SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching P55196 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MSAGGRDEERRKLADIIHHWNANRLDLFEISQPTEDLEFHGVMRFYFQDK    50
51 AAGNFATKCIRVSSTATTQDVIETLAEKFRPDMRMLSSPKYSLYEVHVSG 100
101 ERRLDIDEKPLVVQLNWNKDDREGRFVLKNENDAIPPKKAQSNGPEKQEK 150
151 EGVIQNFKRTLSKKEKKEKKKREKEALRQASDKDDRPFQGEDVENSRLAA 200
201 EVYKDMPETSFTRTISNPEVVMKRRRQQKLEKRMQEFRSSDGRPDSGGTL 250
251 RIYADSLKPNIPYKTILLSTTDPADFAVAEALEKYGLEKENPKDYCIARV 300
301 MLPPGAQHSDEKGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPDH 350
351 IPKKTKKHLEGKTPKGKERADGSGYGSTLPPEKLPYLVELSPGRRNHFAY 400
401 YNYHTYEDGSDSRDKPKLYRLQLSVTEVGTEKLDDNSIQLFGPGIQPHHC 450
451 DLTNMDGVVTVTPRSMDAETYVEGQRISETTMLQSGMKVQFGASHVFKFV 500
501 DPSQDHALAKRSVDGGLMVKGPRHKPGIVQETTFDLGGDIHSGTALPTSK 550
551 STTRLDSDRVSSASSTAERGMVKPMIRVEQQPDYRRQESRTQDASGPELI 600
601 LPASIEFRESSEDSFLSAIINYTNSSTVHFKLSPTYVLYMACRYVLSNQY 650
651 RPDISPTERTHKVIAVVNKMVSMMEGVIQKQKNIAGALAFWMANASELLN 700
701 FIKQDRDLSRITLDAQDVLAHLVQMAFKYLVHCLQSELNNYMPAFLDDPE 750
751 ENSLQRPKIDDVLHTLTGAMSLLRRCRVNAALTIQLFSQLFHFINMWLFN 800
801 RLVTDPDSGLCSHYWGAIIRQQLGHIEAWAEKQGLELAADCHLSRIVQAT 850
851 TLLTMDKYAPDDIPNINSTCFKLNSLQLQALLQNYHCAPDEPFIPTDLIE 900
901 NVVTVAENTADELARSDGREVQLEEDPDLQLPFLLPEDGYSCDVVRNIPN 950
951 GLQEFLDPLCQRGFCRLIPHTRSPGTWTIYFEGADYESHLLRENTELAQP 1000
1001 LRKEPEIITVTLKKQNGMGLSIVAAKGAGQDKLGIYVKSVVKGGAADVDG 1050
1051 RLAAGDQLLSVDGRSLVGLSQERAAELMTRTSSVVTLEVAKQGAIYHGLA 1100
1101 TLLNQPSPMMQRISDRRGSGKPRPKSEGFELYNNSTQNGSPESPQLPWAE 1150
1151 YSEPKKLPGDDRLMKNRADHRSSPNVANQPPSPGGKSAYASGTTAKITSV 1200
1201 STGNLCTEEQTPPPRPEAYPIPTQTYTREYFTFPASKSQDRMAPPQNQWP 1250
1251 NYEEKPHMHTDSNHSSIAIQRVTRSQEELREDKAYQLERHRIEAAMDRKS 1300
1301 DSDMWINQSSSLDSSTSSQEHLNHSSKSVTPASTLTKSGPGRWKTPAAIP 1350
1351 ATPVAVSQPIRTDLPPPPPPPPVHYAGDFDGMSMDLPLPPPPSANQIGLP 1400
1401 SAQVAAAERRKREEHQRWYEKEKARLEEERERKRREQERKLGQMRTQSLN 1450
1451 PAPFSPLTAQQMKPEKPSTLQRPQETVIRELQPQQQPRTIERRDLQYITV 1500
1501 SKEELSSGDSLSPDPWKRDAKEKLEKQQQMHIVDMLSKEIQELQSKPDRS 1550
1551 AEESDRLRKLMLEWQFQKRLQESKQKDEDDEEEEDDDVDTMLIMQRLEAE 1600
1601 RRARLQDEERRRQQQLEEMRKREAEDRARQEEERRRQEEERTKRDAEEKR 1650
1651 RQEEGYYSRLEAERRRQHDEAARRLLEPEAPGLCRPPLPRDYEPPSPSPA 1700
1701 PGAPPPPPQRNASYLKTQVLSPDSLFTAKFVAYNEEEEEEDCSLAGPNSY 1750
1751 PGSTGAAVGAHDACRDAKEKRSKSQDADSPGSSGAPENLTFKERQRLFSQ 1800
1801 GQDVSNKVKASRKLTELENELNTK 1824

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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