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

NucPred

Fetching Q9UKV3 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MWRRKHPRTSGGTRGVLSGNRGVEYGSGRGHLGTFEGRWRKLPKMPEAVG    50
  51  TDPSTSRKMAELEEVTLDGKPLQALRVTDLKAALEQRGLAKSGQKSALVK   100
 101  RLKGALMLENLQKHSTPHAAFQPNSQIGEEMSQNSFIKQYLEKQQELLRQ   150
 151  RLEREAREAAELEEASAESEDEMIHPEGVASLLPPDFQSSLERPELELSR   200
 201  HSPRKSSSISEEKGDSDDEKPRKGERRSSRVRQARAAKLSEGSQPAEEEE   250
 251  DQETPSRNLRVRADRNLKTEEEEEEEEEEEEDDEEEEGDDEGQKSREAPI   300
 301  LKEFKEEGEEIPRVKPEEMMDERPKTRSQEQEVLERGGRFTRSQEEARKS   350
 351  HLARQQQEKEMKTTSPLEEEEREIKSSQGLKEKSKSPSPPRLTEDRKKAS   400
 401  LVALPEQTASEEETPPPLLTKEASSPPPHPQLHSEEEIEPMEGPAPAVLI   450
 451  QLSPPNTDADTRELLVSQHTVQLVGGLSPLSSPSDTKAESPAEKVPEESV   500
 501  LPLVQKSTLADYSAQKDLEPESDRSAQPLPLKIEELALAKGITEECLKQP   550
 551  SLEQKEGRRASHTLLPSHRLKQSADSSSSRSSSSSSSSSRSRSRSPDSSG   600
 601  SRSHSPLRSKQRDVAQARTHANPRGRPKMGSRSTSESRSRSRSRSRSASS   650
 651  NSRKSLSPGVSRDSSTSYTETKDPSSGQEVATPPVPQLQVCEPKERTSTS   700
 701  SSSVQARRLSQPESAEKHVTQRLQPERGSPKKCEAEEAEPPAATQPQTSE   750
 751  TQTSHLPESERIHHTVEEKEEVTMDTSENRPENDVPEPPMPIADQVSNDD   800
 801  RPEGSVEDEEKKESSLPKSFKRKISVVSATKGVPAGNSDTEGGQPGRKRR   850
 851  WGASTATTQKKPSISITTESLKSLIPDIKPLAGQEAVVDLHADDSRISED   900
 901  ETERNGDDGTHDKGLKICRTVTQVVPAEGQENGQREEEEEEKEPEAEPPV   950
 951  PPQVSVEVALPPPAEHEVKKVTLGDTLTRRSISQQKSGVSITIDDPVRTA  1000
1001  QVPSPPRGKISNIVHISNLVRPFTLGQLKELLGRTGTLVEEAFWIDKIKS  1050
1051  HCFVTYSTVEEAVATRTALHGVKWPQSNPKFLCADYAEQDELDYHRGLLV  1100
1101  DRPSETKTEEQGIPRPLHPPPPPPVQPPQHPRAEQREQERAVREQWAERE  1150
1151  REMERRERTRSEREWDRDKVREGPRSRSRSRDRRRKERAKSKEKKSEKKE  1200
1201  KAQEEPPAKLLDDLFRKTKAAPCIYWLPLTDSQIVQKEAERAERAKEREK  1250
1251  RRKEQEEEEQKEREKEAERERNRQLEREKRREHSRERDRERERERERDRG  1300
1301  DRDRDRERDRERGRERDRRDTKRHSRSRSRSTPVRDRGGRR           1341

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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