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

NucPred

Fetching Q8I8U7 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MSVIENVPVNTFRNYLNILNDSSSKDELKLKATQELSEHFEMIMQSPAYP    50
  51  SFLDNSLKIFMRILQDGEPQFIQENTMQHIRKLILEMIHRLPITESLRQH   100
 101  VKTIITMMLKILKTDNEENVLVCLRIIIELHKHFRPSFNSEIQLFLGFVK   150
 151  EIYTNLPNHLTSIFETSNDVWVTDLKDLNLEVLLSESYSVRTIHVEKALD   200
 201  SNSQQQIYNLLPRGILSLKVLQELPIIVVLMYQIYKNAVHQEVSEFIPLI   250
 251  LTTINLQPTVTRRNSPQKEIYVEFMGAQIKTLSFLAYIVRIFQEVVIASS   300
 301  LSVTSGMLNLMKNCPKEAAHLRKELLIAARHIFATDLRQKFIPSIEQLFD   350
 351  EDLLIGKGVTLDSIRPLAYSTLADLAHHVRQSLNIDVLIKAVNLFSKNVH   400
 401  DESLAVGIQTMSCKLLLNLVDCLRHHSETEPQRSKALLSKLLKVFVKKFE   450
 451  TIAKIQLPLIIQKCKGHAFSGALVNSSGNASLSHINAPDLKDDISNIQVS   500
 501  ASGSQWIYSVNVAEFRSLVKTLVGGVKTITWGFFNSKFQLTDTKLANHEK   550
 551  IFGPEIVCSYIDLVYYAMEALDIYTINVNPNQQRTSGLISRSKEEKEVLE   600
 601  HFSGIFLMMHSQNFQEIFSTTINFLVERIYKNQSLQVIANSFLANPTTSP   650
 651  LFATVLVEYLLNKMEEMGSNLERSNLYLRLFKLVFGSVSLFPVENEQMLR   700
 701  PHLHKIVNRSMELALISEEPYNYFLLLRALFRSIGGGSHDLLYQEFLPLL   750
 751  PNLLEGLNRLQSGFHKQHMRDLFVELCLTVPVRLSSLLPYLPMLMDPLVS   800
 801  ALNGSPTLISQGLRTLELCVDNLQPDFLYDHIQPVRAALMQALWKTLRNQ   850
 851  DNAALVAFRVLGKFGGGNRKMMVEPQALSYIINDKPTISIVTYFQEYETP   900
 901  IDFPVDEAIKSAFRALGSNSTDQFYRRQSWEVIRCFLAAFISLDDEKHML   950
 951  LKLFTHVDFVENKIMNWSTFQHKAGNETVRETHQTALIGMLVASATKDLR  1000
1001  DSVCPVMAAVVRHYTMVAIAQQAGPFPQKGYQATHGIDPMILIDALASCM  1050
1051  GHEEKELCKPGIACMGIILDTATNIMGNKDRACKLPIIQYLAEKMVSLCY  1100
1101  DRPWYSKVGGCQAIQFLCKHMSLRALFQNLFNFLKAFMFVLMDLEGDVSN  1150
1151  GAIEITKSYMKSMLEICLTPINECYKNIDLKDLQAKATYEVIHELVRHIT  1200
1201  SPNTIVREESMVLLKHIGTIQSKTVSEVMDPHKDVLADIIPPKKHLLRHQ  1250
1251  PANAQIGLMDGNTFCTTLEPRLFTIDLTNTYHKLFFHELLTLSEAEDATL  1300
1301  AKLDCYKNVPNLIPLRTSALRALAACHYISDIGYKEKIINIIFKVMESDK  1350
1351  SELQTTAFHCMKHFITGVTLEKEKVQSAMRPLLLKLGDHRNLSIPAIKRL  1400
1401  SYFTQIFPQMFNEKLSEQILQHCSKIMEIFVSEYKSTSPNVNFFASSKGG  1450
1451  EYEQKIVILIEMFFYISASVKYIEKLCQLVLKTEKNLMIEASSPYREALI  1500
1501  KFLQRFPTETVDLFLTESLMIDPQWNRLFIYLLKHETGVSFRAVIKSSRY  1550
1551  NNLIHYLNTHTEFPEALKYEIQHQAVLIIFTLMESDDQWIPTRQDIVDAL  1600
1601  KNCWQNYLSTLSSEDVLCDLWHLIGKILLHYFSNNTNDIELLFQLLRALC  1650
1651  FRFIPDVYFLRDFLQHTVAQSFTVNWKRNAFFYFVENFNNSFLSEELKAK  1700
1701  IITAVIIPCFAVSFDKGEGNKLIGAPPTPYQEDEKNIVSVFINKVFDPDK  1750
1751  QYDDAVRIALLQLACLLVERASQHIHDGDANNKRQGNKLRRLMTFAWPCL  1800
1801  LSKSSVDPTARYHGHLLLSHIIARLAIHKKIVLQVFHSLLKGHALEARSI  1850
1851  VKQALDVLTPAMPLRMEDGNTMLTHWTKKIIVEEGHAMQQLFHILQLIIR  1900
1901  HYKVYFPVRHQLVQHLINYMQRLGFPPTASIEHKKLAVDLAEVIIKWELH  1950
1951  RIKDDRETKTDGTEEELIQESSVKRSGIDLVETRKKSFDIIRETTVQGVG  2000
2001  SHTKPDDILRSIDKSYCDTVLNFLIRLACQVNDPQAPILSPGESLSRRCV  2050
2051  MLLKMAMRPEIWPQPFDIKLNWLDKVLATVETPHHNLNNICTGIDFLTFL  2100
2101  TTILSPDQLVSIIRPVQRGLSLCIIHQNTRIVRLMHMFLTRIMAIFPPDT  2150
2151  QHKHEDLDLLYTAVSKMIAENLTSYEKSPQPNASSLFGTLMILKACTTNN  2200
2201  ASYIDRILVQFIRVLNHLTRDHINTIGGNTVISQSPDSNALPLELLVLSL  2250
2251  ELIKNRIFVMSVEIRKLFIGTILVSLIEKSTEVKIIKCIIKMLDEWIKTK  2300
2301  EPNVMTQVPSIREKSALLVKLMQNVEKKFTDEIELNIQFLEIINFIYRDE  2350
2351  ILKQTELTNKLEGAFLNGLRFQNPNVRSKFFEILDSSMRRRLHDRLLYII  2400
2401  CSQAWDTIGSHYWIKQCIELLILTANTMMQIQCSNEQFKIPSITSVIPVN  2450
2451  SSETQENSFVSFLSSHSESFDIIQTVDDKDDVYDIDLNADRKEDCQQILP  2500
2501  NRRVTLVELVYKQAEFLEANRNIRTDQMLVATSQLCHIDTQLAQSVWLSM  2550
2551  FPRIWSIFTEDQRCNITKELIPFLSSGTNVNQKDCHPSTLNTFVESLTKC  2600
2601  APPIYIPPNLLAYLGKSHNLWHRAILVLEDMAVNQSMQSKDIDGGENQFS  2650
2651  DLDVQQSNNIFDSLSKMYSSMHEEDLWAGLWLKFAHYPETNIAVSYEQMG  2700
2701  FFEEAQGAYDLAMTKFKQDLSNGVVNTYVNSELLLWENHWMRCAKELNQW  2750
2751  DILLDYAQTNKDKNMFLILESSWRVPDWNLMKIALAKTEQCYLKHYGFKI  2800
2801  NLYKGYLSILHQEERQTGNIERYVEIASSLCIREWRRLPNIVSHIHLPYL  2850
2851  QASQQIMELHEASQIHQGLAQSRNNSLHDMKAIVKTWRNRLPIISDDLSH  2900
2901  WSDIFTWRQHHYQIITQHLEQQSDQGSTMLGVHASAQAIISFGKIARKHN  2950
2951  LTGVCQETLSRIYTIPSVPIVDCFQKIRQQVKCYLQMPSTSGKNEINEAL  3000
3001  EVIESTNLKYFTGEMNAEFYALKGLLLAQIGRSEEAGKSFSVAAQLHDGL  3050
3051  TKAWAMWGDYMEQIFLKERKITLAVDALICYLQASRNQIESKTRKYIAKV  3100
3101  LWFLSYDNNTKILISTLEKHVAGIPPSYWLPWIPQLLCCLEQFEGDVILN  3150
3151  LLSQIGRLYPQAVYFPIRTLYLTLKIEQREKHKTAEQAVKSSCSNIDGTT  3200
3201  LSFGRGASHGNIPSINPIKATPPMWRCSKVMQLQREVHPTILSSLEGIVD  3250
3251  QMVWFRESWTEEVLRQLRQGLIKCYAIAFEKRDTVQHSTITPHTLHFVKK  3300
3301  LGSTFGIGIENVPGSVTSSISNSAASESLARRAQVTFQDPVFQKMKEQFT  3350
3351  NDFDFSKPGAMKLHNLISKLKTWIKVLETKVKKLPTSFLIEDKCRFLSNF  3400
3401  SQKTAEVELPGELLIPLSSHYYVRIARFMPRVEIVQKNNTAARRLYIRGT  3450
3451  NGKIYPYLVVLDSGLGDARREERVLQLKRMLNYYLEKQKETSRRFLNITV  3500
3501  PRVVPISPQMRLAEDNPNSISLLKIFKKCCQSMQVDYDMPIVKYYDRLSE  3550
3551  VQARGTPTTHTLLREIFSEIQWTMVPKTLLKHWALKTFLAATDFWHFRKM  3600
3601  LTLQLALAFLCEHALNLTRLNADMMYLHQDSGLMNISYFKFDVNDDKCQL  3650
3651  NQHRPVPFRLTPNVGEFITHFGITGPLSAAIVATARCFIQPNYKLSSILQ  3700
3701  TILRDEIIALQKKGFRECKLIEGSEDRYSDGNCMEHSVNIVNSAVDIIMT  3750
3751  RFNKISYFDSIENKKISVLVQSATNIDNLCRMDPAWHPWL            3790

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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