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

NucPred

Fetching Q8N1I0 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MWIPTEHEKYGVVIASFRGTVPYGLSLEIGDTVQILEKCDGWYRGFALKN    50
  51  PNIKGIFPSSYVHLKNACVKNKGQFEMVIPTEDSVITEMTSTLRDWGTMW   100
 101  KQLYVRNEGDLFHRLWHIMNEILDLRRQVLVGHLTHDRMKDVKRHITARL   150
 151  DWGNEQLGLDLVPRKEYAMVDPEDISITELYRLMEHRHRKKDTPVQASSH   200
 201  HLFVQMKSLMCSNLGEELEVIFSLFDSKENRPISERFFLRLNRNGLPKAP   250
 251  DKPERHCSLFVDLGSSELRKDIYITVHIIRIGRMGAGEKKNACSVQYRRP   300
 301  FGCAVLSIADLLTGETKDDLILKVYMCNTESEWYQIHENIIKKLNARYNL   350
 351  TGSNAGLAVSLQLLHGDIEQIRREYSSVFSHGVSITRKLGFSNIIMPGEM   400
 401  RNDLYITIERGEFEKGGKSVARNVEVTMFIVDSSGQTLKDFISFGSGEPP   450
 451  ASEYHSFVLYHNNSPRWSELLKLPIPVDKFRGAHIRFEFRHCSTKEKGEK   500
 501  KLFGFSFVPLMQEDGRTLPDGTHELIVHKCEENTNLQDTTRYLKLPFSKG   550
 551  IFLGNNNQAMKATKESFCITSFLCSTKLTQNGDMLDLLKWRTHPDKITGC   600
 601  LSKLKEIDGSEIVKFLQDTLDTLFGILDENSQKYGSKVFDSLVHIINLLQ   650
 651  DSKFHHFKPVMDTYIESHFAGALAYRDLIKVLKWYVDRITEAERQEHIQE   700
 701  VLKAQEYIFKYIVQSRRLFSLATGGQNEEEFRCCIQELLMSVRFFLSQES   750
 751  KGSGALSQSQAVFLSSFPAVYSELLKLFDVREVANLVQDTLGSLPTILHV   800
 801  DDSLQAIKLQCIGKTVESQLYTNPDSRYILLPVVLHHLHIHLQEQKDLIM   850
 851  CARILSNVFCLIKKNSSEKSVLEEIDVIVASLLDILLRTILEITSRPQPS   900
 901  SSAMRFQFQDVTGEFVACLLSLLRQMTDRHYQQLLDSFNTKEELRDFLLQ   950
 951  IFTVFRILIRPEMFPKDWTVMRLVANNVIITTVLYLSDALRKNFLNENFD  1000
1001  YKIWDSYFYLAVIFINQLCLQLEMFTPSKKKKVLEKYGDMRVTMGCEIFS  1050
1051  MWQNLGEHKLHFIPALIGPFLEVTLIPQPDLRNVMIPIFHDMMDWEQRRS  1100
1101  GNFKQVEAKLIDKLDSLMSEGKGDETYRELFNSILLKKIERETWRESGVS  1150
1151  LIATVTRLMERLLDYRDCMKMGEVDGKKIGCTVSLLNFYKTELNKEEMYI  1200
1201  RYIHKLYDLHLKAQNFTEAAYTLLLYDELLEWSDRPLREFLTYPMQTEWQ  1250
1251  RKEHLHLTIIQNFDRGKCWENGIILCRKIAEQYESYYDYRNLSKMRMMEA  1300
1301  SLYDKIMDQQRLEPEFFRVGFYGKKFPFFLRNKEFVCRGHDYERLEAFQQ  1350
1351  RMLNEFPHAIAMQHANQPDETIFQAEAQYLQIYAVTPIPESQEVLQREGV  1400
1401  PDNIKSFYKVNHIWKFRYDRPFHKGTKDKENEFKSLWVERTSLYLVQSLP  1450
1451  GISRWFEVEKREVVEMSPLENAIEVLENKNQQLKTLISQCQTRQMQNINP  1500
1501  LTMCLNGVIDAAVNGGVSRYQEAFFVKEYILSHPEDGEKIARLRELMLEQ  1550
1551  AQILEFGLAVHEKFVPQDMRPLHKKLVDQFFVMKSSLGIQEFSACMQASP  1600
1601  VHFPNGSPRVCRNSAPASVSPDGTRVIPRRSPLSYPAVNRYSSSSLSSQA  1650
1651  SAEVSNITGQSESSDEVFNMQPSPSTSSLSSTHSASPNVTSSAPSSARAS  1700
1701  PLLSDKHKHSRENSCLSPRERPCSAIYPTPVEPSQRMLFNHIGDGALPRS  1750
1751  DPNLSAPEKAVNPTPSSWSLDSGKEAKNMSDSGKLISPPVPPRPTQTASP  1800
1801  ARHTTSVSPSPAGRSPLKGSVQSFTPSPVEYHSPGLISNSPVLSGSYSSG  1850
1851  ISSLSRCSTSETSGFENQVNEQSAPLPVPVPVPVPSYGGEEPVRKESKTP  1900
1901  PPYSVYERTLRRPVPLPHSLSIPVTSEPPALPPKPLAARSSHLENGARRT  1950
1951  DPGPRPRPLPRKVSQL                                    1966

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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