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

NucPred

Fetching P09547 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MDFFNLNNNNNNNNTTTTTTTTNNNNTNNNNTNNNNNPANNTNNNNSTGH    50
  51  SSNTNNNTNNNNTNTGASGVDDFQNFFDPKPFDQNLDSNNNNSNSNNNDN   100
 101  NNSNTVASSTNFTSPTAVVNNAAPANVTGGKAANFIQNQSPQFNSPYDSN   150
 151  NSNTNLNSLSPQAILAKNSIIDSSNLPLQAQQQLYGGNNNNNSTGIANDN   200
 201  VITPHFITNVQSISQNSSSSTPNTNSNSTPNANQQFLPFNNSASNNGNLT   250
 251  SNQLISNYAASNSMDRSSSASNEFVPNTSDNNNNSNNHNMRNNSNNKTSN   300
 301  NNNVTAVPAATPANTNNSTSNANTVFSERAAMFAALQQKQQQRFQALQQQ   350
 351  QQQQQNQQQQNQQPQQQQQQQQNPKFLQSQRQQQQRSILQSLNPALQEKI   400
 401  STELNNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKF   450
 451  GGADQVTRTQQWSMVAQRLQISDYQQLESIYFRILLPYERHMISQEGIKE   500
 501  TQAKRIFLQQFLQELLKKVQQQQQAAALANANNNINSASSAPTPAAPGAS   550
 551  VPATAAPGTEAGIVPVSANTPKSLNSNININVNNNNIGQQQVKKPRKQRV   600
 601  KKKTKKELELERKEREDFQKRQQKLLEDQQRQQKLLLETKLRQQYEIELK   650
 651  KLPKVYKRSIVRNYKPLINRLKHYNGYDINYISKIGEKIDSNKPIFLFAP   700
 701  ELGAINLHALSMSLQSKNLGEINTALNTLLVTSADSNLKISLVKYPELLD   750
 751  SLAILGMNLLSNLSQNVVPYHRNTSDYYYEDAGSNQYYVTQHDKMVDKIF   800
 801  EKVNNNATLTPNDSNDEKVTILVDSLTGNQLPTPTPTEMEPDLDTECFIS   850
 851  MQSTSPAVKQWDLLPEPIRFLPNQFPLKIHRTPYLTSLKKIKDEIDDPFT   900
 901  KINTRGAEDPKVLINDQLSTISMILRNISFSDNNSRIMSRNFYLKRFISD   950
 951  LLWLVLIHPENFTCNRKILNFKKDLVIVLSNISHLLEIASSIDCLLILIL  1000
1001  VISFGQPKLNPMASSSSFGSESLTFNEFQLQWGKYQTFGVDILAKLFSLE  1050
1051  KPNLNYFKSILLNKNTGNNLYDRNSNNNHKDKKLLRRLLNLYNDNNKNNN  1100
1101  NRHNLLNDVVSFLFSAIPLQQVLSQSADPSLLIDQFSPVISQSLTSILVI  1150
1151  VQKILPLSNEVFEISENNSDSNSNNNGNKDSSFNFNKNLPFVWLSSEENI  1200
1201  GSGLLKLSEIILNINNSTSKNTLLQQQNYSKVLLPSINISCVQLIKCLVE  1250
1251  KSICFENCLNNDPEILKKIASIPNLFPTDLEIFQLFTNPSVDIQIINQYQ  1300
1301  LLYNLKNDILTNLE                                      1314

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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