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

NucPred

Fetching P15205 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MATVVVEATEPEPSGSIGNPAATTSPSLSHRFLDSKFYLLVVVGETVTEE    50
  51  HLRRAIGNIELGIRSWDTNLIECNLDQELKLFVSRHSARFSPEVPGQKIL   100
 101  HHRSDVLETVVLINPSDEAVSTEVRLMITDAARHKLLVLTGQCFENTGEL   150
 151  ILQSGSFSFQNFIEIFTDQEIGELLSTTHPANKASLTLFCPEEGDWKNSN   200
 201  LDRHNLQDFINIKLNSASILPEMEGLSEFTEYLSESVEVPSPFDILEPPT   250
 251  SGGFLKLSKPCCYIFPGGRGDSALFAVNGFNMLINGGSERKSCFWKLIRH   300
 301  LDRVDSILLTHIGDDNLPGINSMLQRKIAELEEERSQGSTSNSDWMKNLI   350
 351  SPDLGVVFLNVPENLKNPEPNIKMKRSTEEACFTLQYLNKLSMKPEPLFR   400
 401  SVGNAIEPVILFQKMGVGKLEMYVLNPVKSSKEMQYFMQQWTGTNKDKAE   450
 451  LILPNGQEVDIPISYLTSVSSLIVWHPANPAEKIIRVLFPGNSTQYNILE   500
 501  GLEKLKHLDFLKQPLATQKDLTGQVSTPPVKQVKLKQRADSRESLKPATK   550
 551  PLSSKSVRKESKEEAPEATKASQVEKTPKVESKEKVIVKKDKPGKVESKP   600
 601  SVTEKEVPSKEEQSPVKAEVAEKAATESKPKVTKDKVVKKEIKTKPEEKK   650
 651  EEKPKKEVAKKEDKTPLKKDEKPKKEEAKKEIKKEIKKEEKKELKKEVKK   700
 701  ETPLKDAKKEVKKDEKKEVKKEEKEPKKEIKKISKDIKKSTPLSDTKKPA   750
 751  ALKPKVAKKEEPTKKEPIAAGKLKDKGKVKVIKKEGKTTEAAATAVGTAA   800
 801  VAAAAGVAASGPAKELEAERSLMSSPEDLTKDFEELKAEEIDVAKDIKPQ   850
 851  LELIEDEEKLKETEPGEAYVIQKETEVSKGSAESPDEGITTTEGEGECEQ   900
 901  TPEELEPVEKQGVDDIEKFEDEGAGFEESSEAGDYEEKAETEEAEEPEED   950
 951  GEDNVSGSASKHSPTEDEEIAKAEADVHIKEKRESVASGDDRAEEDMDEA  1000
1001  LEKGEAEQSEEEGEEEEDKAEDAREEDHEPDKTEAEDYVMAVVDKAAEAG  1050
1051  VTEDQYGFLGTPAKQPGVQSPSREPASSIHDETLPGGSESEATASDEENR  1100
1101  EDQPEEFTATSGYTQSTIEISSEPTPMDEMSTPRDVMSDETNNEETESPS  1150
1151  QEFVNITKYESSLYSQEYSKPVVASFNGLSDGSKTDATDGRDYNASASTI  1200
1201  SPPSSMEEDKFSKSALRDAYRPEETDVKTGAELDIKDVSDERLSPAKSPS  1250
1251  LSPSPPSPIEKTPLGERSVNFSLTPNEIKASAEGEATAVVSPGVTQAVVE  1300
1301  EHCASPEEKTLEVVSPSQSVTGSAGHTPYYQSPTDEKSSHLPTEVTEKPQ  1350
1351  AVPVSFEFTEAKDENERSSISPMDEPVPDSESPIEKVLSPLRSPPLIGSE  1400
1401  SAYEDFLSADDKALGRRSESPFEGKNGKQGFSDKESPVSDLTSDLYQDKQ  1450
1451  EEKSAGFIPIKEDFSPEKKASDAEIMSSQSALALDERKLGGDGSPTQVDV  1500
1501  SQFGSFKEDTKMSISEGTVSDKSATPVDEGVAEDTYSHMEGVASVSTASV  1550
1551  ATSSFPEPTTDDVSPSLHAEVGSPHSTEVDDSLSVSVVQTPTTFQETEMS  1600
1601  PSKEECPRPMSISPPDFSPKTAKSRTPVQDHRSEQSSMSIEFGQESPEHS  1650
1651  LAMDFSRQSPDHPTVGAGMLHITENGPTEVDYSPSDIQDSSLSHKIPPTE  1700
1701  EPSYTQDNDLSELISVSQVEASPSTSSAHTPSQIASPLQEDTLSDVVPPR  1750
1751  DMSLYASLASEKVQSLEGEKLSPKSDISPLTPRESSPTYSPGFSDSTSGA  1800
1801  KESTAAYQTSSSPPIDAAAAEPYGFRSSMLFDTMQHHLALSRDLTTSSVE  1850
1851  KDNGGKTPGDFNYAYQKPESTTESPDEEDYDYESHEKTIQAHDVGGYYYE  1900
1901  KTERTIKSPCDSGYSYETIEKTTKTPEDGGYSCEITEKTTRTPEEGGYSY  1950
1951  EISEKTTRTPEVSGYTYEKTERSRRLLDDISNGYDDTEDGGHTLGDCSYS  2000
2001  YETTEKITSFPESESYSYETTTKTTRSPDTSAYCYETMEKITKTPQASTY  2050
2051  SYETSDRCYTPERKSPSEARQDVDLCLVSSCEFKHPKTELSPSFINPNPL  2100
2101  EWFAGEEPTEESEKPLTQSGGAPPPSGGKQQGRQCDETPPTSVSESAPSQ  2150
2151  TDSDVPPETEECPSITADANIDSEDESETIPTDKTVTYKHMDPPPAPMQD  2200
2201  RSPSPRHPDVSMVDPEALAIEQNLGKALKKDLKEKAKTKKPGTKTKSSSP  2250
2251  VKKGDGKSKPSAASPKPGALKESSDKVSRVASPKKKESVEKAMKTTTTPE  2300
2301  VKATRGEEKDKETKNAANASASKSVKTATAGPGTTKTAKSSTVPPGLPVY  2350
2351  LDLCYIPNHSNSKNVDVEFFKRVRSSYYVVSGNDPAAEEPSRAVLDALLE  2400
2401  GKAQWGSNMQVTLIPTHDSEVMREWYQETHEKQQDLNIMVLASSSTVVMQ  2450
2451  DESFPACKIEL                                         2461

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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