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

NucPred

Fetching P07259 from www.uniprot.org...

The NucPred score for your sequence is 0.20 (see score help below)

   1  MATIAPTAPITPPMESTGDRLVTLELKDGTVLQGYSFGAEKSVAGELVFQ    50
  51  TGMVGYPESVTDPSYEGQILVITYPLVGNYGVPDMHLRDELVEELPRYFE   100
 101  SNRIHIAGLVISHYTDEYSHYLAKSSLGKWLQNEGIPAVYGVDTRSLTKH   150
 151  LRDAGSMLGRLSLEKSGSDRTISRSSSWRSAFDVPEWVDPNVQNLVSKVS   200
 201  INEPKLYVPPADNKHIELQTGPDGKVLRILAIDVGMKYNQIRCFIKRGVE   250
 251  LKVVPWNYDFTKEDYDGLFISNGPGDPSVLDDLSQRLSNVLEAKKTPVFG   300
 301  ICLGHQLIARAAGASTLKLKFGNRGHNIPCTSTISGRCYITSQNHGFAVD   350
 351  VDTLTSGWKPLFVNANDDSNEGIYHSELPYFSVQFHPESTPGPRDTEFLF   400
 401  DVFIQAVKEFKYTQVLKPIAFPGGLLEDNVKAHPRIEAKKVLVLGSGGLS   450
 451  IGQAGEFDYSGSQAIKALKEEGIYTILINPNIATIQTSKGLADKVYFVPV   500
 501  TAEFVRKVILHERPDAIYVTFGGQTALSVGIAMKDEFEALGVKVLGTPID   550
 551  TIITTEDRELFSNAIDEINEKCAKSQAANSVDEALAAVKEIGFPVIVRAA   600
 601  YALGGLGSGFANNEKELVDLCNVAFSSSPQVLVEKSMKGWKEVEYEVVRD   650
 651  AFDNCITVCNMENFDPLGIHTGDSIVVAPSQTLSDEDYNMLRTTAVNVIR   700
 701  HLGVVGECNIQYALNPVSKDYCIIEVNARLSRSSALASKATGYPLAYTAA   750
 751  KLGLNIPLNEVKNSVTKSTCACFEPSLDYCVVKMPRWDLKKFTRVSTELS   800
 801  SSMKSVGEVMSIGRTFEEAIQKAIRSTEYANLGFNETDLDIDIDYELNNP   850
 851  TDMRVFAIANAFAKKGYSVDKVWEMTRIDKWFLNKLHDLVQFAEKISSFG   900
 901  TKEELPSLVLRQAKQLGFDDRQIARFLDSNEVAIRRLRKEYGITPFVKQI   950
 951  DTVAAEFPAYTNYLYMTYNADSHDLSFDDHGVMVLGSGVYRIGSSVEFDW  1000
1001  CAVTAVRTLRANNIKTIMVNYNPETVSTDYDEADRLYFETINLERVLDIY  1050
1051  EIENSSGVVVSMGGQTSNNIAMTLHRENVKILGTSPDMIDSAENRYKFSR  1100
1101  MLDQIGVDQPAWKELTSMDEAESFAEKVGYPVLVRPSYVLSGAAMNTVYS  1150
1151  KNDLESYLNQAVEVSRDYPVVITKYIENAKEIEMDAVARNGELVMHVVSE  1200
1201  HVENAGVHSGDATLIVPPQDLAPETVDRIVVATAKIGKALKITGPYNIQF  1250
1251  IAKDNEIKVIECNVRASRSFPFISKVVGVNLIELATKAIMGLPLTPYPVE  1300
1301  KLPDDYVAVKVPQFSFPRLAGADPVLGVEMASTGEVATFGHSKYEAYLKS  1350
1351  LLATGFKLPKKNILLSIGSYKEKQELLSSVQKLYNMGYKLFATSGTADFL  1400
1401  SEHGIAVQYLEVLNKDDDDQKSEYSLTQHLANNEIDLYINLPSANRFRRP  1450
1451  ASYVSKGYKTRRLAVDYSVPLVTNVKCAKLLIEAISRNITLDVSERDAQT  1500
1501  SHRTITLPGLINIATYVPNASHVIKGPAELKETTRLFLESGFTYCQLMPR  1550
1551  SISGPVITDVASLKAANSVSQDSSYTDFSFTIAGTAHNAHSVTQSASKVT  1600
1601  ALFLPLRELKNKITAVAELLNQWPTEKQVIAEAKTADLASVLLLTSLQNR  1650
1651  SIHITGVSNKEDLALIMTVKAKDPRVTCDVNIYSLFIAQDDYPEAVFLPT  1700
1701  KEDQEFFWNNLDSIDAFSVGALPVALANVTGNKVDVGMGIKDSLPLLLAA  1750
1751  VEEGKLTIDDIVLRLHDNPAKIFNIPTQDSVVEIDLDYSFRRNKRWSPFN  1800
1801  KDMNGGIERVVYNGETLVLSGELVSPGAKGKCIVNPSPASITASAELQST  1850
1851  SAKRRFSITEEAIADNLDAAEDAIPEQPLEQKLMSSRPPRELVAPGAIQN  1900
1901  LIRSNNPFRGRHILSIKQFKRSDFHVLFAVAQELRAAVAREGVLDLMKGH  1950
1951  VITTIFFEPSTRTCSSFIAAMERLGGRIVNVNPLVSSVKKGETLQDTIRT  2000
2001  LACYSDAIVMRHSEEMSVHIAAKYSPVPIINGGNGSREHPTQAFLDLFTI  2050
2051  REEIGTVNGITVTFMGDLKHGRTVHSLCRLLMHYQVRINLVSPPELRLPE  2100
2101  GLREELRKAGLLGVESIELTPHIISKTDVLYCTRVQEERFNSPEEYARLK  2150
2151  DTYIVDNKILAHAKENMAIMHPLPRVNEIKEEVDYDHRAAYFRQMKYGLF  2200
2201  VRMALLAMVMGVDM                                      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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