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

NucPred

Fetching P98081 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MVKSLVAKLSTASSNLSLASTFGGGSGAAEETNYAKHRNDPGRFFGDGVQ    50
  51  FKAKLIGILEVGEARGDRMCQEALQDLKMAIRAAGEHKQRITIHVTIDGL   100
 101  RLRDEKTGDSLYHHPVHKISFIAQDMTDSRAFGYIFGSPDSGHRFFGIKT   150
 151  DKAASQVVLAMRDLFQVVFELKKKEIEMARQQIQGKSLHDHSSQLASLSS   200
 201  LKSSGLGGMGLGHSDLASGGISSGHALTLLGSSLSTTNGTSRLGVSLDVA   250
 251  KASGSAAKEVSPESVADLVDLEQELTSLQRGISQMERITPNEPTTSSTGG   300
 301  AGHPSLAKSASEDDPFGDSFIYVPSYSILPPPPDSGRNRHKPPNKTPDAV   350
 351  TSLDAMLSPPPGTSSSHGSASAGLQAADNDDDNWLQELDQQNDVFDTSKV   400
 401  VSSSGLGSVLAMAPLASSESTATPTQQLTEVAAGSGPLADLDIGLSTALG   450
 451  NEEQTSTILSLDAFTDLDPLGTGRTRPYVDKKYFFQELKNPPKKLLKELS   500
 501  SGSQAGLGLGLSLGQLDGLFPEDSTTISTTTTTATNITAGNPQQNSANTL   550
 551  TSTASTAASLGQLLSTVALNPDPLPAPISIPTSISHSITPSAELKLLLGH   600
 601  VTNPPNPTGHYYTTEPPTLNSLENPHPPADPVLLPRDTDPFSPTRKKSDP   650
 651  DPFQESDLFAKLDAFEFEAPPAVPAPSIPNLATETKANVFNGPLQVQLPP   700
 701  EKELQLQQPPSTVRNRPTASVSALPSGGALDVISSISNKKMPHLFGQARS   750
 751  FGKSGSDIGSSVNMRRLQESDSLSETEAAPEPPPRPDSTPYSEPPPLPPK   800
 801  KQFSDLVIRPSPANTTQPPTSGRYEYLNSNVTARRTASSVDAPPIPLPSR   850
 851  RVGRSDGCFPGPGRPRKPGHTEDDYLAPLGAPPPLLPPPSQGSSARARPQ   900
 901  RQASLGRPQDIYENKAEILQAQAQAQAQAPEVAPSSNTLAPDITLTQLLT   950
 951  LGMDDLAIKLNVPASKLSTMTLVQLTAYLSEYLSSEKSQVHSQERRSSPA  1000
1001  NTAPAPASTAAVFKVNFDQQTSFVAKFDDTFGEDEPVMPSGSSDSTFVAN  1050
1051  FANFNDAPTPVPTVSPVVATVPSADRYAVFREIIDQELQQQQQETDLMGD  1100
1101  LTPPPVDETQAKEISEGLEVNNVGAELPIDALDVKPAPKIDTKITEVVAQ  1150
1151  AKDRYAALRDIILVENLFDKPAIATDTQPEKEKDLLQDFPEFSDEFNEDH  1200
1201  DLRQIMDHQNVQTHARDRHGLVDSRGFPTEPSSSALTVGDYDEDEDADAG  1250
1251  GESSLDSNEKDAEPVSGQDQYEKLSTSTQQLDAAAPALEDVQQLQQQSLP  1300
1301  PKQDQKFLSILTAPGGGTKDDIEIDELMHRAISNLSLDSRDRVSPATSSA  1350
1351  APSRGAPGLHTPSQFNDVSTSPIPLQKPGMGPSPVPSQLSAVSQLIDTAT  1400
1401  KQMMGDKDREKQSWATFDSPKAKGKARLTLPPPPPPASNTSQPDTVESPC  1450
1451  SSDPRDDGWSKQQRRWAKKERQQTSSSSRDLSPWDDETPEYLKRRQLAAA  1500
1501  QMAHPHQPPMQAPPQHTDRHGYYMRHARRMNSCDEDYDYDGEFVARRDQP  1550
1551  QHQQQQRKFKHGLSRSRDNFELESPSWYHHPAHHTWSPQEIEQVRVRSFD  1600
1601  RTAYERSSYGPPPPIYDKRGQLRGKYRGDHRDRERERDRDREYRDYARPS  1650
1651  YDFDYENVYEERGGRSPLAYKPGRGGGDYLYDRERDRDRERDRKSFDRES  1700
1701  LESYESATRRRRSFGSGNDVYGSLDSRDDYRGDRERDRERDREQMKTRSL  1750
1751  RKPTTTSGKLRISGDIDYEQDSEQDFQQRSGVRSLQRPNQLGGDVVLPSN  1800
1801  AVVGPQRLRKSSGSSPWDGEEPALPGQKSWKRPASAAETERRLAESRRAV  1850
1851  ALGQTPSDGEKERRFRKKTRARSAKDLATVGAPSASTSAPSRSSYGRGIR  1900
1901  DNYDYICPGQRNDDDDDDDEDYVDDEPPTDEDKFERLNRRRHEMHQRMLE  1950
1951  SERRQMERHQPPSLAKLPGQNRTRGVVANSDYGFVDSYEQTPTPTPRSNA  2000
2001  SSTGPGGLMMSGGESSAGVTSSKFNFDDGFESDFNQSSPPPAPAGTASSC  2050
2051  NSTPAGPVSANANNGGSKSLFRFSNDFSDREKREQFEMDTPPTSTPPITQ  2100
2101  KLRFDDNVKVSQFDDAAFEDDFAKASFDFEKEQAGSATAGAGGSGAMSRK  2150
2151  QNMRTSKLQQRQELIKKSESVNIFAKKQEDPFEDDEFFKSPDQEQAMDQH  2200
2201  NDDTEGGKFQWSEDANFAKFDENM                            2224

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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