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

NucPred

Fetching P14873 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MATVVVEATEPEPSGSIGNPAASTSPSLSHRFLDSKFYLLVVVGETVTEE    50
  51  HLRRAIGNIELGIRSWDTNLIECNLDQELKLFVSRHSARFSPEVPGQKIL   100
 101  HHRSDVLETVVLINPSDEAVSTEVRLMITDAARHKLLVLTGQCFENTGEL   150
 151  ILQSGSFSFQNFIEIFTDQEIGELLSTTHPANKASLTLFCPEEGDWKNSN   200
 201  LDRHNLQDFINIKLNSASILPEMEGLSEFTEYLSESVEVPSPFDILEPPT   250
 251  SGGFLKLSKPCCYIFPGGRGDSALFAVNGFNMLINGGSERKSCFWKLIRH   300
 301  LDRVDSILLTHIGDDNLPGINSMLQRKIAELEEERSQGSTSNSDWMKNLI   350
 351  SPDLGVVFLNVPENLKDPEPNIKMKRSIEEACFTLQYLNKLSMKPEPLFR   400
 401  SVGNTIEPVILFQKMGVGKLEMYVLNPVKSSKEMQYFMQQWTGTNKDKAE   450
 451  LILPNGQEVDIPISYLTSVSSLIVWHPANPAEKIIRVLFPGNSTQYNILE   500
 501  GLEKLKHLDFLKQPLATQKDLTGQVPTPPVKQVKLKQRADSRESLKPATK   550
 551  PVASKSVRKESKEETPEVTKTSQVEKTPKVESKEKVLVKKDKPVKTESKP   600
 601  SVTEKEVSSKEEQSPVKAEVAEKQATESKPKVTKDKVVKKEIKTKLEEKK   650
 651  EEKPKKEVVKKEDKTPLKKDEKPRKEEVKKEIKKEIKKEERKELKKEVKK   700
 701  ETPLKDAKKEVKKEEKKEVKKEEKEPKKEIKKISKDIKKSTPLSDTKKPS   750
 751  ALKPKVAKKEESTKKEPLAAGKLKDKGKVKVIKKEGKTTEAAATAVGTAA   800
 801  TTAAVVAAAGIAASGPVKELEAERSLMSSPEDLTKDFEELKAEEIDVAKD   850
 851  IKPQLELIEDEEKLKETQPGEAYVIQKETEVSKGSAESPDEGITTTEGEG   900
 901  ECEQTPEELEPVEKQGVDDIEKFEDEGAGFEESSETGDYEEKAETEEAEE   950
 951  PEEDGEDNASGSASKHSPTEDDESAKAEADVHLKEKRESVVSGDDRAEED  1000
1001  MDDVLEKGEAEQSEEEGEEEDKAEDAREEGYEPDKTEAEDYVMAVADKAA  1050
1051  EAGVTEEQYGYLGTSAKQPGIQSPSREPASSIHDETLPGGSESEATASDE  1100
1101  ENREDQPEEFTATSGYTQSTIEISSEPTPMDEMSTPRDVMSDETNNEETE  1150
1151  SPSQEFVNITKYESSLYSQEYSKPAVASFNGLSEGSKTDATDGKDYNASA  1200
1201  STISPPSSMEEDKFSKSALRDAYCSEEKELKASAELDIKDVSDERLSPAK  1250
1251  SPSLSPSPPSPIEKTPLGERSVNFSLTPNEIKVSAEGEARSVSPGVTQAV  1300
1301  VEEHCASPEEKTLEVVSPSQSVTGSAGHTPYYQSPTDEKSSHLPTEVTEK  1350
1351  PQAVPVSFEFSEAKDENERASLSPMDEPVPDSESPVEKVLSPLRSPPLLG  1400
1401  SESPYEDFLSADSKVLGRRSESPFEGKNGKQGFPDRESPVSDLTSTGLYQ  1450
1451  DKQEEKSTGFIPIKEDFGPEKKTSDVETMSSQSALALDERKLGGDVSPTQ  1500
1501  IDVSQFGSFKEDTKMSISEGTVSDKSATPVDEGVAEDTYSHMEGVASVST  1550
1551  ASVATSSFPEPTTDDVSPSLHAEVGSPHSTEVDDSLSVSVVQTPTTFQET  1600
1601  EMSPSKEECPRPMSISPPDFSPKTAKSRTPVQDHRSEQSSMSIEFGQESP  1650
1651  EHSLAMDFSRQSPDHPTLGASVLHITENGPTEVDYSPSDIQDSSLSHKIP  1700
1701  PTEEPSYTQDNDLSELISVSQVEASPSTSSAHTPSQIASPLQEDTLSDVV  1750
1751  PPREMSLYASLASEKVQSLEGEKLSPKSDISPLTPRESSPLYSPGFSDST  1800
1801  SAAKETAAAHQASSSPPIDAATAEPYGFRSSMLFDTMQHHLALNRDLTTS  1850
1851  SVEKDSGGKTPGDFNYAYQKPENAAGSPDEEDYDYESQEKTIRTHDVGGY  1900
1901  YYEKTERTIKSPCDSGYSYETIEKTIKTPEDGGYTCEITEKTTRTPEEGG  1950
1951  YSYEISEKTTRTPEVSGYTYEKTERSRRLLDDISNGYDDTEDGGHTLGDC  2000
2001  SYSYETTEKITSFPESESYSYETSTKTTRSPDTSAYCYETMEKITKTPQA  2050
2051  STYSYETSDRCYTTEKKSPSEARQDVDLCLVSSCEFKHPKTELSPSFINP  2100
2101  NPLEWFAGEEPTEESEKPLTQSGGAPPPSGGKQQGRQCDETPPTSVSESA  2150
2151  PSQTDSDVPPETEECPSITADANIDSEDESETIPTDKTVTYKHMDPPPAP  2200
2201  MQDRSPSPRHPDVSMVDPDALAVDQNLGKALKKDLKEKTKTKKPGTKTKS  2250
2251  SSPVKKGDGKSKPLAASPKPGALKESSDKVSRVASPKKKESVEKATKTTT  2300
2301  TPEVKATRGEEKDKETKNAANASASKSAKTATAGPGTTKTAKSSTVPPGL  2350
2351  PVYLDLCYIPNHSNSKNVDVEFFKRVRSSYYVVSGNDPAAEEPSRAVLDA  2400
2401  LLEGKAQWGSNMQVTLIPTHDSEVMREWYQETHEKQQDLNIMVLASSSTV  2450
2451  VMQDESFPACKIEL                                      2464

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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