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

NucPred

Fetching P13368 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MTMFWQQNVDHQSDEQDKQAKGAAPTKRLNISFNVKIAVNVNTKMTTTHI    50
  51  NQQAPGTSSSSSNSQNASPSKIVVRQQSSSFDLRQQLARLGRQLASGQDG   100
 101  HGGISTILIINLLLLILLSICCDVCRSHNYTVHQSPEPVSKDQMRLLRPK   150
 151  LDSDVVEKVAIWHKHAAAAPPSIVEGIAISSRPQSTMAHHPDDRDRDRDP   200
 201  SEEQHGVDERMVLERVTRDCVQRCIVEEDLFLDEFGIQCEKADNGEKCYK   250
 251  TRCTKGCAQWYRALKELESCQEACLSLQFYPYDMPCIGACEMAQRDYWHL   300
 301  QRLAISHLVERTQPQLERAPRADGQSTPLTIRWAMHFPEHYLASRPFNIQ   350
 351  YQFVDHHGEELDLEQEDQDASGETGSSAWFNLADYDCDEYYVCEILEALI   400
 401  PYTQYRFRFELPFGENRDEVLYSPATPAYQTPPEGAPISAPVIEHLMGLD   450
 451  DSHLAVHWHPGRFTNGPIEGYRLRLSSSEGNATSEQLVPAGRGSYIFSQL   500
 501  QAGTNYTLALSMINKQGEGPVAKGFVQTHSARNEKPAKDLTESVLLVGRR   550
 551  AVMWQSLEPAGENSMIYQSQEELADIAWSKREQQLWLLNVHGELRSLKFE   600
 601  SGQMVSPAQQLKLDLGNISSGRWVPRRLSFDWLHHRLYFAMESPERNQSS   650
 651  FQIISTDLLGESAQKVGESFDLPVEQLEVDALNGWIFWRNEESLWRQDLH   700
 701  GRMIHRLLRIRQPGWFLVQPQHFIIHLMLPQEGKFLEISYDGGFKHPLPL   750
 751  PPPSNGAGNGPASSHWQSFALLGRSLLLPDSGQLILVEQQGQAASPSASW   800
 801  PLKNLPDCWAVILLVPESQPLTSAGGKPHSLKALLGAQAAKISWKEPERN   850
 851  PYQSADAARSWSYELEVLDVASQSAFSIRNIRGPIFGLQRLQPDNLYQLR   900
 901  VRAINVDGEPGEWTEPLAARTWPLGPHRLRWASRQGSVIHTNELGEGLEV   950
 951  QQEQLERLPGPMTMVNESVGYYVTGDGLLHCINLVHSQWGCPISEPLQHV  1000
1001  GSVTYDWRGGRVYWTDLARNCVVRMDPWSGSRELLPVFEANFLALDPRQG  1050
1051  HLYYATSSQLSRHGSTPDEAVTYYRVNGLEGSIASFVLDTQQDQLFWLVK  1100
1101  GSGALRLYRAPLTAGGDSLQMIQQIKGVFQAVPDSLQLLRPLGALLWLER  1150
1151  SGRRARLVRLAAPLDVMELPTPDQASPASALQLLDPQPLPPRDEGVIPMT  1200
1201  VLPDSVRLDDGHWDDFHVRWQPSTSGGNHSVSYRLLLEFGQRLQTLDLST  1250
1251  PFARLTQLPQAQLQLKISITPRTAWRSGDTTRVQLTTPPVAPSQPRRLRV  1300
1301  FVERLATALQEANVSAVLRWDAPEQGQEAPMQALEYHISCWVGSELHEEL  1350
1351  RLNQSALEARVEHLQPDQTYHFQVEARVAATGAAAGAASHALHVAPEVQA  1400
1401  VPRVLYANAEFIGELDLDTRNRRRLVHTASPVEHLVGIEGEQRLLWVNEH  1450
1451  VELLTHVPGSAPAKLARMRAEVLALAVDWIQRIVYWAELDATAPQAAIIY  1500
1501  RLDLCNFEGKILQGERVWSTPRGRLLKDLVALPQAQSLIWLEYEQGSPRN  1550
1551  GSLRGRNLTDGSELEWATVQPLIRLHAGSLEPGSETLNLVDNQGKLCVYD  1600
1601  VARQLCTASALRAQLNLLGEDSIAGQLAQDSGYLYAVKNWSIRAYGRRRQ  1650
1651  QLEYTVELEPEEVRLLQAHNYQAYPPKNCLLLPSSGGSLLKATDCEEQRC  1700
1701  LLNLPMITASEDCPLPIPGVRYQLNLTLARGPGSEEHDHGVEPLGQWLLG  1750
1751  AGESLNLTDLLPFTRYRVSGILSSFYQKKLALPTLVLAPLELLTASATPS  1800
1801  PPRNFSVRVLSPRELEVSWLPPEQLRSESVYYTLHWQQELDGENVQDRRE  1850
1851  WEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNSSERLHVRSFA  1900
1901  ELPELQLLELGPYSLSLTWAGTPDPLGSLQLECRSSAEQLRRNVAGNHTK  1950
1951  MVVEPLQPRTRYQCRLLLGYAATPGAPLYHGTAEVYETLGDAPSQPGKPQ  2000
2001  LEHIAEEVFRVTWTAARGNGAPIALYNLEALQARSDIRRRRRRRRRNSGG  2050
2051  SLEQLPWAEEPVVVEDQWLDFCNTTELSCIVKSLHSSRLLLFRVRARSLE  2100
2101  HGWGPYSEESERVAEPFVSPEKRGSLVLAIIAPAAIVSSCVLALVLVRKV  2150
2151  QKRRLRAKKLLQQSRPSIWSNLSTLQTQQQLMAVRNRAFSTTLSDADIAL  2200
2201  LPQINWSQLKLLRFLGSGAFGEVYEGQLKTEDSEEPQRVAIKSLRKGASE  2250
2251  FAELLQEAQLMSNFKHENIVCLVGICFDTESISLIMEHMEAGDLLSYLRA  2300
2301  ARATSTQEPQPTAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCL  2350
2351  VTESTGSTDRRRTVKIGDFGLARDIYKSDYYRKEGEGLLPVRWMSPESLV  2400
2401  DGLFTTQSDVWAFGVLCWEILTLGQQPYAARNNFEVLAHVKEGGRLQQPP  2450
2451  MCTEKLYSLLLLCWRTDPWERPSFRRCYNTLHAISTDLRRTQMASATADT  2500
2501  VVSCSRPEFKVRFDGQPLEEHREHNERPEDENLTLREVPLKDKQLYANEG  2550
2551  VSRL                                                2554

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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