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

NucPred

Fetching Q7YQM3 from www.uniprot.org...

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

   1  MTAEPMSESKLNTLVQKLHDFLAHSSEESEETSSPPRLAMNQNTDKISGS    50
  51  GSNSDMMENSKEEGTSSSEKSKSSGSSRSKRKPSIVTKYVESDDEKPLDD   100
 101  ETVNEDASNENSENDITMQSLPKGTVIVQPEPVLNEDKDDFKGPEFRSRS   150
 151  KMKTENLKKRGEDGLHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNC   200
 201  FKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGR   250
 251  KELSTIMDENNQWYCYICHPEPLLDLVTACNSVFDNLEQLLQQNKKKIKV   300
 301  DSEKSNKVYEHTSRFSPKKTSSNCNGEEKKLDDSCSGSVTYSYSALIVPK   350
 351  EMIKKAKKLIETTANMNSSYVKFLKQATDNSEINSATKLRQLKAFKSVLA   400
 401  DIKKAHLALEEDLNSEFRAMDAVSKEKNTKEHKVIEAKFETKARKGEKPC   450
 451  ALEKKDISKSEAKLSRKQVDSEHMYQNVPTEEQRANKSTGGEHKKSDRKE   500
 501  EPQYEPANTSEDLDMDIVSVPSSVPEDIFENLETAMEVQSSVDHQGDGSS   550
 551  GTEQEVESSSVKLSISSKDNRGGIKSKTTAKVTKELYVKLTPVSLSNSPI   600
 601  KGADCQEVPQDKDGYKSCGLNPKLEKCGLGQENSDNEHLVENEVSLLLEE   650
 651  SDLRRSPRVKTTPLRRQTETNPVTSNSDEECNETVKEKQKLSVPVRKKDK   700
 701  RNSSDSAIDNPKPNKLPKSKQSETVDQNSDSDEMLAILKEVSRMSHSSSS   750
 751  DTDINEIHTNHKTLYDLKTQAGKDDKGKRKRKSSTSGSDFDTKKGKSAKS   800
 801  SIISKKKRQTQSESSNYDSELEKEIKSMSKIGAARTTKKRIPNTKDFDSS   850
 851  EDEKHSKKGMDNQGHKNLKTSQEGSSDDAERKQERENFSSAEGTVDKDTT   900
 901  IMELRDRLPKKQQASASTDGVDKLSGKEEGFTSLEVRKVAETKEKSKHLK   950
 951  TKICKKVQDGLSDITEKFLKKDQSDETSEDDKKQSKKGTEEKKKTSDFKK  1000
1001  KVIKMEQQYESSSDGTEKLPEREEICHFPKGIKQIKNGTTDGEKKNKKIR  1050
1051  DKTSKKKDELSDYAEKSTGKGDSCDSSEDKKSKNGAYGREKKRCTLLGKS  1100
1101  SRKRQDCSSSDTEKYSMKEDGCNSSDKRLKRIELRERRNLSSKRNTKEIQ  1150
1151  SGSSSSDAEESSEDNKKKKQRTSSKKKAVIVKEKKRNSLRTSTKRKQADI  1200
1201  TSSSSSDIEDDDQNSIGEGSSDEQKIKPVTENLVLSSHTGFCQSSGDEAL  1250
1251  SKSVPVTVDDDDDDNDPENRIAKKMLLEEIKANLSSDEDGSSDDEPEEGK  1300
1301  KRTGKQNEENPGDEEAKNQVNSESDSDSEESKKPRYRHRLLRHKLTVSDG  1350
1351  ESGEEKKTKPKEHKEVKGRNRRKVSSEDSEDSDFQESGVSEEVSESEDEQ  1400
1401  RPRTRSAKKAELEENQRSYKQKKKRRRIKVQEDSSSENKSNSEEEEEEKE  1450
1451  EEEEEEEEEEEEEEDENDDSKSPGKGRKKIRKILKDDKLRTETQNALKEE  1500
1501  EERRKRIAEREREREKLREVIEIEDASPTKCPITTKLVLDEDEETKEPLV  1550
1551  QVHRNMVIKLKPHQVDGVQFMWDCCCESVKKTKKSPGSGCILAHCMGLGK  1600
1601  TLQVVSFLHTVLLCDKLDFSTALVVCPLNTALNWMNEFEKWQEGLKDDEK  1650
1651  LEVSELATVKRPQERSYMLQRWQEDGGVMIIGYEMYRNLAQGRNVKSRKL  1700
1701  KEIFNKALVDPGPDFVVCDEGHILKNEASAVSKAMNSIRSRRRIILTGTP  1750
1751  LQNNLIEYHCMVNFIKENLLGSIKEFRNRFINPIQNGQCADSTMVDVRVM  1800
1801  KKRAHILYEMLAGCVQRKDYTALTKFLPPKHEYVLAVRMTSIQCKLYQYY  1850
1851  LDHLTGVGNNSEGGRGKAGAKLFQDFQMLSRIWTHPWCLQLDYISKENKG  1900
1901  YFDEDSMDEFIASDSDETSMSLSSDDYTKKKKKGKKGKKDSSSSGSGSDN  1950
1951  DVEVIKVWNSRSRGGGEGNVDETGNNPSVSLKLEESKATSSSNPSSPAPD  2000
2001  WYKDFVTDADAEVLEHSGKMVLLFEILRMAEEIGDKVLVFSQSLISLDLI  2050
2051  EDFLELASREKTEDKDKPLIYKGEGKWLRNIDYYRLDGSTTAQSRKKWAE  2100
2101  EFNDETNVRGRLFIISTKAGSLGINLVAANRVIIFDASWNPSYDIQSIFR  2150
2151  VYRFGQTKPVYVYRFLAQGTMEDKIYDRQVTKQSLSFRVVDQQQVERHFT  2200
2201  MNELTELYTFEPDLLDDPNSEKKKKRDTPMLPKDTILAELLQIHKEHIVG  2250
2251  YHEHDSLLDHKEEEELTEEERKAAWAEYEAEKKGLTMRFNIPTGTNLPPV  2300
2301  SFNSQTPYIPFNLGALSAMSNQQLEDLINQGREKVVEATNSVTAVRIQPL  2350
2351  EDIISAVWKENMNLSEAQVQALALSRQASQELDVKRREAIYNDVLTKQQM  2400
2401  LISCVQRILMNRRLQQQYNQQQQQQMTYQQATLGHLMMPKPPNLIMNPSN  2450
2451  YQQIDMRGMYQPVAGGMQPPPLQRAPPPMRSKNPGPSQGKSM          2492

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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