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

NucPred

Fetching Q61115 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MASAGNAAGALGRQAGGGRRRRTGGPHRAAPDRDYLHRPSYCDAAFALEQ    50
  51  ISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAV   100
 101  GLKAANLETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKE   150
 151  EGANVLTTEALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETG   200
 201  YMDQIIEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEF   250
 251  LEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNST   300
 301  KPLDVALVLNGGCQGLSRKYMHWQEELIVGGTVKNATGKLVSAHALQTMF   350
 351  QLMTPKQMYEHFRGYDYVSHINWNEDRAAAILEAWQRTYVEVVHQSVAPN   400
 401  STQKVLPFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSK   450
 451  SQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDD   500
 501  VFLLAHAFSETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAAL   550
 551  IPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDLYRREDRRLDIFCCF   600
 601  TSPCVSRVIQVEPQAYTEPHSNTRYSPPPPYTSHSFAHETHITMQSTVQL   650
 651  RTEYDPHTHVYYTTAEPRSEISVQPVTVTQDNLSCQSPESTSSTRDLLSQ   700
 701  FSDSSLHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVILLFLGLLGVS   750
 751  LYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPN   800
 801  IQHLLYDLHKSFSNVKYVMLEENKQLPQMWLHYFRDWLQGLQDAFDSDWE   850
 851  TGRIMPNNYKNGSDDGVLAYKLLVQTGSRDKPIDISQLTKQRLVDADGII   900
 901  NPSAFYIYLTAWVSNDPVAYAASQANIRPHRPEWVHDKADYMPETRLRIP   950
 951  AAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRVICNNYTSLGLSSYPNGYP  1000
1001  FLFWEQYISLRHWLLLSISVVLACTFLVCAVFLLNPWTAGIIVMVLALMT  1050
1051  VELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNHR  1100
1101  AMLALEHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTVLGV  1150
1151  LNGLVLLPVLLSFFGPCPEVSPANGLNRLPTPSPEPPPSVVRFAVPPGHT  1200
1201  NNGSDSSDSEYSSQTTVSGISEELRQYEAQQGAGGPAHQVIVEATENPVF  1250
1251  ARSTVVHPDSRHQPPLTPRQQPHLDSGSLSPGRQGQQPRRDPPREGLRPP  1300
1301  PYRPRRDAFEISTEGHSGPSNRDRSGPRGARSHNPRNPTSTAMGSSVPSY  1350
1351  CQPITTVTASASVTVAVHPPPGPGRNPRGGPCPGYESYPETDHGVFEDPH  1400
1401  VPFHVRCERRDSKVEVIELQDVECEERPWGSSSN                  1434

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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