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

NucPred

Fetching Q8NB66 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MVANFFKSLILPYIHKLCKGMFTKKLGNTNKNKEYRQQKKDQDFPTAGQT    50
  51  KSPKFSYTFKSTVKKIAKCSSTHNLSTEEDEASKEFSLSPTFSYRVAIAN   100
 101  GLQKNAKVTNSDNEDLLQELSSIESSYSESLNELRSSTENQAQSTHTMPV   150
 151  RRNRKSSSSLAPSEGSSDGERTLHGLKLGALRKLRKWKKSQECVSSDSEL   200
 201  STMKKSWGIRSKSLDRTVRNPKTNALEPGFSSSGCISQTHDVMEMIFKEL   250
 251  QGISQIETELSELRGHVNALKHSIDEISSSVEVVQSEIEQLRTGFVQSRR   300
 301  ETRDIHDYIKHLGHMGSKASLRFLNVTEERFEYVESVVYQILIDKMGFSD   350
 351  APNAIKIEFAQRIGHQRDCPNAKPRPILVYFETPQQRDSVLKKSYKLKGT   400
 401  GIGISTDILTHDIRERKEKGIPSSQTYESMAIKLSTPEPKIKKNNWQSPD   450
 451  DSDEDLESDLNRNSYAVLSKSELLTKGSTSKPSSKSHSARSKNKTANSSR   500
 501  ISNKSDYDKISSQLPESDILEKQTTTHYADATPLWHSQSDFFTAKLSRSE   550
 551  SDFSKLCQSYSEDFSENQFFTRTNGSSLLSSSDRELWQRKQEGTATLYDS   600
 601  PKDQHLNGGVQGIQGQTETENTETVDSGMSNGMVCASGDRSHYSDSQLSL   650
 651  HEDLSPWKEWNQGADLGLDSSTQEGFDYETNSLFDQQLDVYNKDLEYLGK   700
 701  CHSDLQDDSESYDLTQDDNSSPCPGLDNEPQGQWVGQYDSYQGANSNELY   750
 751  QNQNQLSMMYRSQSELQSDDSEDAPPKSWHSRLSIDLSDKTFSFPKFGST   800
 801  LQRAKSALEVVWNKSTQSLSGYEDSGSSLMGRFRTLSQSTANESSTTLDS   850
 851  DVYTEPYYYKAEDEEDYTEPVADNETDYVEVMEQVLAKLENRTSITETDE   900
 901  QMQAYDHLSYETPYETPQDEGYDGPADDMVSEEGLEPLNETSAEMEIRED   950
 951  ENQNIPEQPVEITKPKRIRPSFKEAALRAYKKQMAELEEKILAGDSSSVD  1000
1001  EKARIVSGNDLDASKFSALQVCGGAGGGLYGIDSMPDLRRKKTLPIVRDV  1050
1051  AMTLAARKSGLSLAMVIRTSLNNEELKMHVFKKTLQALIYPMSSTIPHNF  1100
1101  EVWTATTPTYCYECEGLLWGIARQGMKCLECGVKCHEKCQDLLNADCLQR  1150
1151  AAEKSSKHGAEDKTQTIITAMKERMKIREKNRPEVFEVIQEMFQISKEDF  1200
1201  VQFTKAAKQSVLDGTSKWSAKITITVVSAQGLQAKDKTGSSDPYVTVQVG  1250
1251  KNKRRTKTIFGNLNPVWDEKFYFECHNSTDRIKVRVWDEDDDIKSRVKQH  1300
1301  FKKESDDFLGQTIVEVRTLSGEMDVWYNLEKRTDKSAVSGAIRLKINVEI  1350
1351  KGEEKVAPYHIQYTCLHENLFHYLTEVKSNGGVKIPEVKGDEAWKVFFDD  1400
1401  ASQEIVDEFAMRYGIESIYQAMTHFSCLSSKYMCPGVPAVMSTLLANINA  1450
1451  FYAHTTVSTNIQVSASDRFAATNFGREKFIKLLDQLHNSLRIDLSKYREN  1500
1501  FPASNTERLQDLKSTVDLLTSITFFRMKVLELQSPPKASMVVKDCVRACL  1550
1551  DSTYKYIFDNCHELYSQLTDPSKKQDIPREDQGPTTKNLDFWPQLITLMV  1600
1601  TIIDEDKTAYTPVLNQFPQELNMGKISAEIMWTLFALDMKYALEEHENQR  1650
1651  LCKSTDYMNLHFKVKWFYNEYVRELPAFKDAVPEYSLWFEPFVMQWLDEN  1700
1701  EDVSMEFLHGALGRDKKDGFQQTSEHALFSCSVVDVFAQLNQSFEIIKKL  1750
1751  ECPNPEALSHLMRRFAKTINKVLLQYAAIVSSDFSSHCDKENVPCILMNN  1800
1801  IQQLRVQLEKMFESMGGKELDSEASTILKELQVKLSGVLDELSVTYGESF  1850
1851  QVIIEECIKQMSFELNQMRANGNTTSNKNSAAMDAEIVLRSLMDFLDKTL  1900
1901  SLSAKICEKTVLKRVLKELWKLVLNKIEKQIVLPPLTDQTGPQMIFIAAK  1950
1951  DLGQLSKLKEHMIREDARGLTPRQCAIMEVVLATIKQYFHAGGNGLKKNF  2000
2001  LEKSPDLQSLRYALSLYTQTTDALIKKFIDTQTSQSRSSKDAVGQISVHV  2050
2051  DITATPGTGDHKVTVKVIAINDLNWQTTAMFRPFVEVCILGPNLGDKKRK  2100
2101  QGTKTKSNTWSPKYNETFQFILGKENRPGAYELHLSVKDYCFAREDRIIG  2150
2151  MTVIQLQNIAEKGSYGAWYPLLKNISMDETGLTILRILSQRTSDDVAKEF  2200
2201  VRLKSETRSTEESA                                      2214

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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