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

NucPred

Fetching Q02224 from www.uniprot.org...

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

   1  MAEEGAVAVCVRVRPLNSREESLGETAQVYWKTDNNVIYQVDGSKSFNFD    50
  51  RVFHGNETTKNVYEEIAAPIIDSAIQGYNGTIFAYGQTASGKTYTMMGSE   100
 101  DHLGVIPRAIHDIFQKIKKFPDREFLLRVSYMEIYNETITDLLCGTQKMK   150
 151  PLIIREDVNRNVYVADLTEEVVYTSEMALKWITKGEKSRHYGETKMNQRS   200
 201  SRSHTIFRMILESREKGEPSNCEGSVKVSHLNLVDLAGSERAAQTGAAGV   250
 251  RLKEGCNINRSLFILGQVIKKLSDGQVGGFINYRDSKLTRILQNSLGGNA   300
 301  KTRIICTITPVSFDETLTALQFASTAKYMKNTPYVNEVSTDEALLKRYRK   350
 351  EIMDLKKQLEEVSLETRAQAMEKDQLAQLLEEKDLLQKVQNEKIENLTRM   400
 401  LVTSSSLTLQQELKAKRKRRVTWCLGKINKMKNSNYADQFNIPTNITTKT   450
 451  HKLSINLLREIDESVCSESDVFSNTLDTLSEIEWNPATKLLNQENIESEL   500
 501  NSLRADYDNLVLDYEQLRTEKEEMELKLKEKNDLDEFEALERKTKKDQEM   550
 551  QLIHEISNLKNLVKHAEVYNQDLENELSSKVELLREKEDQIKKLQEYIDS   600
 601  QKLENIKMDLSYSLESIEDPKQMKQTLFDAETVALDAKRESAFLRSENLE   650
 651  LKEKMKELATTYKQMENDIQLYQSQLEAKKKMQVDLEKELQSAFNEITKL   700
 701  TSLIDGKVPKDLLCNLELEGKITDLQKELNKEVEENEALREEVILLSELK   750
 751  SLPSEVERLRKEIQDKSEELHIITSEKDKLFSEVVHKESRVQGLLEEIGK   800
 801  TKDDLATTQSNYKSTDQEFQNFKTLHMDFEQKYKMVLEENERMNQEIVNL   850
 851  SKEAQKFDSSLGALKTELSYKTQELQEKTREVQERLNEMEQLKEQLENRD   900
 901  STLQTVEREKTLITEKLQQTLEEVKTLTQEKDDLKQLQESLQIERDQLKS   950
 951  DIHDTVNMNIDTQEQLRNALESLKQHQETINTLKSKISEEVSRNLHMEEN  1000
1001  TGETKDEFQQKMVGIDKKQDLEAKNTQTLTADVKDNEIIEQQRKIFSLIQ  1050
1051  EKNELQQMLESVIAEKEQLKTDLKENIEMTIENQEELRLLGDELKKQQEI  1100
1101  VAQEKNHAIKKEGELSRTCDRLAEVEEKLKEKSQQLQEKQQQLLNVQEEM  1150
1151  SEMQKKINEIENLKNELKNKELTLEHMETERLELAQKLNENYEEVKSITK  1200
1201  ERKVLKELQKSFETERDHLRGYIREIEATGLQTKEELKIAHIHLKEHQET  1250
1251  IDELRRSVSEKTAQIINTQDLEKSHTKLQEEIPVLHEEQELLPNVKEVSE  1300
1301  TQETMNELELLTEQSTTKDSTTLARIEMERLRLNEKFQESQEEIKSLTKE  1350
1351  RDNLKTIKEALEVKHDQLKEHIRETLAKIQESQSKQEQSLNMKEKDNETT  1400
1401  KIVSEMEQFKPKDSALLRIEIEMLGLSKRLQESHDEMKSVAKEKDDLQRL  1450
1451  QEVLQSESDQLKENIKEIVAKHLETEEELKVAHCCLKEQEETINELRVNL  1500
1501  SEKETEISTIQKQLEAINDKLQNKIQEIYEKEEQFNIKQISEVQEKVNEL  1550
1551  KQFKEHRKAKDSALQSIESKMLELTNRLQESQEEIQIMIKEKEEMKRVQE  1600
1601  ALQIERDQLKENTKEIVAKMKESQEKEYQFLKMTAVNETQEKMCEIEHLK  1650
1651  EQFETQKLNLENIETENIRLTQILHENLEEMRSVTKERDDLRSVEETLKV  1700
1701  ERDQLKENLRETITRDLEKQEELKIVHMHLKEHQETIDKLRGIVSEKTNE  1750
1751  ISNMQKDLEHSNDALKAQDLKIQEELRIAHMHLKEQQETIDKLRGIVSEK  1800
1801  TDKLSNMQKDLENSNAKLQEKIQELKANEHQLITLKKDVNETQKKVSEME  1850
1851  QLKKQIKDQSLTLSKLEIENLNLAQKLHENLEEMKSVMKERDNLRRVEET  1900
1901  LKLERDQLKESLQETKARDLEIQQELKTARMLSKEHKETVDKLREKISEK  1950
1951  TIQISDIQKDLDKSKDELQKKIQELQKKELQLLRVKEDVNMSHKKINEME  2000
2001  QLKKQFEAQNLSMQSVRMDNFQLTKKLHESLEEIRIVAKERDELRRIKES  2050
2051  LKMERDQFIATLREMIARDRQNHQVKPEKRLLSDGQQHLTESLREKCSRI  2100
2101  KELLKRYSEMDDHYECLNRLSLDLEKEIEFQKELSMRVKANLSLPYLQTK  2150
2151  HIEKLFTANQRCSMEFHRIMKKLKYVLSYVTKIKEEQHESINKFEMDFID  2200
2201  EVEKQKELLIKIQHLQQDCDVPSRELRDLKLNQNMDLHIEEILKDFSESE  2250
2251  FPSIKTEFQQVLSNRKEMTQFLEEWLNTRFDIEKLKNGIQKENDRICQVN  2300
2301  NFFNNRIIAIMNESTEFEERSATISKEWEQDLKSLKEKNEKLFKNYQTLK  2350
2351  TSLASGAQVNPTTQDNKNPHVTSRATQLTTEKIRELENSLHEAKESAMHK  2400
2401  ESKIIKMQKELEVTNDIIAKLQAKVHESNKCLEKTKETIQVLQDKVALGA  2450
2451  KPYKEEIEDLKMKLVKIDLEKMKNAKEFEKEISATKATVEYQKEVIRLLR  2500
2501  ENLRRSQQAQDTSVISEHTDPQPSNKPLTCGGGSGIVQNTKALILKSEHI  2550
2551  RLEKEISKLKQQNEQLIKQKNELLSNNQHLSNEVKTWKERTLKREAHKQV  2600
2601  TCENSPKSPKVTGTASKKKQITPSQCKERNLQDPVPKESPKSCFFDSRSK  2650
2651  SLPSPHPVRYFDNSSLGLCPEVQNAGAESVDSQPGPWHASSGKDVPECKT  2700
2701  Q                                                   2701

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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