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Effector Prediction Tool

This tool performs the prediction using a Naive Bayes classifier model generated in the Waikato Environment for Knowledge Analysis (WEKA, version 3.6.2). The model was trained with a positive dataset of 100 experimentally known effectors from 28 species and negative dataset of 100 non-effector protein sequences from 10 species. The training was restricted to only the 100 amino acids (aa) region of the N-terminal of these sequences and based on three physico-chemical properties, namely hydrophobicity, polarity and beta-turns to discriminate highly diverse effectors from non-effectors. Testing of the Naive Bayes model with experimentally validated effectors (positive dataset of 68 sequences from 19 species) and non-effector protein sequences (negative dataset of 68 sequences from 7 species) that were not part of the training data returned an excellent Aroc of 93%, demonstrating the utility of the model for prediction of effectors. The model has been integrated in T3SEdb as prediction tool to allow users to scan thier sequences of interest against the model for presence of functional signals indicative of a T3SE.

The model will be updated periodically as more experimentally verified effector sequence data are deposited in T3SEdb and may include more features to discriminate effectors from non-effectors as the database records get enriched with more annotations.

*Click here for alternative prediction using a BayesNet model

Enter your query sequence here to perform a prediction:
- Please input a gram-negative bacterial raw protein sequence (One sequence at a time in single letter code)
- Please enter N-terminal sequences of 100 amino-acids or longer

Sample N-terminal effector sequences (truncated) Sample N-terminal non-effector sequences (truncated)
Click following sample sequence to copy into textbox Click following sample sequence to copy into textbox
>Q6LAD6|P. syringae | avrRpt2
>YP_002280912|R. leguminosarum | Methyltransferase type 11
MKIAPVAINHSPLSREVPSHAAPTQAKQTNLQSEAGDLD
ARKSSASSPETRALLATKTVLGRHKIEVPAFGGWFKKKS
SKHETGGSSANADSSSVASDSTEKPLFRLTHVPYVSQG
NERMGCWYACARMVGHSVEAGPRLGLPELYEGREGPA
GLQDFSDVERFIH
MTISADIENGAPATSAPPFDEGMAELYQTLLVPILFAPYA
TEMAIAADQSKPGSVLELAAGTGALTRALRATLDPPTEI
VATDLSQAMIDIGAPTVTMSRTHWMHADAQNLPFAPEM
FDLVICQFGAMFFPDKVKAYSEAERVLRSKGRFLFSTW
DSLSV
 
>1G4U_S|S. typhimurium | Secreted effector protein sptP
>EDR31828|Y. pestis | Transporter, major facilitator family
NDVGAESKQPLLDIALKGLKRTLPQLEQMDGNSLRENFQ
EMASGNGPLRSLMTNLQNLNKIPEAKQLNDYVTTLTNIQV
GVARFSQWGTCGGEVERWVDKASTHELTQAVKKIHVIA
KELKNVTAELEKIEAGAPMPQTMSGPTLGLARFAVS
MALVSQARSLGKYFLLFDNLLVVLGFFVVFPLISIRFVD
QLGWAALVVGLALGLRQLVQQGLGIFGGAIADRFGAK
PMIVTGMLMRAAGFALMAMADEPWILWLACALSGLGG
TLFDPPRTALVIKLTRPHERGRFYSLLMMQDSAGAVI
 
>AAS48654|X. oryzae | Leucine rich hrp associated protein
>YP_003365619|C. rodentium | N-assimilation regulatory protein
MFNINRLLRSRPQTDNADQAPAQDRPSRQPSPAQGLLSPL
LARPRRRESRSAADTSTPRNAAQGRFSRSPLHPSSQPEA
LAGASSAPPRSIEHDIDDWLAQSLPMAERIPTGYNLHDGS
RDTSRDVLQSAAEAIRRAATRRSTELLVDGLPATR
MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATL
EGELNQQLLIRTKRGVTPTEAGKILYAHARTILRQCEQAQ
LAVVNVGQTLTGQVSIGLAPGTAASSVTMPLLQAVRA
ELPEVLVYLHENSGAVLNDKIMSGQLDMAVLYER
 
Indeterminate prediction of effector status
Click following sample sequence to copy into textbox
>2J0N_A|S. flexneri | Invasin ipaD
ELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLY
PANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKN
 
Click following sample sequence to copy into textbox
>Q500C1|P. syringae | Regulator of nucleoside diphosphate kinase
MTTAPSIILTRLDVQRLEKFIADQNEDTPGIQALQAELDRADQVVGHDEVPAGVVTMNSRVHCREEVSGK
DYHLKLVYPQDAGADGTVSVLAPMGSALLGLQIGQHIDWPAPGGKTLKLTLLAVEYQPEAAGEYE