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

NucPred

Fetching Q9FKS4 from www.uniprot.org...

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

   1  MAKDDNNLSSLVHELRERVAASASTPANNLRHSSGDEDALEIRFRAVIPN    50
  51  LLNTYVVPSLGNGREVTAVLKLVGHTARNIPGVFYHGTPSAILPVIARII   100
 101  PFFAEPEFVPGHGVLLETVGSLLMLLRSNSRKAYRIFFHDALQAIQDMQP   150
 151  IASLHSIEPEVCESHIPFRCFCMSFSGIGGDLPDANKPRDGDGLVLNLLG   200
 201  ANRWQPFATCILKLICKCLTEGTLYVQGLIHTSFFKAACSLVCCGGADVQ   250
 251  MACFEFATLVGSILTFNILPHVALIQSIILLLSADEGLPVYRNTIYDSTI   300
 301  GRFLTAVYSSCSDAAVKLTAESLVLVLSHALQRTKSEELKASLCSAYVRI   350
 351  VKSCPPCIWKIHCLLELLHLPEPCFQLIECFKAVLIVLGPGCVRVETTKC   400
 401  GSHTSATSDRPVQGINAGKKRHIEDESTYKRKRQKVGDDIRRGVYFAPEF   450
 451  ADETDGKDAASLREMLISTVESLKPPPAGPSLSQTESSIVALSMLTNAFC   500
 501  FCPWTDMTHRLFNQMYAWIPWIAGQVEETNPIMFDISIYLEGIHNLLLVG   550
 551  VDPQYEYTSKGNDLVAIQFLLKLPWTHYMLFKTPSSLVKSKCLSVGIWTK   600
 601  LGLQDGSDFDIFSWSLSDDFEQVQAVAAISMPLKVLFSGLGALLHMFPKL   650
 651  EHLLEEKELMIKKAIPQSLGFLSCLYGSSTTDSEKTACHLLLHEDLKKDE   700
 701  TLNSLLQGFRCSKCDKFIEREDEKHFRIIETPEMVKLKMDHHRDYFNLQS   750
 751  LYFNLLYDESSEETQLACVEVIRRILGHTSPDILVRTRSQWIRCLQYLLV   800
 801  HVNTDVREAFCAQIGIFVQHPIVSCLFLSEDATEKSCERNFFNLIEHSLA   850
 851  AAKDLLVIQTLLETTAEVMVAVDVTSELFLICLFLLIDQLDHPNLIVRIN   900
 901  ASKLINRSCYIHVKGGFATLLSTASHIQNELFDNLSVRLTSRPNVVREFA   950
 951  EAVLGVETEELVRKMVPAVLPKLLVYWQENAQAANTLNELAKLIDTDVVP  1000
1001  LIVNWLPRVLAFALNQEEDKNLLSVLQLYHSQIGSDNQEIFAAALPALLD  1050
1051  ELVCFVDIADTPETDRRLQRLPDAIKKISKVLTNAEDLPGFLQNHFVGLL  1100
1101  NSIDRKMLHADDIFLQKQALKRIKLLIEMMGHYLSTYVPKLMVLLMHAIE  1150
1151  KDALQSEGLLVLHFFTRKLADVSPSSIKYVISQIFAALIPFLEKEKEGPH  1200
1201  VYLDEVVKILEELVLKNRDIVKEHICEFPLLPSIPSLGELNNAIQEARGL  1250
1251  MSLKDQLRDIVNGMKHENLNVRYMVACELSKLLYNRNEDVAALIAGELVS  1300
1301  DMEILSSLITYLLQGCAEESRTTVGQRLKLVCADCLGAIGAIDPAKVRVA  1350
1351  SCSRFKIQCSDDDLIFELIHKHLARAFRAAQDTIIQDSAALAIQELLKIA  1400
1401  GCEPSLAGNVVVLTPQEHVQVNVSGSRRCGGNNEVKDRGQKLWDRFSNYV  1450
1451  KELIAPCLTSRFQLPNVSDPGSAGPIYRPSMSFRRWLSYWIRKLTAFATG  1500
1501  SRVSIFAACRGIVRHDMQTATYLLPYLVLDVVCHGTEAARLSISEEILSV  1550
1551  LDAAASENSGVTINSFGVGQSEVCVQAVFTLLDNLGQWVDDVKQGVALSS  1600
1601  SLQSSGGRQVAPKSKDQVSNSTTEQDHLLVQCKYVLELLLAIPKVTLARA  1650
1651  SFRCQAYARSLMYLESHVRGKSGSLNPAAEKTGIFENADVSSLMGIYSCL  1700
1701  DEPDGLSGFASLSKSLNLQDQLLINKKSGNWADVFTACEQALQMEPTSVQ  1750
1751  RHSDVLNCLLNMCHHQTMVTHVDGLISRVPEYKKTWCTQGVQAAWRLGKW  1800
1801  DLMDEYLDGADAEGLLFSSSDSNASFDRDVAKILHAMMKKDQYSVAEGIA  1850
1851  ISKQALIAPLAAAGMDSYTRAYPFVVKLHLLRELEDFQAVLNGDSYLEKS  1900
1901  FSTSDQVFSKAVDNWENRLRFTQSSLWTREPLLAFRRLVFGASGLGAQVG  1950
1951  NCWLQYAKLCRLAGHYETAHRAILEAQASGAPNVHMEKAKLLWITKRSDS  2000
2001  AIIELQQSLLNMPEGVVDSTVISSINSLLMAPPNPEPTVRNTQSFKEKKD  2050
2051  VAKTLLLYSKWIHHSGQKQKKDVLNLYTQVKELLPWEKGYFHLAKYYDEL  2100
2101  YVDARKCQQESSVFSSAGSKKGSVSSNLSTEKAGWDYLFKGMYFYAKALH  2150
2151  SGHKNLFQALPRLLTLWFDFGTIYKTSGSAGNKELKSTHMKIMSLMRGCL  2200
2201  KDLPTYQWLTVLPQLVSRICHQNADTVLMVKNIITSVLHQFPQQGLWIMA  2250
2251  AVSKSTVPARREAAAEIIQGARKGFNQSDRGHNLFIQFASLTDHFIKLCF  2300
2301  HGGQPRSKVINIATEFSALKRMMPLDIIMPIQQSLTISLPAFHMNNNERH  2350
2351  SASVFSGSDLPTISGIADEAEILSSLQRPKKIILLGNDGIEYPFLCKPKD  2400
2401  DLRKDARMMEFTAMINRLLSKYPESRRRKLYIRTFAVAPLTEDCGLVEWV  2450
2451  PHTRGLRHILQDIYISCGKFDRQKTNPQIKRIYDQCAVKKEYEMLKTKIL  2500
2501  PMFPPVFHKWFLTTFSEPAAWFRSRVAYAHTTAVWSMVGHIVGLGDRHGE  2550
2551  NILFDSTSGDCVHVDFSCLFDKGLQLEKPELVPFRLTQNMIDGLGITGYE  2600
2601  GIFMRVCEITLTVLRTHRETLMSILETFIHDPLVEWTKSHKSSGVEVQNP  2650
2651  HAQRAISSIEARLQGVVVGVPLPVEGQARRLIADAVSLENLGKMYIWWMP  2700
2701  WF                                                  2702

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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