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

NucPred

Fetching Q3UH53 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MARARPSVAGGGVAAPPERAGPGRPRRSRTGHHCDPECPGLRAAPRTPGP    50
  51  GAGRRAAKLRPGRGWWALLLLQLHLLRALAQDDVAPYFKTEPGLPQIHLE   100
 101  GNRLVLTCLAEGSWPLEFKWIRNDSELTTYSSEYKYIIPSLQKLDAGFYR   150
 151  CVVRNRMGALLQRKSEIQVAYMGNFMDTDQRKTVSQGHAALLNLLPIVSC   200
 201  PQPQVTWFREGHKIIPSSRIAITLENQLVILATTASDAGAYYVQAVNEKN   250
 251  GENKTSPFIHLSVARDTGTHEAMAPIIVVAPGNRSVVAGSSETTLECIAN   300
 301  ARPVEELSVHWKRNGVRLTSGLHSYGRRLTITNPTSADTGMYVCEATLRG   350
 351  STFEPARARAFLSIIEPPYFTAEPESRILGEVEETMDIPCRAMGVPLPTL   400
 401  QWYKDAVPLSKLQNPRYKVLPSGGLHIQKLSPEDSGIFQCFASNEGGEVQ   450
 451  THTYLDVTNIAPAFTQRPVDTTVTDGMTAVLRCEVSGAPKPAITWKRGNH   500
 501  ILASGSVRIPRFMLLESGGLRIAPVFIQDAGNYTCYAANTEASVNASAML   550
 551  TVWNRTSIVHPPEDRVVIKGTTATLCCGATHDPRTSLRYVWKKDNVVITA   600
 601  SSSSRIVVEKDGSLVISQTWSGDIGDYTCEIISEGGSDSRTARLEVIELP   650
 651  HPPQNLLASLSPARSHSVTLSWVRPFDGNSPVLYYIVQVSENNSPWKVHL   700
 701  SNVGPEMTGVTVSGLTPARTYQFRVCAVNQVGKGQYSTETSRLMLPEEPP   750
 751  SAPPKNIVASGRTNQSIMVQWQPPPETEHNGVLRGYILRYRLAGLPGEHQ   800
 801  QRNISSPEVNYCLVTDLIIWTQYEIQVAAYNGAGLGVFSRAVTEYTLQGV   850
 851  PTAPPQNVQAEAVNSTTVHFLWNPPPQQFINGINQGYKLLAWPADAPETV   900
 901  TVVTIAPDFHGIHHGYITNLKKFTAYFTSVLCFTTPGDGPPSSPQLVWTH   950
 951  EDKPGAVGHLSFTEILDTSLKVSWQEPLERNGIIMGYQISWEVYGRNDSR  1000
1001  LTHTLNSTMHEYKIQGLSSLTTYTIDVAALTAAGVGVTTSSTISSGVPPD  1050
1051  LPGAPSNLVISNISPRSATLQFRPGYDGKTAICRWIVEGQVGAIGDEEEW  1100
1101  VTLYEEENEPDAQMLEIPNLTPYTHYRFRMRQVNIVGPSPFSQSSRVIQT  1150
1151  LQAPPDVAPTSLTVRTASETSLRLRWVPLPDSQYNGNPESVGYRVKYWRS  1200
1201  DQPSSALAQVVSDRLERELTIEELEEWTEYELRMQAFNAIGAGPWSELVR  1250
1251  GRTRESVPSAAPENVSAEAVSSTQILLTWASVPEQDQNGLILGYKVLYCA  1300
1301  KDLDPEPRSHVVRGNHTQSALLAGLRKFVVYELQVLAFTRIGNGVPSSPL  1350
1351  ILERTKDDTPGPPVRLVFPEVRLTAVRIVWQPPEEPNGVILGYQIAYRLA  1400
1401  SGSPHTFTTVEVGATVRQFTATELAPESAYIFRLSAKTRQGWGEPLEATV  1450
1451  ITTEKRERPAPPRELLVPQAEVTARSLRLQWVPGSDGASPIRYFTVQVRE  1500
1501  LPGGEWQTYSSSISHEATACAVERLRPFTSYKLRLKATNDIGDSDFSAET  1550
1551  EAVTTLQDVPGEPPGSVSATPHTTSSVLIQWQPPRDESLNGLLQGYRIYY  1600
1601  RELESETGMSPEPKTLKSPSALRAELTAQSSFKTVNSSSSLTTYELTHLK  1650
1651  KYRRYEVIMTAYNIIGESPASVPVEVFVGEAAPAMAPQNVQVTPLTASQL  1700
1701  EVTWDPPPPESQNGNIQGYKVYYWEADSRNETEKMKVLFLPEPVVKIKDL  1750
1751  TSHTKYLISISAFNAAGDGPKSDPCQGRTHQAAPGPPSFLAFSEITSTTL  1800
1801  NVSWGEPSAANGILQGYRVVYEPLAPVQGVSKVVTVDVKGNWQRWLKVRD  1850
1851  LTKGVTYFFRVQARTIAYGPELQANVTAGPAEGSPGSPRNVLVTKSASEL  1900
1901  TLQWTEGNAGTTPTTGYVIEARPSDEGLWDMFAKDIPRSATSYTVDLDKL  1950
1951  RQGVTYEFRVVAVNKAGFGEPSRPSIAVSAQAEAPFYEEWWFLLVMALSS  2000
2001  LLLILLVVFVLVLHGQSKKYKSCSTGKGISNMEETVTLDNGGFAALELNS  2050
2051  RHLNVKSTFSKKNGTRSPPRPSPGGLHYSDEDICNKYNGAVLTESVNLKE  2100
2101  KSVDGSESEASDSDYEEALPKHSFVNHYMSDPTYYNSWKRRPPAAAPHRY  2150
2151  EAVAGAEAGPHLHTVITTQSAGGVYTPAGPGARAPLTGFSSFV         2193

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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