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

NucPred

Fetching P51123 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MEMESDNSDDEGSIGNGLDLTGILFGNIDSEGRLLQDDDGEGRGGTGFDA    50
  51  ELRENIGSLSKLGLDSMLLEVIDLKEAEPPSDDEEEEDARPSAVSASEGM   100
 101  SAFDALKAGVKREDGAVKAQDDAIDYSDITELSEDCPRTPPEETSTYDDL   150
 151  EDAIPASKVEAKLTKDDKELMPPPSAPMRSGSGGGIEEPAKSNDASSPSD   200
 201  DSKSTDSKDADRKLDTPLADILPSKYQNVDVRELFPDFRPQKVLRFSRLF   250
 251  GPGKPTSLPQIWRHVRKRRRKRNQSRDQKTTNTGGSDSPSDTEEPRKRGF   300
 301  SLHYAAEPTPAECMSDDEDKLLGDFNSEDVRPEGPDNGENSDQKPKVADW   350
 351  RFGPAQIWYDMLEVPDSGEGFNYGFKTKAASTSSQPQLKDERRVKSPEDD   400
 401  VEDPSIADDAFLMVSQLHWEDDVVWDGNDIKAKVLQKLNSKTNAAGWLPS   450
 451  SGSRTAGAFSQPGKPSMPVGSGSSKQGSGASSKKAQQNAQAKPAEAPDDT   500
 501  WYSLFPVENEELIYYKWEDEVIWDAQQVSKVPKPKVLTLDPNDENIILGI   550
 551  PDDIDPSKINKSTGPPPKIKIPHPHVKKSKILLGKAGVINVLAEDTPPPP   600
 601  PKSPDRDPFNISNDTYYTPKTEPTLRLKVGGNLIQHSTPVVELRAPFVPT   650
 651  HMGPMKLRAFHRPPLKKYSHGPMAQSIPHPVFPLLKTIAKKAKQREVERI   700
 701  ASGGGDVFFMRNPEDLSGRDGDIVLAEFCEEHPPLINQVGMCSKIKNYYK   750
 751  RKAEKDSGPQDFVYGEVAFAHTSPFLGILHPGQCIQAIENNMYRAPIYPH   800
 801  KMAHNDFLVIRTRNNYWIRSVNSIYTVGQECPLYEVPGPNSKRANNFTRD   850
 851  FLQVFIYRLFWKSRDNPRRIRMDDIKQAFPAHSESSIRKRLKQCADFKRT   900
 901  GMDSNWWVIKPEFRLPSEEEIRAMVSPEQCCAYFSMIAAEQRLKDAGYGE   950
 951  KFLFAPQEDDDEEAQLKLDDEVKVAPWNTTRAYIQAMRGKCLLQLSGPAD  1000
1001  PTGCGEGFSYVRVPNKPTQTKEEQESQPKRSVTGTDADLRRLPLQRAKEL  1050
1051  LRQFKVPEEEIKKLSRWEVIDVVRTLSTEKAKAGEEGMDKFSRGNRFSIA  1100
1101  EHQERYKEECQRIFDLQNRVLASSEVLSTDEAESSASEESDLEELGKNLE  1150
1151  NMLSNKKTSTQLSREREELERQELLRQLDEEHGGPSGSGGAKGAKGKDDP  1200
1201  GQQMLATNNQGRILRITRTFRGNDGKEYTRVETVRRQPVIDAYIKIRTTK  1250
1251  DEQFIKQFATLDEQQKEEMKREKRRIQEQLRRIKRNQERERLAQLAQNQK  1300
1301  LQPGGMPTSLGDPKSSGGHSHKERDSGYKEVSPSRKKFKLKPDLKLKCGA  1350
1351  CGQVGHMRTNKACPLYSGMQSSLSQSNPSLADDFDEQSEKEMTMDDDDLV  1400
1401  NVDGTKVTLSSKILKRHGGDDGKRRSGSSSGFTLKVPRDAMGKKKRRVGG  1450
1451  DLHCDYLQRHNKTANRRRTDPVVVLSSILEIIHNELRSMPDVSPFLFPVS  1500
1501  AKKVPDYYRVVTKPMDLQTMREYIRQRRYTSREMFLEDLKQIVDNSLIYN  1550
1551  GPQSAYTLAAQRMFSSCFELLAEREDKLMRLEKAINPLLDDDDQVALSFI  1600
1601  FDKLHSQIKQLPESWPFLKPVNKKQVKDYYTVIKRPMDLETIGKNIEAHR  1650
1651  YHSRAEYLADIELIATNCEQYNGSDTRYTKFSKKILEYAQTQLIEFSEHC  1700
1701  GQLENNIAKTQERARENAPEFDEAWGNDDYNFDRGSRASSPGDDYIDVEG  1750
1751  HGGHASSSNSIHRSMGAEAGSSHTAPAVRKPAPPGPGEVKRGRGRPRKQR  1800
1801  DPVEEVKSQNPVKRGRGRPRKDSLASNMSHTQAYFLDEDLQCSTDDEDDD  1850
1851  EEEDFQEVSEDENNAASILDQGERINAPADAMDGMFDPKNIKTEIDLEAH  1900
1901  QMAEEPIGEDDSQQVAEAMVQLSGVGGYYAQQQQDESMDVDPNYDPSDFL  1950
1951  AMHKQRQSLGEPSSLQGAFTNFLSHEQDDNGPYNPAEASTSAASGADLGM  2000
2001  DASMAMQMAPEMPVNTMNNGMGIDDDLDISESDEEDDGSRVRIKKEVFDD  2050
2051  GDYALQHQQMGQAASQSQIYMVDSSNEPTTLDYQQPPQLDFQQVQEMEQL  2100
2101  QHQVMPPMQSEQLQQQQTPQGDNDYAWTF                       2129

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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