvum cgd2_2120   high mobility group small protein
Cryptosporidium parvum cgd2_3070   high mobility group (HMG)-box
Dictyostelium discoideum DDB_G0270260   HMG1/2 box-containing protein
Drosophila melanogaster Dmel_CG12223   Dorsal switch protein 1
Drosophila melanogaster Dmel_CG17921   HMG protein Z
Echinococcus granulosus EgrG_001049000   high mobility group protein dsp1
Echinococcus granulosus EgrG_000941400   SWI:SNF chromatin binding protein
Echinococcus granulosus EgrG_000768300   high mobility group protein dsp1
Entamoeba histolytica EHI_045480   high mobility group (HMG) box domain containing protein
Entamoeba histolytica EHI_093800   high mobility group (HMG) box domain containing protein
Echinococcus multilocularis EmuJ_000430600   High mobility group, HMG1 HMG2
Echinococcus multilocularis EmuJ_001049000   high mobility group protein dsp1 high mobility group protein b1 high mobility group b3 protein
Echinococcus multilocularis EmuJ_000768300   high mobility group protein dsp1 high mobility group protein b2 high mobility group protein b1 high mobility group b3 protein
Echinococcus multilocularis EmuJ_000941400   SWI:SNF chromatin binding protein
Giardia lamblia GL50803_14064   Hypothetical protein
Homo sapiens ENSG00000189403   high mobility group box 1
Homo sapiens 3148   high mobility group box 2
Homo sapiens ENSG00000029993   high mobility group box 3
Leishmania braziliensis LbrM.29.0880   high mobility group protein homolog tdp-1, putative
Leishmania donovani LdBPK_290890.1   High mobility group protein TDP1
Leishmania infantum LinJ.29.0890   high mobility group protein homolog tdp-1, putative
Leishmania major LmjF.29.0850   high mobility group protein homolog tdp-1, putative
Leishmania mexicana LmxM.08_29.0850   high mobility group protein homolog tdp-1, putative
Loa Loa (eye worm) LOAG_14354   high mobility group protein 1
Loa Loa (eye worm) LOAG_07813   hypothetical protein
Loa Loa (eye worm) LOAG_04936   high mobility group protein 1.2
Mus musculus 667284   predicted gene 8556
Mus musculus 102642363   high mobility group protein B1-like
Mus musculus 619937   predicted gene 6115
Mus musculus ENSMUSG00000066551   high mobility group box 1
Mus musculus 100862258   predicted gene, 21596
Mus musculus ENSMUSG00000015217   high mobility group box 3
Mus musculus ENSMUSG00000054717   high mobility group box 2
Mus musculus 102641638   high mobility group protein B1-like
Neospora caninum NCLIV_024230   Zgc:123215, related
Neospora caninum NCLIV_043680   hypothetical protein
Neospora caninum NCLIV_060790   High mobility group protein 1, related
Neospora caninum NCLIV_043670   High mobility group protein, related
Oryza sativa 4342129   Os06g0728000
Onchocerca volvulus OVOC213   FACT complex subunit SSRP1 homolog
Plasmodium berghei PBANKA_0601900   high mobility group protein B1, putative
Plasmodium berghei PBANKA_0712900   high mobility group protein B2
Plasmodium falciparum PF3D7_0817900   high mobility group protein B2
Plasmodium falciparum PF3D7_1202900   high mobility group protein B1
Plasmodium knowlesi PKNH_1302800   high mobility group protein B1, putative
Plasmodium vivax PVX_084190   high mobility group protein B1, putative
Plasmodium vivax PVX_089520   high mobility group protein B2, putative
Plasmodium yoelii PY07077   high mobility group protein
Plasmodium yoelii PY05184   high mobility group protein
Saccharomyces cerevisiae YPR052C   Nhp6ap
Saccharomyces cerevisiae YBR089C-A   Nhp6bp
Schistosoma japonicum Sjp_0099540   expressed protein
Schistosoma japonicum Sjp_0051340   High mobility group protein DSP1, putative
Schistosoma japonicum Sjp_0205610   High mobility group protein DSP1, putative
Schistosoma japonicum Sjp_0306300   High mobility group protein DSP1, putative
Schistosoma mansoni Smp_100090   SWI/SNF-related chromatin binding protein
Schistosoma mansoni Smp_103530   SWI/SNF-related chromatin binding protein
Schistosoma mansoni Smp_000980   high mobility group protein
Schmidtea mediterranea mk4.027518.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.022878.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.008573.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.001463.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.034399.01   High mobility group protein 1.2
Schmidtea mediterranea mk4.004809.00  
Schmidtea mediterranea mk4.001697.02   High mobility group protein 1.2
Schmidtea mediterranea mk4.008831.01   High mobility group protein 1.2
Schmidtea mediterranea mk4.017967.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.016635.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.001670.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.004256.03   High mobility group protein 1.2
Schmidtea mediterranea mk4.012220.01   High mobility group protein 1.2
Schmidtea mediterranea mk4.002022.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.001688.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.012314.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.016158.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.008034.01   High mobility group protein 1.2
Schmidtea mediterranea mk4.002022.04   High mobility group protein 1.2
Schmidtea mediterranea mk4.030107.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.000004.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.002293.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.001283.05   High mobility group protein 1.2
Schmidtea mediterranea mk4.002209.07   High mobility group protein 1.2
Schmidtea mediterranea mk4.000004.09   High mobility group protein 1.2
Schmidtea mediterranea mk4.011813.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.000503.05   High mobility group protein 1.2
Schmidtea mediterranea mk4.003405.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.002076.02   High mobility group protein 1.2
Schmidtea mediterranea mk4.016720.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.009554.02   High mobility group protein 1.2
Schmidtea mediterranea mk4.000438.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.013558.03   High mobility group protein 1.2
Schmidtea mediterranea mk4.017510.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.002076.06   High mobility group protein 1.2
Schmidtea mediterranea mk4.016971.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.032327.00   High mobility group protein 1.2
Schmidtea mediterranea mk4.000097.13   High mobility group-1
Schmidtea mediterranea mk4.000382.06   High mobility group-2
Trypanosoma brucei gambiense Tbg972.3.3740   high mobility group protein, putative
Trypanosoma brucei Tb927.3.3490   High mobility group protein TDP1
Trypanosoma congolense TcIL3000_3_2190   High mobility group protein TDP1
Trypanosoma congolense TcIL3000_0_11270   high mobility group protein, putative
Trypanosoma cruzi TcCLB.504431.64   Trypanosome DNA binding protein 1
Trypanosoma cruzi TcCLB.507951.114   High mobility group protein TDP1
Toxoplasma gondii TGME49_263720   HMG (high mobility group) box domain-containing protein
Toxoplasma gondii TGME49_210408   HMG (high mobility group) box domain-containing protein
Theileria parva TP03_0469   high mobility group protein, putative
Trichomonas vaginalis TVAG_346400   high mobility group protein, putative
Trichomonas vaginalis TVAG_325010   high mobility group protein, putative
Trichomonas vaginalis TVAG_125540   high mobility group protein, putative
Trichomonas vaginalis TVAG_161660   high mobility group protein, putative
Trichomonas vaginalis TVAG_302620   high mobility group protein, putative

Essentiality

PF3D7_0817900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.3490 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.3.3490 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.3.3490 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.3490 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F47D12.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_F47D12.4 Caenorhabditis elegans larval lethal wormbase
CELE_F47D12.4 Caenorhabditis elegans slow growth wormbase
CELE_F47D12.4 Caenorhabditis elegans sterile wormbase
YBR089C-A Saccharomyces cerevisiae inviable yeastgenome
TGME49_263720 Toxoplasma gondii Essentiality uncertain sidik
TGME49_210408 Toxoplasma gondii Essentiality uncertain sidik
TGME49_263720 Toxoplasma gondii Probably non-essential sidik
TGME49_210408 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.

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
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

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.

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

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Gene identifier PF3D7_0817900 (Plasmodium falciparum), high mobility group protein B2
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