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

NucPred

Fetching Q9JIS7 from www.uniprot.org...

The NucPred score for your sequence is 0.46 (see score help below)

   1  MSESEVGKDTTPEPSPANGTGPGPEWGLCPGPPTVGTDTSGASGLGTPRR    50
  51  RTQHNKHKTVAVASAQRSPRALFCLTLTNPIRRSCISIVEWKPFDILILL   100
 101  TIFANCVALGVYIPFPEDDSNTANHNLEQVEYVFLVIFTVETVLKIVAYG   150
 151  LVLHPSAYIRNGWNLLDFIIVVVGLFSVLLEQGPGRPGDAPHTGGKPGGF   200
 201  DVKALRAFRVLRPLRLVSGVPSLHIVVNSIMKALVPLLHIALLVLFVIII   250
 251  YAIIGLELFLGRMHKTCYFLGSDMEAEEDPSPCASSGSGRSCTLNHTECR   300
 301  GRWPGPNGGITNFDNFFFAMLTVFQCITMEGWTDVLYWMQDAMGYELPWV   350
 351  YFVSLVIFGSFFVLNLVLGVLSGEFSKEREKAKARGDFQKLREKQQMEED   400
 401  LRGYLDWITQAEELDLHDPSVDGNLASLAEEGRAGHRPQLSELTNRRRGR   450
 451  LRWFSHSTRSTHSTSSHASLPASDTGSMTDTPGDEDEEEGTMASCTRCLN   500
 501  KIMKTRICRHFRRANRGLRARCRRAVKSNACYWAVLLLVFLNTLTIASEH   550
 551  HGQPLWLTQTQEYANKVLLCLFTVEMLLKLYGLGPSVYVASFFNRFDCFV   600
 601  VCGGILETTLVEVGAMQPLGISVLRCVRLLRIFKVTRHWASLSNLVASLL   650
 651  NSMKSIASLLLLLFLFIIIFSLLGMQLFGGKFNFDQTHTKRSTFDTFPQA   700
 701  LLTVFQILTGEDWNVVMYDGIMAYGGPFFPGMLVCVYFIILFICGNYILL   750
 751  NVFLAIAVDNLASGDAGTAKDKGREKSSEGNPPKENKVLVPGGENEDAKG   800
 801  ARSEGAAPGMEEEEEEEEEEEEEEEEEEENGAGHVELLQEVVPKEKVVPI   850
 851  PEGSAFFCLSQTNPLRKACHTLIHHHIFTSLILVFIILSSVSLAAEDPIR   900
 901  AHSFRNHILGYFDYAFTSIFTVEILLKMTVFGAFLHRGSFCRSWFNLLDL   950
 951  LVVSVSLISFGIHSSAISVVKILRVLRVLRPLRAINRAKGLKHVVQCVFV  1000
1001  AIRTIGNIMIVTTLLQFMFACIGVQLFKGKFYSCTDEAKHTLKESKGSFL  1050
1051  IYPDGDVSRPLVRERLWVNSDFNFDNVLSAMMALFTVSTFEGWPALLYKA  1100
1101  IDANAEDEGPIYNYHVEISVFFIVYIIIIAFFMMNIFVGFVIITFRAQGE  1150
1151  QEYQNCELDKNQRQCVEYALKAQPLRRYIPKNPHQYRVWATVNSRAFEYL  1200
1201  MFLLILLNTVALAMQHYEQTAPFNYAMDILNMVFTGLFTIEMVLKIIAFK  1250
1251  PKHYFADAWNTFDALIVVGSVVDIAVTEVNNGGHLGESSEDTSRISITFF  1300
1301  RLFRVMRLVKLLSKGEGIRTLLWTFIKSFQALPYVALLIAMIFFIYAVIG  1350
1351  MQMFGLVALQDGTQINRNNNFQTFPQAVLLLFRCATGEAWQEIMLASLPG  1400
1401  NRCDPESDFGPGEEFTCGSSFAIVYFISFFMLCAFLIINLFVAVIMDNFD  1450
1451  YLTRDWSILGPHHLDEFKRIWSEYDPGAKGRIKHLDVVALLRRIQPPLGF  1500
1501  GKLCPHRVACKRLVAMNVPLNSDGTVTFNATLFALVRTSLKIKTEGNLDQ  1550
1551  ANQELRMVIKKIWKRIKQKLLDEVIPPPDEEEVTVGKFYATFLIQDYFRK  1600
1601  FRRRKEKGLLGREAPTSTSSALQAGLRSLQDLGPEIRQALTYVTEEEEEE  1650
1651  EEAVGQEAEEEEAENNPEPYKDSIDSQPQSRWNSRISVSLPVKEKLPDSL  1700
1701  STGPSDDDGLAPNSRQPSVIQAGSQPHRRSSGVFMFTIPEEGSIQLKGTQ  1750
1751  GQDNQNEEQELPDWTPDLDRAGRDSFEPSPFTTSLVQQHVNGHMSTPTFA  1800
1801  APHACRSEPSFTIQCLQRLGSCEDLPIPGTYHRGRTSGPSRAQGSWAAPP  1850
1851  QKGRLLYAPLLLVEESTVGEGYLGKLGGPLRTFTCLQVPGAHPNPSHRKR  1900
1901  GSADSLVEAVLISEGLGLFAQDPRFVALAKQEIADACHLTLDEMDSAASD  1950
1951  LLAQRTISLYSDEESILSRFDEEDLGDEMACVHAL                 1985

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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