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

NucPred

Fetching Q00449 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MVKKEESRLPQAGDFQLKEGSVVDATRKYSYFDLFRYSTRCERFLLVVSL    50
  51  LVATAASAFIPYFMIIYGEFTSLLVDRTVGVGTSSPAFALPMFGGGQQLT   100
 101  NASKEENNQAIIDDATAFGIGSLVGSVAMFLLITLAIDLANRIALNQIDR   150
 151  IRKLFLEAMLRQDIAWYDTSSGSNFASKMTEDLDKLKEGIGEKIVIVVFL   200
 201  IMTFVIGIVSAFVYGWKLTLVVLSCVPFIIAATSVVARLQGSLAEKELKS   250
 251  YSDAANVVEEVFSGIRTVFAFSGQEKEKERFGKLLIPAENTGRKKGLYSG   300
 301  MGNALSWLIIYLCMALAIWYGVTLILDERDLPDRVYTPAVLVIVLFAVIM   350
 351  GAQNLGFASPHVEAIAVATAAGQTLFNIIDRPSQVDPMDEKGNRPENTAG   400
 401  HIRFEGIRFRYPARPDVEILKGLTVDVLPGQTVAFVGASGCGKSTLIQLM   450
 451  QRFYDPEAGSVKLDGRDLRTLNVGWLRSQIGVVGQEPVLFATTIGENIRY   500
 501  GRPSATQADIEKAARAANCHDFITRLPKGYDTQVGEKGAQISGGQKQRIA   550
 551  IARALVRQPQVLLLDEATSALDPTSEKRVQSALELASQGPTTLVVAHRLS   600
 601  TITNADKIVFLKDGVVAEQGTHEELMERRGLYCELVSITQRKEATEADEG   650
 651  AVAGRPLQKSQNLSDEETDDDEEDEEEDEEPELQTSGSSRDSGFRASTRR   700
 701  KRRSQRRKKKKDKEVVSKVSFTQLMKLNSPEWRFIVVGGIASVMHGATFP   750
 751  LWGLFFGDFFGILSDGDDDVVRAEVLKISMIFVGIGLMAGLGNMLQTYMF   800
 801  TTAGVKMTTRLRKRAFGTIIGQDIAYFDDERNSVGALCSRLASDCSNVQG   850
 851  ATGARVGTMLQAVATLVVGMVVGFVFSWQQTLLTLVTLPLVCLSVYLEGR   900
 901  FIMKSAQKAKASIEEASQVAVEAITNIRTVNGLCLERQVLDQYVQQIDRV   950
 951  DIACRRKVRFRGLVFALGQAAPFLAYGISMYYGGILVAEERMNYEDIIKV  1000
1001  AEALIFGSWMLGQALAYAPNVNDAILSAGRLMDLFKRTSTQPNPPQSPYN  1050
1051  TVEKSEGDIVYENVGFEYPTRKGTPILQGLNLTIKKSTTVALVGPSGSGK  1100
1101  STCVQLLLRYYDPVSGSVNLSGVPSTEFPLDTLRSKLGLVSQEPVLFDRT  1150
1151  IAENIAYGNNFRDDVSMQEIIEAAKKSNIHNFISALPQGYDTRLGKTSQL  1200
1201  SGGQKQRIAIARALVRNPKILILDEATSALDLESEKVVQQALDEARSGRT  1250
1251  CLTIAHRLTTVRNADLICVLKRGVVVEHGTHDELMALNKIYANLYLMQQV  1300
1301  SG                                                  1302

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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