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

NucPred

Fetching Q6V3V8 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MSLGDVKEQLRGSRTEAKNAAKLIQVQFERVRNGGTTSVALRALKYELNI    50
  51  LRQLCCALQENFHQHADIYCDIAADMLPHVAPHLPQPDYWVNHLMSLQYI   100
 101  HHALCREQTIKQCQRFYELINAQSCQMQNKSEYKYYIDIHIRHVYFFGHQ   150
 151  LGKQSAASEAKAQLCQALQALGKLLENMLQLKAEQNEGYSELMGELNQLL   200
 201  GKRSIGYLKNLASLPLTAMNRLWKPLFKLIACNGGTTDQLNAQFSEYLSA   250
 251  LLALLQLDDNVWQLQQSEAQAQTPLSLQLLHSCRELYKNQTAQNNVLQLL   300
 301  YNYLKLLNTQSADLKRSYIDLAKKFVHFFEHKAVSHVQEQWYLDFLFVLV   350
 351  RVQKHLHQIDNKVPSLERFWQCLGGQDSATAYAAHFELLQCLTSRVMKIG   400
 401  RGSPLAASCSGNDASCPSVLKHCVFTLGCCATVAYSSWQPEAQATLPKAS   450
 451  QLCLASIIHYAIDVAKVTKCLTPNSSELVTFAWYLINMAEKVTTATQMYL   500
 501  LEHLLKPLQELRPLLSPPYAQQLVRRLFKASAHSSNPELSALLHGAYIVS   550
 551  MSCPARQFQQLCVFYHTPKNDTEQCLLELCEKSPLCSPLNATEKRKLYEL   600
 601  DMLAVLANKKTPKLLQSLLRHCQTDYQMVLLGRQMRTDKRSAGQQIEELR   650
 651  VRLQRLGRKQQLTRLQQLILGHATVTKLLEAAETQKIKIHIKEMTEKTLE   700
 701  VLLVKYKLFDLTISSEMPLLELATTAIGAFESFYEQADAEPLSSDEALID   750
 751  WEALIDDGIAAAMALSTMGYIPQADNAWLLLLRICRLLGDRFNYLRALSH   800
 801  FLPRYTQHALFDLPAEVSHAEQLLDELWPQLHAAHLLKRHHTTVLLCLCN   850
 851  LALYYARLDCVRHAQLLLLHAQRLRLEFEERAGKCDIIQLTIQTVRFRMC   900
 901  YQQRHCRSLARLPTALQQLDTLTESVRSFTCISSMDNGALILLLGDMVRD   950
 951  TTECTANRLSELPNFSNSLLQLLLQSGLVLRAVELLISWLWTNLRMECLD  1000
1001  KAHSKLRLIEHFLGMQPLLESRAALEQTSNKGSLTLAPMDAQSKHMTELV  1050
1051  GKMLVMQLEQSGACVEPIRKQQQLTMSSPRRELPLPSARPKLQRYVSLDM  1100
1101  QQSHPMLRSSVQLQCIYFMAGCLHARLYFLNREHEQLDDFYALANAWLQQ  1150
1151  NAARGNALGHMLLVLHIYQANYLRARRRQQQAIELTETALKLAGSEQLQQ  1200
1201  RIDVNYRYNLLLQLRTAQLELEPPSKPQNPRRALTFNISPEEKLPRPVRK  1250
1251  VATASKKPAKFAIYTEDVRPASSTTSSSSSSSSSENASSPERKSTKSKSP  1300
1301  KRLDLNACQLIDIIDLSDDETEAVVQLQPAKSTSALSTRSTRTRAQRQPD  1350
1351  TLVAPLRRTATAPNPLSAEATPKTIGTRARARRQNTAEQPTTTTTATPKV  1400
1401  DSVSSRRRHRN                                         1411

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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