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

NucPred

Fetching Q8QG78 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSSSGYPPNQGAFSTEQGRYSSHPVQYTFPSSRHQQEYSVSEYRTAHLEA    50
  51  SQLIQQQQLRRRPSLLSEFHPVSDRPQDRRSGYDQQYHSISQNEHEALES   100
 101  KRPRLDQVSDSHYRLNPAMVLLVPTIQEGVRVQSEVKKEQGLSSKHESSS   150
 151  SPLSGQPGDDQDASPSKLSKEELIQSMDRVDREIAKVEQQILKLKKKQQQ   200
 201  LEEEAAKPPEPEKPVSPPPVEQKHRSVVQIIYDENRKKAEEAHKFLEGLG   250
 251  PKVELPLYNQPSDTKVYHENIKTNQVMRKKLILFFKRRNHARKLREQNIC   300
 301  QRYDQLMEAWEKKVDRIENNPRRKAKESKTREYYEKQFPEIRKQREQQER   350
 351  FQRVGQRGTGMSATIARSEHEISEIIDGLSEQENNEKQMRQLSVIPPMMF   400
 401  DAEQRRVKFINTNGLMEDPMKVYKDRQFMNVWTDHEKEIFKEKFVRHPKN   450
 451  FGLIASYLERKNVSDCVLYYYLTKKNENLKSLVRRNYPKRRGRNQQQITR   500
 501  PSQEEKEIEKVEEEKADRNDKKEDERREEEEKEEKEELREGAKDKIDAVA   550
 551  EDGDEKDQSMPRGRKTANNQGRRKGRVTRSMASEAAAANAVTTATTAPVT   600
 601  TTSTATTVAPVPVAPPPEEPTPPPPPQEQSLVDHGRNWGAIAKMVGSKSE   650
 651  SQCKNFYFNYKRRHNLDNLLQQHKQKSSRRPREERDVSQCDSIASTVSAQ   700
 701  EDDENEASNEEENPEDSEGAENSSDTESAPSPSPAEAARLGDDSVDRTTS   750
 751  SVSMEAPPEQDAASKPASDSSPSPIVENTKPPETQYAELKVKEEISTENE   800
 801  QTMEVEERSQSAELKSALNLQVQTKAEPYETEAKPTESTTQVKTEVDSKE   850
 851  DDSMERLMDRAEAADMGYAPPQNISQARQESQPDNDSSATCSADEEVDGE   900
 901  PDRPRMYSFGSRPSLLNQAGTFLKQGPMDLQQLQHRAAVIPPMTSCSPCN   950
 951  LTTGTAIAASNFSMYQRHLYENSLLEEQRQRQEQLTLENRMSASPGNMSK  1000
1001  SPNMDWEGKSVYMPYTEVKHPFEHEAQMQNVARSVSPYRLSPRDVGRVSP  1050
1051  QVDMNPSRYCVPPVLQPAPHQVITSLSDSARLPVTRPTRPPPPLIPSSKT  1100
1101  SATSSDKPSFITGGSISQGTPGTYLASLSQPYSQETLKPSVGSISLGLPR  1150
1151  QHESTKIGCVTYIKQEEFPSRGQSSQPEGLLVRAQHEGVVRGSMAAIQEG  1200
1201  SIARGTPATKVPLEAVSTLRGSITQGTPALSQSGIAADVLLKSTITRLAA  1250
1251  EDIGSPERCREDTSAKGHVIYEGKSGHIVSYDTIKNMREGTRSPRTAPEV  1300
1301  ALKRAYDTMEGNIKQAMSVREAAVSGPMEGLICRTLPKGSPHPELKDRQV  1350
1351  LSGSIMKGTPRTTSDNFDDGLKYAKQIKLESPPIRSFEGAISKGKPYEGV  1400
1401  TTIKELGRSIHEIPRQDLVSQESRKTPESSRQIMEGSISQGTPIKYESTS  1450
1451  GQSAIKHNVKSLITGPSNLSWGVPQMDNMPENLKMGERSKHEDTKSSDAI  1500
1501  RSRHTSVVSSGPSVLRSTLHEASKSQLSPGIYEDNNARRTPVNYPSPMSR  1550
1551  SSPMARSAEGCLTPSKSSSHERKSTLTPTQRESIVVKSPVPGVDPSAAHS  1600
1601  PFDTHLRSAPPGDVYRAHLPPHLDPALQFHRPLDPAAAAYLFQRQLSPTP  1650
1651  GYPSQYQLYAMENTRQTILNDYITSQQMQVNLRPDVARGLSPRDQGLGIP  1700
1701  YPGARGIIDLTNMPPAILVPHPGGTSTPPMDRITYIPGTQLAFPPRPYNP  1750
1751  ASMSPGHPAHLANSVSAERERERERERERDREREKEQRERESDRERERDR  1800
1801  LAHAAAAAAAASAPSEHYLRPVSEQPSRPSSRPSSHGYVRSPSPSVRAQE  1850
1851  SIMQQRPSIFLGTNGKSVITPLDAAQFRIMPPTPGAASITQGIPASRYST  1900
1901  AADALAALVDAATSAPQMEVAKPKESKNDSARSEENLSRRNALEQQQQID  1950
1951  CERRVMQSPYTSSSFSSSKSQSQPSSAVYSEAGKERTAHTKSRYVEELRM  2000
2001  RGKTTITAANFIDVIITQQIASDKDGRERNSQSSDASSSHSSHRYEAPRE  2050
2051  TIEVISPANSPVQEKESYPQEMPKSSQTETGEGSRKYDGQPNRYRQQQES  2100
2101  PPQQTIPGHVPQTHRLITLADHICHIITQDFARNQPVNQPLQQPPASTFQ  2150
2151  STNPTSTAVRTKASSRFSPESQVQPMHSPRPASRVSPENIPDKPRGRPGK  2200
2201  SPDRGHISEPYEPISPPQAPMLHTKQDNMMLLSQRQEPPEQRNDSRSPGN  2250
2251  INYLPSFFTKLENTSPMVMYKKQEIFRKLNSSGGGDSDMAAAQPGTEIFN  2300
2301  LPAVTTSGAISSRGHSFADPASNLGLEDIIRKALMGNFDDKSEDHGVLVG  2350
2351  VPQGNQSGTPNSEARREEANPSPNSGGGTHKQKLISKYGSRKTKSPISGS  2400
2401  QTYLGAERPSSVSSVHSEGDYRQASAWAWEDRPSSTGSTQFPYNPLTMGM  2450
2451  LNSTPPSSMSCIPTSMTQTSAHQQSRIWEREPAPLLSEQYETLSDSDE    2498

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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