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

NucPred

Fetching Q14008 from www.uniprot.org...

The NucPred score for your sequence is 0.57 (see score help below)

   1  MGDDSEWLKLPVDQKCEHKLWKARLSGYEEALKIFQKIKDEKSPEWSKFL    50
  51  GLIKKFVTDSNAVVQLKGLEAALVYVENAHVAGKTTGEVVSGVVSKVFNQ   100
 101  PKAKAKELGIEICLMYIEIEKGEAVQEELLKGLDNKNPKIIVACIETLRK   150
 151  ALSEFGSKIILLKPIIKVLPKLFESREKAVRDEAKLIAVEIYRWIRDALR   200
 201  PPLQNINSVQLKELEEEWVKLPTSAPRPTRFLRSQQELEAKLEQQQSAGG   250
 251  DAEGGGDDGDEVPQIDAYELLEAVEILSKLPKDFYDKIEAKKWQERKEAL   300
 301  ESVEVLIKNPKLEAGDYADLVKALKKVVGKDTNVMLVALAAKCLTGLAVG   350
 351  LRKKFGQYAGHVVPTILEKFKEKKPQVVQALQEAIDAIFLTTTLQNISED   400
 401  VLAVMDNKNPTIKQQTSLFIARSFRHCTASTLPKSLLKPFCAALLKHIND   450
 451  SAPEVRDAAFEALGTALKVVGEKAVNPFLADVDKLKLDKIKECSEKVELI   500
 501  HGKKAGLAADKKEFKPLPGRTAASGAAGDKDTKDISAPKPGPLKKAPAAK   550
 551  AGGPPKKGKPAAPGGAGNTGTKNKKGLETKEIVEPELSIEVCEEKASAVL   600
 601  PPTCIQLLDSSNWKERLACMEEFQKAVELMDRTEMPCQALVRMLAKKPGW   650
 651  KETNFQVMQMKLHIVALIAQKGNFSKTSAQVVLDGLVDKIGDVKCGNNAK   700
 701  EAMTAIAEACMLPWTAEQVVSMAFSQKNPKNQSETLNWLSNAIKEFGFSG   750
 751  LNVKAFISNVKTALAATNPAVRTAAITLLGVMYLYVGPSLRMFFEDEKPA   800
 801  LLSQIDAEFEKMQGQSPPAPTRGISKHSTSGTDEGEDGDEPDDGSNDVVD   850
 851  LLPRTEISDKITSELVSKIGDKNWKIRKEGLDEVAGIINDAKFIQPNIGE   900
 901  LPTALKGRLNDSNKILVQQTLNILQQLAVAMGPNIKQHVKNLGIPIITVL   950
 951  GDSKNNVRAAALATVNAWAEQTGMKEWLEGEDLSEELKKENPFLRQELLG  1000
1001  WLAEKLPTLRSTPTDLILCVPHLYSCLEDRNGDVRKKAQDALPFFMMHLG  1050
1051  YEKMAKATGKLKPTSKDQVLAMLEKAKVNMPAKPAPPTKATSKPMGGSAP  1100
1101  AKFQPASAPAEDCISSSTEPKPDPKKAKAPGLSSKAKSAQGKKMPSKTSL  1150
1151  KEDEDKSGPIFIVVPNGKEQRMKDEKGLKVLKWNFTTPRDEYIEQLKTQM  1200
1201  SSCVAKWLQDEMFHSDFQHHNKALAVMVDHLESEKEGVIGCLDLILKWLT  1250
1251  LRFFDTNTSVLMKALEYLKLLFTLLSEEEYHLTENEASSFIPYLVVKVGE  1300
1301  PKDVIRKDVRAILNRMCLVYPASKMFPFIMEGTKSKNSKQRAECLEELGC  1350
1351  LVESYGMNVCQPTPGKALKEIAVHIGDRDNAVRNAALNTIVTVYNVHGDQ  1400
1401  VFKLIGNLSEKDMSMLEERIKRSAKRPSAAPIKQVEEKPQRAQNISSNAN  1450
1451  MLRKGPAEDMSSKLNQARSMSGHPEAAQMVRREFQLDLDEIENDNGTVRC  1500
1501  EMPELVQHKLDDIFEPVLIPEPKIRAVSPHFDDMHSNTASTINFIISQVA  1550
1551  SGDINTSIQALTQIDEVLRQEDKAEAMSGHIDQFLIATFMQLRLIYNTHM  1600
1601  ADEKLEKDEIIKLYSCIIGNMISLFQIESLAREASTGVLKDLMHGLITLM  1650
1651  LDSRIEDLEEGQQVIRSVNLLVVKVLEKSDQTNILSALLVLLQDSLLATA  1700
1701  SSPKFSELVMKCLWRMVRLLPDTINSINLDRILLDIHIFMKVFPKEKLKQ  1750
1751  CKSEFPIRTLKTLLHTLCKLKGPKILDHLTMIDNKNESELEAHLCRMMKH  1800
1801  SMDQTGSKSDKETEKGASRIDEKSSKAKVNDFLAEIFKKIGSKENTKEGL  1850
1851  AELYEYKKKYSDADIEPFLKNSSQFFQSYVERGLRVIEMEREGKGRISTS  1900
1901  TGISPQMEVTCVPTPTSTVSSIGNTNGEEVGPSVYLERLKILRQRCGLDN  1950
1951  TKQDDRPPLTSLLSKPAVPTVASSTDMLHSKLSQLRESREQHQHSDLDSN  2000
2001  QTHSSGTVTSSSSTANIDDLKKRLERIKSSRK                    2032

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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