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

NucPred

Fetching P48423 from www.uniprot.org...

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

   1  MLLKKKRYMFDERDDNNINSPVAVEPSSNNNKMADTREVRIEEQLKVKIG    50
  51  EAKNLSSRNAANTSCSTQGTRDVYCTIALDQEEICRTPTIERTLTPFFGE   100
 101  EHQFKIPRRFRYLTIYLWDRDMKQDKPIGKIAIKREELHMYNHKDHWFSL   150
 151  RPVDQDSEVQGMVNVEVAFTEAQQTQSLSEGIDLGQHTLRHHQNLPHHSH   200
 201  QQRAHLNDYKENSELSNIQRASAAAASSSSAAMTLKTRAAGLFGHVHHPP   250
 251  SQTQHFPIINTTSTSSDQLSNWKSHGRFVGVTIKVPACVDLAKKQGTCDP   300
 301  FVVCTAHYSNKHQVTRRTKQRKKTVDPEFDEAMYFDLHIDADAGSTNTTG   350
 351  SNKSAGSLESSANKGYSIYPVGGADLVEIVVSVWHDAHGAMSDKVFLGEV   400
 401  RLPMLNKQEQQAVNPSAWYYLQPRSMTHSSRSLNATPRSCATPPGTRLSV   450
 451  DSTIGSLRLNLNYTADHVFPLATYDDLMNLLLESVDQRPITVSAVSILGE   500
 501  LVSGKTEVAQPLVRLFTHTERIAPIIKALADHEISHLTDPTTIFRGNTLV   550
 551  SKMMDEAMRLSGLHYLHQTLRPVLSQIVAEKKPCEIDPSKIKDRSAVDTN   600
 601  LHNLQDYVERVFEAITKSADRCPKVLCQIFHDLRECAGEHFPSNREVRYS   650
 651  VVSGFIFLRFFAPAILGPKLFDLTTERLDAQTSRTLTLISKTIQSLGNLV   700
 701  SSRSSQQTCKEEFTVELYKKFCTEQHVDAVKHFLEVISTPSHASSSVHPA   750
 751  AAAATPLEPVLLKEGLMTKYPTSRKRFGRQFKQRHFRLTTHSLSYAKSKG   800
 801  KQPICDIPLQEIASVEQLKDKSFKMQNCFKIVHNDRSLIVQTTNCVEERE   850
 851  WFDLLHKICLMNSIRMQYFHPSAFVSGFYSCCGRSDENSPGCKKVLDKTM   900
 901  DYFQMDLVTALDPALDLQRIHTLIMSNMSVLESLLDPLTYHQSLSQTQHQ   950
 951  QHNPLVPLATDLQKHSPQAFAEFKRTIEKLREKAYAIDRDHRDYKQGITR  1000
1001  QLKYGSRQAPIGDDNYWHMMRAAGQLNQQHHQQQQHQQQQQQQQQQQLQQ  1050
1051  FQPQPVLPQMQNVRAYPYQPATSNMNAYCLHNMQYQQQRLPFHQQQQQHH  1100
1101  QQLQQQQSQFQPLRSHQLQRHNNNLNNNNCGNGSSSSPSSTTSSVVAAPP  1150
1151  STTSSSQPAPPIY                                       1163

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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