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

NucPred

Fetching Q61CW2 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MLTSKNNDIGNLIEIFRQRDITYKERKATLQKIEELIPKVPDLEALNTKW    50
  51  IYLLDNAVWPLIVKSDRMDLKSLAGKVTRHVGALLFDSPFYPEFLLWLGT   100
 101  LLQNTPKKNDDARADIVFSVYYIVGAISQKSENRLGKNDEEYVRKSLEWL   150
 151  IRVIPNSSSAVYNNCLKGIILISNTFRKVTDDLYESCLRAIVSNFPDFNS   200
 201  HEKNFERLLDTVNLFSDHFSKDPVLAEEMVRIIRPDIKKNGLRNTRELKK   250
 251  RLKLTMAIVKMAKSQQILVETNEMMCELQAELEGNGGKWSSAALITIICD   300
 301  LLNELLILGKNDAEMRQSVEESLGNLLKDLNLSKQNTKEKQAFFNSLAKI   350
 351  VKQLPAESDVKTRIHHIVFNSDTGLFNIQNDDNRIFGHNTIYRDLVNLIS   400
 401  VLLTPTSLSHLQATYTDLRKIMMESMSKLKQSERWHESILLLFFSALQGI   450
 451  SCAKSSLIVMIGIRPSIFELFCDELPLTEYWLASNHPEVYHIFITILVGH   500
 501  LKAHDFYVSQSDYLVHGETPTGHAYGQTKREYVRKQVIALHKIIGGFGNR   550
 551  LWKKTRFLISTWLHSLVVIARDQKISAESFRLKEWVRLRNTVIQHSVLDW   600
 601  NNESINQALTVLSTVTNWSALPLELNKDITDKTKKATWKEATTIWESGDF   650
 651  KTYIRQSLSTTYQMSQERQQKQIGSTSFGAEEFNLVTNFLLKQIVPTTFK   700
 701  KGPYVWMDEVLETAIQGCKNISQEKSDVPETFMEKWDWIINQTANFCIVN   750
 751  KMKTPLGKPMQTFAAFENEIKRLAKEVINRKSSDKKPKSTTEDVPPPATP   800
 801  PLKFSIQWLRVHLLLKLIEVLEKIMISSIRGGSSIFNLTEIPVTARQFFI   850
 851  MNSSSCEVWLNRVYYPALIVAYFNGYYGLVIRFGSNALNHYARQKGSDEK   900
 901  MITNGVCTACLMSLSMAVLGEPMEIVGLRRRVREEFGTEMGQKLMEALGE   950
 951  MASARYEIALVQLEAILVVDSSINETLRIIIQIAITDMLNRIRLPDAVRY  1000
1001  YKKTLFGEDEEAQVAEDFRSIEMLTKFEKLNYGVAEKRQVVDWSARERLQ  1050
1051  LVESAYSQTMKRNELLELQKEMSAMGALALSADSSCKLYSDISSTSLVIA  1100
1101  NLVDRMTGTSHWKNQLTDVEMFDRAEEGNEGDKLTICRKLMHWGRHMKHH  1150
1151  RGQSFAAHGEIIRFSRKTSNCELAFFHINSAIRGEKLEAWQRLEVERQRL  1200
1201  KLVKSQHFDVRVREMNEVFGSLADVFSTSIEMKQKFQNLDDQTKDLMVAN  1250
1251  GYLSDIAKREEHMSRASIQLADFFDTLPTIDTVLTPNLYNTIIWSEIQSR  1300
1301  SNSLSCGYAGLVGALYNLSADLCPSLAKAHLKMAKWTYEMAKIENFPNIS  1350
1351  PFALYQFGQTAQENEELWRSLDATSLVNLEKQVRKIVPDAMRASVLLSPN  1400
1401  NPYLLLWEAASAHRRKFLCITVSSYFQFIHNMSGDFECLPYSKREETTLA  1450
1451  TLRILEMLVKHGEVLVDVINDGLSRTNVHVWKEILPQLFARLSHPSDHIR  1500
1501  KTLVDLISRVCTAAPHAVVFQVVSGAASSTEVSDLEEQQNDDRNRVRACC  1550
1551  EQLETKMAQSYPNLVRDVRQFVAELERINLLNEEKWSVVLGTMEHEMEKR  1600
1601  LALIKAENAKTDFSMHLMPKQKDEIISKKTKLLTRQIFDVLDELYEKTIV  1650
1651  AQPETENEKEFFNTFSEMLTKAHTESKNNRYNSPEASWAPFKNLVSNFAH  1700
1701  RTNKKGMQTFQTADISQYLATLGKSCVPMPGQESVEFDRVVSIARVADNV  1750
1751  TILPTKTRPKKLGFIGSDGKQLAFLFKGREDLHLDERVMQFLRLCNVMLQ  1800
1801  SEKGKSRQIAEYQAHHYAVIPLGPRSGLIKWVEGATPIFHIYRKWQMKEK  1850
1851  ALKQATKKNGETVPEIEKPTNMYHNMIRQAFTAHNIDAIIASDRSKWPAQ  1900
1901  ILEEVFDGLCSKTPTDLISREIWMRANDSTAWWAVTKRYARSLAVMSMVG  1950
1951  SVLGLGDRHLDNLLVDLKYGHVVHIDYNICFDKGKILRIPETVPFRLSRN  2000
2001  MRHALGPSDMYGTFRESCVHVLSTLRSGHQVLTMLLDAFVFDPLVDWTSH  2050
2051  DNISTSGGVSLALQLAVYGSSWKAKARERLTDTIELFQLRVTELQALWMS  2100
2101  NREDLYHWMKQVTDCLLAEQSIMGMNGAYAQQRVKAGTELREAVARHQAL  2150
2151  AKEFRPLIRVIGKEKEEFADYLKFYKQAFIDPLLKGHSALRHELDIDTCV  2200
2201  QNFNIVMQNIDVVFMSLISLSTMPIDSVSSRASQKQFNAPPGLENVWVLQ  2250
2251  QEQQENSQAREVVRRVERRLNGWLDGSAPDRKLSPREEADVLIAEATSSA  2300
2301  NLAQMYEGWTAWV                                       2313

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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