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

NucPred

Fetching P21519 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MDAGGLPVFQSASQAAAVAQQQQQQQQQQQQHLNLQLHQQHLGLHLQQQQ    50
  51  QLQLQQQQHNAQAQQQQIQVQQQQQQQQQQQQQQHSPYNANLGATGGIAG   100
 101  ITGGNGAGGPTNPGAVPTAPGDTMPTKRMPVVDRLRRRMENYRRRQTDCV   150
 151  PRYEQAFNTVCEQQNQETTVLQKRFLESKNKRAAKKTDKKLPDPSQQHQQ   200
 201  QQHQQQQQHQQHQQHQQAQTMLAGQLQSSVHVQQKFLKRPAEDVDNGPDS   250
 251  FEPPHKLPNNNNNSNSNNNNGNANANNGGNGSNTGNNTNNNGNSTNNNGG   300
 301  SNNNGSENLTKFSVEIVQQLEFTTSAANSQPQQISTNVTVKALTNTSVKS   350
 351  EPGVGGGGGGGGGGGSGNNNNNGGGGGGGNGNNNNNGGDHHQQQHQQQQQ   400
 401  QQGGGLGGLGNNGRGGGPGGMATGPGGVAGGLGGMGMPPNMMSAQQKSAL   450
 451  GNLANLVECKREPDHDFPDLGSLDKDGGGGQFPGFPDLLGDDNSENNDTF   500
 501  KDLINNLQDFNPSFLDGFDEKPLLDIKTEDGIKVEPPNAQDLINSLNVKS   550
 551  EGGLGHGFGGFGLGLDNPGMKMRGGNPGNQGGFPNGPNGGTGGAPNAGGN   600
 601  GGNSGNLMSEHPLAAQTLKQMAEQHQHKNAMGGMGGFPRPPHGMNPQQQQ   650
 651  QQQQQQQQQQAQQQHGQMMGQGQPGRYNDYGGGFPNDFGLGPNGPQQQQQ   700
 701  AQQQQPQQQHLPPQFHQQKGPGPGAGMNVQQNFLDIKQELFYSSQNDFDL   750
 751  KRLQQQQAMQQQQQQQHHQQQQQQQQPKMGGVPNFNKQQQQQQVPQQQLQ   800
 801  QQQQQQQQQQQQQQQQYSPFSNQNPNAAANFLNCPPRGGPNGNQQPGNLA   850
 851  QQQQQPGAGPQQQQQRGNAANGQQNNPNAGPGGNTPNAPQQQQQQSTTTT   900
 901  LQMKQTQQLHISQQGGGAHGIQVSAGQHLHLSGDMKSNVSVAAQQGVFFS   950
 951  QQQAQQQQQQQQPGGTNGPNPQQQQQQPHGGNAGGGVGVGVGVGVGNGGP  1000
1001  NPGQQQQQPNQNMSNANVPSDGFSLSQSQSMNFNQQQQQQAAAQQQQVQP  1050
1051  NMRQRQTQAQAAAAAAAAAAQAQAAANASGPNVPLMQQPQVGVGVGVGVG  1100
1101  VGVGVGNGGVVGGPGSGGPNNGAMNQMGGPMGGMPGMQMGGPMNPMQMNP  1150
1151  NAAGPTAQQMMMGSGAGGPGQVPGPGQGPNPNQAKFLQQQQMMRAQAMQQ  1200
1201  QQQHMSGARPPPPEYNATKAQLMQAQMMQQTVGGGGVGVGGVGVGVGVGG  1250
1251  VGGANGGRFPNSAAQAAAMRRMTQQPIPPSGPMMRPQHAMYMQQHGGAGG  1300
1301  GPRTGMGVPYGGGAGGPMGGPQQQQRPPNVQVTPDGMPMGSQQEWRHMMM  1350
1351  TQQQTQMGFGGPGPGGPMRQGPGGFNGGNFMPNGAPNGAAGSGPNAGGMM  1400
1401  SGPNVPQMQLTPAQMQQQLMRQQQQQQQQQQQHMGPGAANNMQMQQLLQQ  1450
1451  QQSGGGGNMMASQMQMTSMHMTQTQQQITMQQQQQFVQSTTTTTHQQQQM  1500
1501  MQMGPGGGGGGGGPGSANNNNGGGGGGAAGGGNSASTIASASSISQTINS  1550
1551  VVANSNDFGLEFLDNLPVDSNFSTQDLINSLDNDNFNLQDFNMP        1594

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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