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

NucPred

Fetching Q7PC87 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MLGRDEDLVRTMSGRGSLGSTSHRSLAGAASKSFRDVFAPPTDDVFGRSD    50
  51  RREEDDVELRWAALERLPTYDRLRKGMLPQTMVNGKIGLEDVDVTNLAPK   100
 101  EKKHLMEMILKFVEEDNEKFLRRLRERTDRVGIEVPKIEVRYENLSVEGD   150
 151  VRSASRALPTLFNVTLNTIESILGLFHLLPSKKRKIEILKDISGIIKPSR   200
 201  MTLLLGPPSSGKTTLLQALAGKLDDTLQMSGRITYCGHEFREFVPQKTCA   250
 251  YISQHDLHFGEMTVRESLDFSGRCLGVGTRYQLLTELSRREREAGIKPDP   300
 301  EIDAFMKSIAISGQETSLVTDYVLKLLGLDICADTLVGDVMRRGISGGQR   350
 351  KRLTTGEMLVGPATALFMDEISTGLDSSTTFQICKFMRQLVHIADVTMVI   400
 401  SLLQPAPETFELFDDIILLSEGQIVYQGSRDNVLEFFEYMGFKCPERKGI   450
 451  ADFLQEVTSKKDQEQYWNRREHPYSYVSVHDFSSGFNSFHAGQQLASEFR   500
 501  VPYDKAKTHPAALVTQKYGISNKDLFKACFDREWLLMKRNSFVYVFKTVQ   550
 551  ITIMSLIAMTVYFRTEMHVGTVQDGQKFYGALFFSLINLMFNGMAELAFT   600
 601  VMRLPVFFKQRDFLFYPPWAFALPGFLLKIPLSLIESVIWIALTYYTIGF   650
 651  APSAARFFRQLLAYFCVNQMALSLFRFLGALGRTEVIANSGGTLALLVVF   700
 701  VLGGFIISKDDIPSWLTWCYYTSPMMYGQTALVINEFLDERWGSPNNDTR   750
 751  INAKTVGEVLLKSRGFFTEPYWFWICIGALLGFTVLFNFCYIIALMYLNP   800
 801  LGNSKATTVVEEGKDKHKGSHSGTGGSVVELTSTSSHGPKKGMVLPFQPL   850
 851  SLAFNNVNYYVDMPAEMKAQGVEGDRLQLLRDVGGAFRPGVLTALVGVSG   900
 901  AGKTTLMDVLAGRKTGGYVEGSINISGYPKNQATFARVSGYCEQNDIHSP   950
 951  HVTVYESLIYSAWLRLSADIDTKTREMFVEEVMELVELKPLRNSIVGLPG  1000
1001  VDGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTV  1050
1051  DTGRTVVCTIHQPSIDIFESFDELLLMKRGGQVIYAGTLGHHSQKLVEYF  1100
1101  EAIEGVPKIKDGYNPATWMLDVTTPSMESQMSVDFAQIFVNSSVNRRNQE  1150
1151  LIKELSTPPPGSNDLYFRTKYAQPFSTQTKACFWKMYWSNWRYPQYNAIR  1200
1201  FLMTVVIGVLFGLLFWQTGTKIEKEQDLNNFFGAMYAAVLFLGATNAATV  1250
1251  QPAVAIERTVFYREKAAGMYSAIPYAISQVAVEIMYNTIQTGVYTLILYS  1300
1301  MIGYDWTVVKFFWFYYYMLTCFVYFTLYGMMLVALTPNYQIAGICLSFFL  1350
1351  SFWNLFSGFLIPRPQIPIWWRWYYWASPVAWTLYGIITSQVGDRDSIVHI  1400
1401  TGVGDMSLKTLLKNGFGFDYDFLPVVAVVHIAWILIFLFAFAYGIKFLNF  1450
1451  QRR                                                 1453

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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