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

NucPred

Fetching P78559 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MDGVAEFSEYVSETVDVPSPFDLLEPPTSGGFLKLSKPCCYIFPGGRGDS    50
  51  ALFAVNGFNILVDGGSDRKSCFWKLVRHLDRIDSVLLTHIGADNLPGING   100
 101  LLQRKVAELEEEQSQGSSSYSDWVKNLISPELGVVFFNVPEKLRLPDASR   150
 151  KAKRSIEEACLTLQHLNRLGIQAEPLYRVVSNTIEPLTLFHKMGVGRLDM   200
 201  YVLNPVKDSKEMQFLMQKWAGNSKAKTGIVLPNGKEAEISVPYLTSITAL   250
 251  VVWLPANPTEKIVRVLFPGNAPQNKILEGLEKLRHLDFLRYPVATQKDLA   300
 301  SGAVPTNLKPSKIKQRADSKESLKATTKTAVSKLAKREEVVEEGAKEARS   350
 351  ELAKELAKTEKKAKESSEKPPEKPAKPERVKTESSEALKAEKRKLIKDKV   400
 401  GKKHLKEKISKLEEKKDKEKKEIKKERKELKKDEGRKEEKKDAKKEEKRK   450
 451  DTKPELKKISKPDLKPFTPEVRKTLYKAKVPGRVKIDRSRAIRGEKELSS   500
 501  EPQTPPAQKGTVPLPTISGHRELVLSSPEDLTQDFEEMKREERALLAEQR   550
 551  DTGLGDKPFPLDTAEEGPPSTAIQGTPPSVPGLGQEEHVMKEKELVPEVP   600
 601  EEQGSKDRGLDSGAETEEEKDTWEEKKQREAERLPDRTEAREESEPEVKE   650
 651  DVIEKAELEEMEEVHPSDEEEEDATKAEGFYQKHMQEPLKVTPRSREAFG   700
 701  GRELGLQGKAPEKETSLFLSSLTTPAGATEHVSYIQDETIPGYSETEQTI   750
 751  SDEEIHDEPEERPAPPRFHTSTYDLPGPEGAGPFEASQPADSAVPATSGK   800
 801  VYGTPETELTYPTNIVAAPLAEEEHVSSATSITECDKLSSFATSVAEDQS   850
 851  VASLTAPQTEETGKSSLLLDTVTSIPSSRTEATQGLDYVPSAGTISPTSS   900
 901  LEEDKGFKSPPCEDFSVTGESEKRGEIIGKGLSGERAVEEEEEETANVEM   950
 951  SEKLCSQYGTPVFSAPGHALHPGEPALGEAEERCLSPDDSTVKMASPPPS  1000
1001  GPPSATHTPFHQSPVEEKSEPQDFQEADSWGDTKRTPGVGKEDAAEETVK  1050
1051  PGPEEGTLEKEEKVPPPRSPQAQEAPVNIDEGLTGCTIQLLPAQDKAIVF  1100
1101  EIMEAGEPTGPILGAEALPGGLRTLPQEPGKPQKDEVLRYPDRSLSPEDA  1150
1151  ESLSVLSVPSPDTANQEPTPKSPCGLTEQYLHKDRWPEVSPEDTQSLSLS  1200
1201  EESPSKETSLDVSSKQLSPESLGTLQFGELNLGKEEMGHLMQAEDTSHHT  1250
1251  APMSVPEPHAATASPPTDGTTRYSAQTDITDDSLDRKSPASSFSHSTPSG  1300
1301  NGKYLPGAITSPDEHILTPDSSFSKSPESLPGPALEDIAIKWEDKVPGLK  1350
1351  DRTSEQKKEPEPKDEVLQQKDKTLEHKEVVEPKDTAIYQKDEALHVKNEA  1400
1401  VKQQDKALEQKGRDLEQKDTALEQKDKALEPKDKDLEEKDKALEQKDKIP  1450
1451  EEKDKALEQKDTALEQKDKALEPKDKDLEQKDRVLEQKEKIPEEKDKALD  1500
1501  QKVRSVEHKAPEDTVAEMKDRDLEQTDKAPEQKHQAQEQKDKVSEKKDQA  1550
1551  LEQKYWALGQKDEALEQNIQALEENHQTQEQESLVQEDKTRKPKMLEEKS  1600
1601  PEKVKAMEEKLEALLEKTKALGLEESLVQEGRAREQEEKYWRGQDVVQEW  1650
1651  QETSPTREEPAGEQKELAPAWEDTSPEQDNRYWRGREDVALEQDTYWREL  1700
1701  SCERKVWFPHELDGQGARPHYTEERESTFLDEGPDDEQEVPLREHATRSP  1750
1751  WASDFKDFQESSPQKGLEVERWLAESPVGLPPEEEDKLTRSPFEIISPPA  1800
1801  SPPEMVGQRVPSAPGQESPIPDPKLMPHMKNEPTTPSWLADIPPWVPKDR  1850
1851  PLPPAPLSPAPGPPTPAPESHTPAPFSWGTAEYDSVVAAVQEGAAELEGG  1900
1901  PYSPLGKDYRKAEGEREEEGRAEAPDKSSHSSKVPEASKSHATTEPEQTE  1950
1951  PEQREPTPYPDERSFQYADIYEQMMLTGLGPACPTREPPLGAAGDWPPCL  2000
2001  STKEAAAGRNTSAEKELSSPISPKSLQSDTPTFSYAALAGPTVPPRPEPG  2050
2051  PSMEPSLTPPAVPPRAPILSKGPSPPLNGNILSCSPDRRSPSPKESGRSH  2100
2101  WDDSTSDSELEKGAREQPEKEAQSPSPPHPIPMGSPTLWPETEAHVSPPL  2150
2151  DSHLGPARPSLDFPASAFGFSSLQPAPPQLPSPAEPRSAPCGSLAFSGDR  2200
2201  ALALAPGPPTRTRHDEYLEVTKAPSLDSSLPQLPSPSSPGAPLLSNLPRP  2250
2251  ASPALSEGSSSEATTPVISSVAERFSPSLEAAEQESGELDPGMEPAAHSL  2300
2301  WDLTPLSPAPPASLDLALAPAPSLPGDMGDGILPCHLECSEAATEKPSPF  2350
2351  QVPSEDCAANGPTETSPNPPGPAPAKAENEEAAACPAWERGAWPEGAERS  2400
2401  SRPDTLLSPEQPVCPAGGSGGPPSSASPEVEAGPQGCATEPRPHRGELSP  2450
2451  SFLNPPLPPSIDDRDLSTEEVRLVGRGGRRRVGGPGTTGGPCPVTDETPP  2500
2501  TSASDSGSSQSDSDVPPETEECPSITAEAALDSDEDGDFLPVDKAGGVSG  2550
2551  THHPRPGHDPPPLPQPDPRPSPPRPDVCMADPEGLSSESGRVERLREKEK  2600
2601  VQGRVGRRAPGKAKPASPARRLDLRGKRSPTPGKGPADRASRAPPRPRST  2650
2651  TSQVTPAEEKDGHSPMSKGLVNGLKAGPMALSSKGSSGAPVYVDLAYIPN  2700
2701  HCSGKTADLDFFRRVRASYYVVSGNDPANGEPSRAVLDALLEGKAQWGEN  2750
2751  LQVTLIPTHDTEVTREWYQQTHEQQQQLNVLVLASSSTVVMQDESFPACK  2800
2801  IEF                                                 2803

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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