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

NucPred

Fetching P15442 from www.uniprot.org...

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

   1  MSLSHLTLDQYYEIQCNELEAIRSIYMDDFTDLTKRKSSWDKQPQIIFEI    50
  51  TLRSVDKEPVESSITLHFAMTPMYPYTAPEIEFKNVQNVMDSQLQMLKSE   100
 101  FKKIHNTSRGQEIIFEITSFTQEKLDEFQNVVNTQSLEDDRLQRIKETKE   150
 151  QLEKEEREKQQETIKKRSDEQRRIDEIVQRELEKRQDDDDDLLFNRTTQL   200
 201  DLQPPSEWVASGEAIVFSKTIKAKLPNNSMFKFKAVVNPKPIKLTSDIFS   250
 251  FSKQFLVKPYIPPESPLADFLMSSEMMENFYYLLSEIELDNSYFNTSNGK   300
 301  KEIANLEKELETVLKAKHDNVNRLFGYTVERMGRNNATFVWKIRLLTEYC   350
 351  NYYPLGDLIQSVGFVNLATARIWMIRLLEGLEAIHKLGIVHKCINLETVI   400
 401  LVKDADFGSTIPKLVHSTYGYTVLNMLSRYPNKNGSSVELSPSTWIAPEL   450
 451  LKFNNAKPQRLTDIWQLGVLFIQIISGSDIVMNFETPQEFLDSTSMDETL   500
 501  YDLLSKMLNNDPKKRLGTLELLPMKFLRTNIDSTINRFNLVSESVNSNSL   550
 551  ELTPGDTITVRGNGGRTLSQSSIRRRSFNVGSRFSSINPATRSRYASDFE   600
 601  EIAVLGQGAFGQVVKARNALDSRYYAIKKIRHTEEKLSTILSEVMLLASL   650
 651  NHQYVVRYYAAWLEEDSMDENVFESTDEESDLSESSSDFEENDLLDQSSI   700
 701  FKNRTNHDLDNSNWDFISGSGYPDIVFENSSRDDENEDLDHDTSSTSSSE   750
 751  SQDDTDKESKSIQNVPRRRNFVKPMTAVKKKSTLFIQMEYCENRTLYDLI   800
 801  HSENLNQQRDEYWRLFRQILEALSYIHSQGIIHRDLKPMNIFIDESRNVK   850
 851  IGDFGLAKNVHRSLDILKLDSQNLPGSSDNLTSAIGTAMYVATEVLDGTG   900
 901  HYNEKIDMYSLGIIFFEMIYPFSTGMERVNILKKLRSVSIEFPPDFDDNK   950
 951  MKVEKKIIRLLIDHDPNKRPGARTLLNSGWLPVKHQDEVIKEALKSLSNP  1000
1001  SSPWQQQVRESLFNQSYSLTNDILFDNSVPTSTPFANILRSQMTEEVVKI  1050
1051  FRKHGGIENNAPPRIFPKAPIYGTQNVYEVLDKGGTVLQLQYDLTYPMAR  1100
1101  YLSKNPSLISKQYRMQHVYRPPDHSRSSLEPRKFGEIDFDIISKSSSESG  1150
1151  FYDAESLKIIDEILTVFPVFEKTNTFFILNHADILESVFNFTNIDKAQRP  1200
1201  LVSRMLSQVGFARSFKEVKNELKAQLNISSTALNDLELFDFRLDFEAAKK  1250
1251  RLYKLMIDSPHLKKIEDSLSHISKVLSYLKPLEVARNVVISPLSNYNSAF  1300
1301  YKGGIMFHAVYDDGSSRNMIAAGGRYDTLISFFARPSGKKSSNTRKAVGF  1350
1351  NLAWETIFGIAQNYFKLASGNRIKKRNRFLKDTAVDWKPSRCDVLISSFS  1400
1401  NSLLDTIGVTILNTLWKQNIKADMLRDCSSVDDVVTGAQQDGIDWILLIK  1450
1451  QQAYPLTNHKRKYKPLKIKKLSTNVDIDLDLDEFLTLYQQETGNKSLIND  1500
1501  SLTLGDKADEFKRWDENSSAGSSQEGDIDDVVAGSTNNQKVIYVPNMATR  1550
1551  SKKANKREKWVYEDAARNSSNMILHNLSNAPIITVDALRDETLEIISITS  1600
1601  LAQKEEWLRKVFGSGNNSTPRSFATSIYNNLSKEAHKGNRWAILYCHKTG  1650
1651  KSSVIDLQR                                           1659

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.)

Go back to the NucPred Home Page.