Information and Help......!!!



Frequently asked questions (FAQs)???


General information about Efflux Mechanism:-

Efflux is a mechanism responsible for moving compounds, like neurotransmitters, toxic substances, and antibiotics, out of the cell; this is considered to be a vital part of xenobiotic metabolism. This mechanism is important in medicine as it can contribute to bacterial antibiotic resistance.

Stepwise Help: How to Use

Query title:

This is an optional field. User may or may not enter the title of the query.

Input Sequence Format:

Users may select the input sequence format as a FASTA format

Query Sequence(s):

BacEffluxPred process only protein sequence file (fasta file). Users have option to cut and paste in the text box or directly upload the sequence file. The limits of BacEffluxPred is maximum 5 sequences at a time. If user submit more than 5 sequences, BacEffluxPred predict only first 5 sequences. Following figure 1 is an example showing how to submit a query in BacEffluxPred.

SVM Threshold Value:

User also have the option to set the threshold. If user select high threshold, the number of prediction will be low but rate of false positive prediction will also be low. If the user select low threshold, the number of prediction will be high and the false positive prediction will also be high.

Example Sequences:
>1120928.3.peg.3378_RND MSISRKQLTLSAVIVAIFATGGSFILFQEKADAKATPTASAAPAATVDVANVISQTITDWQEYSGRLEAIDQVDVRPQVSGKLIAVHFKD GSLVNKGDLLFTIDPRPFEAELNRAKAQLASAEAQVTYSSANLGRNQRLIQSNAIAHQELDQAENEARSANANLQAAKAAVETARLNLEY TRITAPVSGRISRAEVTVGNVVSAGNGAQVLTSLVSVSRLYASFDVDEQTYLKYISNQRNSAQVPVYLGLANESGFSREGFISSIDNNLN TTSGTIRVRATFDNPKGVMLPGLYARIRLGGGQPRAAILISPTAIGVDQDKRFVVVVDAKNQTAYREVKLGAQQDGLQIINSGLQVGDRI VVNGLQRIRPGDPVSPHLVSMPNPQIITDNTAQQPQPTEKTPTSAKG

>Q3B5J7_ABC MAPTTPLLELVDVHRTYPVGESTVNALRGVSLEIREGEFVAIMGSSGSGKSSLLHILGLLDNPDRGEYRILGRNVNALPEDGQAGLRNHV AGFVFQQFHLLKRMSIVDNVRLPHIYSGLKGDFRHEALESLKKVGLMHRLDHTPGQLSGGEQQRVAIARALIGNPMILFADEPTGNLDSR NSLEIMKILEELHREGRTIVMVTHEDEIAAYADRVITMRDGLVVSDQRRDRVCLPAGPSVPLTLDPHAMMDASRNLSVWQDGRFIGFVQQ AFQSIFANKVRSLLSVLGILVGVASVIAMMALGEGAKVSIEEELKSMGSNLISVRGGSARVRGAAQGDGAVARFTFKDVKDISRMHSLVK GAAGTVNGSGQIVFGNRNWSTTLDGVGYEYGSMRAFVPSIGRWFTRDEIRKREKVAVIGVTVARELFGNNNPIGHTVKINRINFKVIGIA PAKGFSTHRDQDDVVLVPVTTAMYRVLGRDYLNSIYVEVRSAEGIDGAKEAVSDLIVKNHRLREGDDSFNIRDMTEIQEMLSSTTRTMSM LLGAIAAISLLVGGIGIMNIMLVSVTERTREIGLRKAIGARREDIMLQFLVESVGLTLSGGIIGIIAGIGISALLAVFAGWAVKTSIVSI VLATFFSAITGIFFGLWPARKAAELRPVEALRYE

>Q9KEJ2_MATE MKPTETLQEKGKLFLVVMMPILITQIGLYAMNFFDTVMSGQAGANDLAGVAIGSSLWVPVFTGLNGVLLALTPIIAQSIGAEKRDDVPYVF LQGLYLSIAISIAVILIGAVVLDPILSAMSLEDEVGRIAKEYLIGLAFGIVPLFIYTTIRCLIDSLGETRVTMFITLLSLPINIFFNYVLI FGKLGFPRLGGVGAGYASAITYWFILAVAIVVVVKVRPFTDFQLFKKLYHVSLKKWKEILLLGLPIGFTIFFETSIFAAVTLLMSTFDTAT IAAHQAAVNFASFLYMIPLSIAFTLTIAVGYEVGAKRVEDARQYSRLGITFALIMGLVAGVIIYVLRAPVASLYTNDSQVAWLIQQFLIYS IFFQLSDALATPIQGVLRGHKDVNVPFVMALVSFWIIGLPTGYLLANFSPLGPYGYWIGLITGLASCAIALSWRLKQMQRKFERAARLSQNGNS

>1006000.3.peg.2818_MFS MIKSSPHCGRFLSLLAQFLDIYSYKPNFYKVISEMKRDRNVNILVMLVLLVAVGQMAQTIYIPAIAQMANDLNVREGAVQSVMAAYLLTYG VSQLFYGPLSDRVGRRPVILVGMSIFMLATLVAITTHSLTVLIIASAMQGMGTGVGGVMARTLPRDLYEGSQLRHANSLLNMGILVSPLLAP LIGGVLETLINWRACYGFLLVLCAGVTFSMARWMPETRPTGAPKTRLISNYKTLFGNSGFNCYLLMLIGGLAGIAVFEASSGVLMGGVLGLS SMTVSILFILPIPAAFFGAWFAGRPKKRFPTLMWQSVVCCLAAGVMMWIPGLLGVMNIWTLLVPAALFFFGAGMLFPLATSGAMEPFPFLAG TAGALVGGLQNIGSGVLAWLSAMMPQTGQASIGLLMTLMGLLIFLCWLPLASRFAHQGQAV


Figure 1. BacEffluxPred submission page showing how to insert input sequences and select the threshold.


Prediction Result:

In response to the submitted protein sequence(s), BacEffluxPred generates theprediction result in tabular form. The prediction results are shown in user-friendly format. The prediction results provides information at two separate tiers for classifying bacterial efflux/non-efflux conferring AR proteins i.e. the predicted sequence belong to bacterial efflux conferring AR class or not (tier-I). At tier-II, it predicts those predicted sequence belongs to which sub-family. When you submit a job then we also provide a job number, if user have any query regarding their result, he/she can contact us. Here is a sample of prediction done in response to query sequences (Figure 2).

Figure 2. Screenshot of BacEffluxPred prediction result.
Citing BacEffluxPred: Pandey D, Kumari B, Singhal N, Kumar M (2020) BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins. Scientific Reports 10:9287; https://doi.org/10.1038/s41598-020-65981-3



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