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

NucPred

Fetching Q01513 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MPRNDASSRFSSMTGSSTDSARSNITVKPLPSLPPSASSSSPFAASSNQT    50
  51  SNASRSASHGSRRAAPSRLKTDENGQLSRSFKDSDAQVSPTSTSPCVSPS   100
 101  SITSSNSIREHRMSDLADYRRDLAILDPAGGRASRTQQNNPSSGSLSQIA   150
 151  PWMAAAPTPASSGPLPTSFFNDSTDNLSLSSQTSPGLRNATARPSQTTTG   200
 201  STESPETLYFTDERRPSIASITTTASSQGSRASGARGGIRKLQGFFGEEF   250
 251  PGRDSSEISLSHPIVGKEHRSHSYSHARPHRDRNYSNATDHGRDASPASR   300
 301  PRTPVPKPEVVPFLYQEADDIARYGEAPVRDILSGPDRERFVNDSSQQNN   350
 351  PPKTSGSGRSGHSIGVHLTGHHHRHNKSNEDPRSLRPTVSREDSTISVPK   400
 401  DRNGSSTMYGTRSRAQSPAPSTTGSYWGHKSGSTDGQTSPGQPKKSFLGR   450
 451  LGRRLKEKDDAPDLKKLGPASQSSLHSRPSRQELSKADGQFARGADGKYQ   500
 501  PDVRDGIRPDLARPANGPQTFNKFSLSKKAPRSKTQDDLDEAIGPTDRQD   550
 551  VGTVFHLDTNLNNMDGILSKPAPLTPMNAHEIFDEVGSGKGSISYPSSNG   600
 601  AWNAPDSWAVLRDDDAGAQLPDTEDIGSPPRPEEKQHNYCIRVFRADGTF   650
 651  ATLQMPLLTSVSELINQIVKKSYLQDPDKFKLVLKKHDLYKVLQSTDRPL   700
 701  LLQKRLLEQVGFEERDRIEDIGREDNSYLCRFLFYPFTDNSYEVMDQMEF   750
 751  LRSQKNNHIDLSGRSLSAIPVQLYPRANEIISLNLSRNLSLQVPRDFISV   800
 801  CPNLRDIKFNNNEARALPKSFGYASRLTMLDASNNRLESLESAALHNLTG   850
 851  LLKLNLANNKLKQLPREFEAFAVLRTLNISSNLLNNFPPFLAKLENLVDL   900
 901  DLSFNTIQSLPDNVGQMTSLERLVITNNELSGSLPPSFKNLRSLRELDIK   950
 951  YNAISNIDVISQLPKLEILSATRNNISQFSGTFERVRSIKLNWNPITKFE  1000
1001  IKAPVPTLKALNLSNAQLASIDESFHNMSNLERLELDKNYFVSLPAHIGN  1050
1051  LRRLEYFSIAHNSVGELPPEIGCLTELKRLDVRGNNIRKLPMELWWANKL  1100
1101  DYLNASSNVLENFPKPASRAPHPPGETNGNTSFPTGRIGPPTGALSQTPS  1150
1151  AEELNDPSRRPSQASSSLLSVGPSPVPGGADRKSSMVSVYGKGGRKTSVI  1200
1201  SRSTTQSSTALATPTASSRKDSSHTQRLTNTFAGSLRYLYMADNQLDDDC  1250
1251  FDQLCMLENLRVLNLSYNDLSDMPQRSIKSWPQLVELYLSGNELASLPAD  1300
1301  DLEEYSMLQTLHINGNKFTNLPADISRAKKLTVFDCGSNSLKYNIANVPY  1350
1351  DWNWNLNPNLRYLNLSGNRRLEIKQSSVPTAAQNREQYTDFGRLTNLRVL  1400
1401  GLMDVTVLNSTLPDQSEDRRVRTSGSLAGYMPYGMADTLGSKNEHLSTID  1450
1451  LVVPRFNSNDSETLLGLFDGQALSSGGSKIAKYLQENFGHIFSQELRDLK  1500
1501  NTENPADALRRSFLSLNKDLIAAGNTHTEDRSLMVHRGSTAPLVLSREDM  1550
1551  NSGGVATIVYIQNQDLYVANVGDVQAMIIKSDSTHVMLTKKHDPADPNER  1600
1601  TRIREAGGWVSRNGRLNDLLEVSRAFGYLDLMPAVQSAPNIEKHTIGEHD  1650
1651  EMILIATREVWEYLPKDVLVDVTRSVRQDPDPMRAAQKVRDLAMAYGCSN  1700
1701  KMTVQMLGVSNLKARRERSRQHKGQSMPVYASLQDDGGSSTGMRRARKAR  1750
1751  DGPLDSTLGRLDAEVPAPTGLIAIVFTDIKNSTQLWETYPEAMRTAIKNH  1800
1801  NELMRRQLRTIGGFEVKTEGDAFMVSFPTATSALLWCFAVQCKLLHLDWP  1850
1851  AELYNSVNCQPVYDRDNNLIFKGLSVRMGIHWGEPLSEPDPVTRRMDYYG  1900
1901  PMVNKASRISACADGGQIAVSSDFIAEIQRCLEHYQEPTSTAVDLNEDSF  1950
1951  ATAIRSELRSLSGQGFEVKDMGEKKLKGLENPEFIYSLYPHALSGRIETH  2000
2001  SKHEKEQAQDLREIRPAILSPGSELSVEPDDIWSLWRVALRLEMLCSMLE  2050
2051  DNSKALQPPETGLLDRMRQRGGEVSEDFLVNFLDHQVSRIETCINTIYMR  2100
2101  HLVSQSSIGSNFGALRGPMDEVLKVVAEQFQLVAEYKARYGDLRA       2145

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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