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

NucPred

Fetching O14002 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MSLYKSLDVAIDYAISQLGEFQFQPIRTQSNPSSLLSACLVRAVHVETRR    50
  51  KVIFKFSQQTFKLENEYFLLRQLSSHPNGRNYAIAPAYILLLNETLGALI   100
 101  YDDPGPNILDEWLGNPNPLDLKLFLKFALGVSYVLCFLHEKKIVHGEIRL   150
 151  DTFHYDLNAPIHAKLLTIGSSVSPIRFTLSSLNWKRLYQVQNICHKLQFF   200
 201  SPEQIGNVGRPLDSRSDIYSLGILFYVILTKQYPWGGQSMRIVQSIHMRQ   250
 251  FPSVLPRRPDAFPALDQLIQKMTAKSMNSRISSATDLCYTIVELMQEFST   300
 301  ITSSPLLDQKLLSINKPQQEKLKFPKLLLTNSSDYVRIFHELVAFSSKRD   350
 351  LLTSAKRVDKLPKQHLFKYRPVDNEATYCQVVTVTGEKGSGKSNLLNAVA   400
 401  DEARKFGYFAMSSFKGHHFSPYSAIFKCVSLIMQQTLREEKQLVTDYFTS   450
 451  LWEFLGFQLIYMGELFEYVPELNSLLSPKYNLHCKRENYFKLKKRDPQQF   500
 501  RSASGRLGFMVCLLEILSFTSRVRPVIIILDELHLADHPSLSLIIGMISH   550
 551  RLPILLILAWDEPVMFKDFSKCLHEAPYAMVTDIRMNLFDRKNITEFLDS   600
 601  TLESPTQALGPLVLLMQKLSKGNPLVLKSLLLIAFANNGFAFHPKSSSWT   650
 651  YDLPVINRSFEALSSYDIPPLLASLLDALLPARCIEFLLWAALLVEPFPF   700
 701  ELLRLITTSMHLFIPKEEILDFPLNVLQFDNDNESCQFSETFFREGILSK   750
 751  ISLRRAESMHAQIAKELITGTAKEFYDIRTVHHILKGLGVIKKFDNTKPY   800
 801  ILALKESADALMQFGSYEYATELLKSCLFLLPRNFWNSKLYTRKDLISIH   850
 851  ISLAMCYWWSKDHENAIKVLKNPKLSSSNVYDYLPAFRLLTKIEYYKYQS   900
 901  LRSIDKAQELLSNLGLKLKEPTDDVLREFYDRLSTKFLECDFLVKQSEPL   950
 951  DRKRIDAISVILSECGFVLFNFSQPYYYYFSFLLAEMYLRYGNPSLRYSV  1000
1001  MFLASYCFVTRRKPEFLLRISQVDSDLFVIKDRSAVAHAELIYWGLKREL  1050
1051  CSTETGSAVTLESILLQCVMFGDKIYGAYCLACLMAQRVFRGDHIHQLLL  1100
1101  DQENSETLLLLWDCEPPFTYYLMLIRNSLLALFGLTNNDDPNNILTTKQR  1150
1151  TQKDLHDKLTSKKVPCTFCCWYYAGIIFLNTLFHHYEYVMSIAQEVRKLV  1200
1201  DGKLYERYYLITRSFIGVAALQLLFYKKNISEFEREKVEDVAHWAQSSLS  1250
1251  EMAKCFHAELYKLWVCLLEGLRQRNLGNYMEALRLFEKVTSMGASVFSPI  1300
1301  EFPFVLELIGEFYYGRGHKFLAKSYITRALSCLKNIGCYGVENKLRSRYS  1350
1351  DLISDVESRGTTVVSIATTTGDYAEKLKLLRNQDINDFSLGLASYSDIFD  1400
1401  KPLVTLPVKKSSAVDESENDFYDRNDEESFDIVSLVSVIKCGQLLSSKLR  1450
1451  LGPLLTTVIKLVIEYSQAKHAAIILKDASNYTLAAHGNVEKAESFEPPVI  1500
1501  LSQSDVKIPDSLLSEVFDHCRIVSLYTVSASQDAELLRWLQEEHDMDFFA  1550
1551  IIPLQFKESVIGALYLCLSRRAIRTGNVTFLKLLSQQIAISVSNALLFQS  1600
1601  LRRTITDNVTLIELQRLSYQRYKAIEEKCITLLDSLPCIVWTLDSDIGEI  1650
1651  EYTNASKRNYFGVPEDCHDSLSWKTFIHPDHHHQFQEKLLNLKTLELGDI  1700
1701  ELLLRMEDGNYHWHLCRGLSFKEDANAKKWIVVCIDINDEKEAREAAMHA  1750
1751  VNLKTNFLANMSHELRTPFSSFYGMLSLLSDTKLNEEQYDIVSTAKQSCT  1800
1801  SLVQIIDDLLNFSELKSGKMKLEPDKVFDVEENIADCIELVYPSLSSKPV  1850
1851  QISYDIYPNVPALLAGDSAKLRQVITNLLGNSVKFTTEGHILLRCMAIDE  1900
1901  EINAEENQCKLRFEIEDTGIGLKEEQLKLLFNPFTQVDGSTTRIYGGSGL  1950
1951  GLSICLQICKIMDGDIGVQSVYGEGSTFWFHVQLRNVTSKLSQKHFEESH  2000
2001  ERFANIRQSLKNAKILVVKSFTTSRSIFRSLFSLAVVDTTTIYSDIEQQL  2050
2051  IDSLDKRQPYDFLCIEAASGQTEQIITQILSNQKLNKVLLIVLLPSIQRT  2100
2101  KVRSDGDPFITSLNKNQSRIFCFREPIRISKLLQNFPALLSKWSTPTKLV  2150
2151  EPSQFRASPRKVDQAVVLSSEEKEILQKKYALIAEDNLIARKLLTKQLSN  2200
2201  LGFQVHAAVDGVELVKMYEAKQFGFYSVIFADYHMPIRDGAEAVMDIRAY  2250
2251  ERENNCSTPIPVIALTADIQKSAKQRCLEVGMNFYLTKPFTQKQLVNAVR  2300
2301  EFVLLEKSAR                                          2310

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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