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

NucPred

Fetching Q9BTC0 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MDDKGDPSNEEAPKAIKPTSKEFRKTWGFRRTTIAKREGAGDAEADPLEP    50
  51  PPPQQQLGLSLRRSGRQPKRTERVEQFLTIARRRGRRSMPVSLEDSGEPT   100
 101  SCPATDAETASEGSVESASETRSGPQSASTAVKERPASSEKVKGGDDHDD   150
 151  TSDSDSDGLTLKELQNRLRRKREQEPTERPLKGIQSRLRKKRREEGPAET   200
 201  VGSEASDTVEGVLPSKQEPENDQGVVSQAGKDDRESKLEGKAAQDIKDEE   250
 251  PGDLGRPKPECEGYDPNALYCICRQPHNNRFMICCDRCEEWFHGDCVGIS   300
 301  EARGRLLERNGEDYICPNCTILQVQDETHSETADQQEAKWRPGDADGTDC   350
 351  TSIGTIEQKSSEDQGIKGRIEKAANPSGKKKLKIFQPVIEAPGASKCIGP   400
 401  GCCHVAQPDSVYCSNDCILKHAAATMKFLSSGKEQKPKPKEKMKMKPEKP   450
 451  SLPKCGAQAGIKISSVHKRPAPEKKETTVKKAVVVPARSEALGKEAACES   500
 501  STPSWASDHNYNAVKPEKTAAPSPSLLYKSTKEDRRSEEKAAAMAASKKT   550
 551  APPGSAVGKQPAPRNLVPKKSSFANVAAATPAIKKPPSGFKGTIPKRPWL   600
 601  SATPSSGASAARQAGPAPAAATAASKKFPGSAALVGAVRKPVVPSVPMAS   650
 651  PAPGRLGAMSAAPSQPNSQIRQNIRRSLKEILWKRVNDSDDLIMTENEVG   700
 701  KIALHIEKEMFNLFQVTDNRYKSKYRSIMFNLKDPKNQGLFHRVLREEIS   750
 751  LAKLVRLKPEELVSKELSTWKERPARSVMESRTKLHNESKKTAPRQEAIP   800
 801  DLEDSPPVSDSEEQQESARAVPEKSTAPLLDVFSSMLKDTTSQHRAHLFD   850
 851  LNCKICTGQVPSAEDEPAPKKQKLSASVKKEDLKSKHDSSAPDPAPDSAD   900
 901  EVMPEAVPEVASEPGLESASHPNVDRTYFPGPPGDGHPEPSPLEDLSPCP   950
 951  ASCGSGVVTTVTVSGRDPRTAPSSSCTAVASAASRPDSTHMVEARQDVPK  1000
1001  PVLTSVMVPKSILAKPSSSPDPRYLSVPPSPNISTSESRSPPEGDTTLFL  1050
1051  SRLSTIWKGFINMQSVAKFVTKAYPVSGCFDYLSEDLPDTIHIGGRIAPK  1100
1101  TVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYISLYSYFSSRGRFGVVA  1150
1151  NNNRHVKDLYLIPLSAQDPVPSKLLPFEGPGLESPRPNIILGLVICQKIK  1200
1201  RPANSGELDKMDEKRTRLQPEEADVPAYPKVATVPQSEKKPSKYPLCSAD  1250
1251  AAVSTTPPGSPPPPPPLPEPPVLKVLSSLKPAAPSPATAATTAAAASTAA  1300
1301  SSTASSASKTASPLEHILQTLFGKKKSFDPSAREPPGSTAGLPQEPKTTA  1350
1351  EDGVPAPPLLDPIVQQFGQFSKDKALEEEEDDRPYDPEEEYDPERAFDTQ  1400
1401  LVERGRRHEVERAPEAAAAEREEVAYDPEDETILEEAKVTVDDLPNRMCA  1450
1451  DVRRNSVERPAEPVAGAATPSLVEQQKMLEELNKQIEEQKRQLEEQEEAL  1500
1501  RQQRAAVGVSMAHFSVSDALMSPPPKSSLPKAELFQQEQQSADKPASLPP  1550
1551  ASQASNHRDPRQARRLATETGEGEGEPLSRLSARGAQGALPERDASRGGL  1600
1601  VGQAPMPVPEEKEPASSPWASGEKPPAGSEQDGWKAEPGEGTRPATVGDS  1650
1651  SARPARRVLLPTPPCGALQPGFPLQHDGERDPFTCPGFASQDKALGSAQY  1700
1701  EDPRNLHSAGRSSSPAGETEGDREPQARPGEGTAPLPPPGQKVGGSQPPF  1750
1751  QGQREPGPHALGMSGLHGPNFPGPRGPAPPFPEENIASNDGPRGPPPARF  1800
1801  GAQKGPIPSLFSGQHGPPPYGDSRGPSPSYLGGPRGVAPSQFEERKDPHG  1850
1851  EKREFQDAPYNEVTGAPAQFEGTEQAPFLGSRGGAPFQFGGQRRPLLSQL  1900
1901  KGPRGGPPPSQFGGQRGPPPGHFVGPRGPHPSQFETARGPHPNQFEGPRG  1950
1951  QAPNFMPGPRGIQPQQFEDQRVHSPPRFTNQRAPAPLQFGGLRGSAPFSE  2000
2001  KNEQTPSRFHFQGQAPQVMKPGPRPLLELPSHPPQHRKDRWEEAGPPSAL  2050
2051  SSSAPGQGPEADGQWASADFREGKGHEYRNQTFEGRQRERFDVGPKEKPL  2100
2101  EEPDAQGRASEDRRRERERGRNWSRERDWDRPREWDRHRDKDSSRDWDRN  2150
2151  RERSANRDREREADRGKEWDRSRERSRNRERERDRRRDRDRSRSRERDRD  2200
2201  KARDRERGRDRKDRSKSKESARDPKPEASRASDAGTASQA            2240

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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