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

NucPred

Fetching O61213 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MRSKHVLYIAILFSSIFGGKGIQQNEEFQRYDGWYNNLANSEWGSAGSRL    50
  51  HRDARSYYSDGVYSVNNSLPSARELSDILFKGESGIPNTRGCTTLLAFFS   100
 101  QVVAYEIMQSNGVSCPLETLKIQVPLCDNVFDKECEGKTEIPFTRAKYDK   150
 151  ATGNGLNSPREQINERTSWIDGSFIYGTTQPWVSSLRSFKQGRLAEGVPG   200
 201  YPPLNNPHIPLNNPAPPQVHRLMSPDRLFMLGDSRVNENPGLLSFGLILF   250
 251  RWHNYNANQIHREHPDWTDEQIFQAARRLVIASMQKIIAYDFVPGLLGED   300
 301  VRLSNYTKYMPHVPPGISHAFGAAAFRFPHSIVPPAMLLRKRGNKCEFRT   350
 351  EVGGYPALRLCQNWWNAQDIVKEYSVDEIILGMASQIAERDDNIVVEDLR   400
 401  DYIFGPMHFSRLDVVASSIMRGRDNGVPPYNELRRTFGLAPKTWETMNED   450
 451  FYKKHTAKVEKLKELYGGNILYLDAYVGGMLEGGENGPGELFKEIIKDQF   500
 501  TRIRDGDRFWFENKLNGLFTDEEVQMIHSITLRDIIKATTDIDETMLQKD   550
 551  VFFFKEGDPCPQPFQVNTTGLEPCVPFMQSTYWTDNDTTYVFTLIGLACV   600
 601  PLICYGIGRYLVNRRIAIGHNSACDSLTTDFANDDCGAKGDIYGVNALEW   650
 651  LQEEYIRQVRIEIENTTLAVKKPRGGILRKIRFETGQKIELFHSMPNPSA   700
 701  MHGPFVLLSQKNNHHLVIRLSSDRDLSKFLDQIRQAASGINAEVIIKDEE   750
 751  NSILLSQAITKERRQDRLDLFFREAYAKAFNDSELQDSETSFDSSNDDIL   800
 801  NETISREELASAMGMKANNEFVKRMFAMTAKHNEDSLSFNEFLTVLREFV   850
 851  NAPQKQKLQTLFKMCDLEGKNKVLRKDLAELVKSLNQTAGVHITESVQLR   900
 901  LFNEVLHYAGVSNDAKYLTYDDFNALFSDIPDKQPVGLPFNRKNYQPSIG   950
 951  ETSSLNSFAVVDRSINSSAPLTLIHKVSAFLETYRQHVFIVFCFVAINLV  1000
1001  LFFERFWHYRYMAENRDLRRVMGAGIAITRGAAGALSFCMALILLTVCRN  1050
1051  IITLLRETVIAQYIPFDSAIAFHKIVALFAAFWATLHTVGHCVNFYHVGT  1100
1101  QSQEGLACLFQEAFFGSNFLPSISYWFFSTITGLTGIALVAVMCIIYVFA  1150
1151  LPCFIKRAYHAFRLTHLLNIAFYALTLLHGLPKLLDSPKFGYYVVGPIVL  1200
1201  FVIDRIIGLMQYYKKLEIVNAEILPSDIIYIEYRRPREFKYKSGQWVTVS  1250
1251  SPSISCTFNESHAFSIASSPQDENMKLYIKAVGPWTWKLRSELIRSLNTG  1300
1301  SPFPLIHMKGPYGDGNQEWMDYEVAIMVGAGIGVTPYASTLVDLVQRTSS  1350
1351  DSFHRVRCRKVYFLWVCSTHKNYEWFVDVLKNVEDQARSGILETHIFVTQ  1400
1401  TFHKFDLRTTMLYICEKHFRATNSGISMFTGLHAKNHFGRPNFKAFFQFI  1450
1451  QSEHKEQSKIGVFSCGPVNLNESIAEGCADANRQRDAPSFAHRFETF     1497

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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