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

NucPred

Fetching O77086 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MPQFDESFLSDCALADRWHFYSYTVKQLPPHPSPKPNRNRNPYPSGASHD    50
  51  DHQHQLHHHHHQQHHHNHHRLWKTQRQSWSPRDTNNNHSLTSNNCNCNSS   100
 101  NTCNSISATGNTLHSIKFHRRRKYKKLARLALSTPAIPLQMDVDVDVNVT   150
 151  VDREFDMEMDTPVPLKNAVCHGSISSPSTPGTCSSGIGVGGGGCSSSSNN   200
 201  SINSGSYSTACTPPPPTHQHHSQHQQLQGTPGGSSRVGGAGAGGGGGVPP   250
 251  APPSAGSSGHKNSLKGTKLARRARSFKDDLIEKISLMRTTNNTLGRSHSP   300
 301  HSPRTKHGTKAPPTTEEVLRSTQTLETHVKDISNALKHFRDVILKKKLEV   350
 351  LPGNGTVILETIASMYSVIQTYTLNENSAIMSSATLQVYQSLGKLIKLCD   400
 401  EVMLSEDSGECASLSNENVREVIDLLEDAVRNLVTLAQGKLKEQDQCAFR   450
 451  YSGSGLGGIGAAAEIMGAVTASPGASVPGTGVMRVSAAESAAQRTSLPDI   500
 501  ALTPKERDILEQHNVNPMRGSHSTESILRDTSPPPKPPLPNRASNPPPLP   550
 551  PKRRSQPSASAGTVGVGCSSSTSTSNQASPLPYAQSHNISLNSDLDCSSN   600
 601  ISLLNYGVDRLSVRSRSPDENSQCSFDSALNHSREEEDQQQQHQHLRSFP   650
 651  KLAAMMDEDMDKMVSYSAAIDDKTQTPLSTGGGIAGVAGGTGGAGEGVAA   700
 701  AASGDGETNSNRHSNESGFVSMREFRTSTQTTDYSVQSSTKSSSSNSEIA   750
 751  FSISESTAVGSSSEYQQISQLVSHSQRHISSSSSSCTTTTTSSSTTTGYG   800
 801  SSEVEQLQQQQQQQTTTTPADLAPALPPKSIQRSSLTRHDSPGVGDELDE   850
 851  VQSSSGWASHRSSQSEVAELRQLSPLHHLNHHPHTASAGQLQQWHSKHHS   900
 901  LIEGPRLQLAGSGSCSAFDQRHLDQEPPPLPIKKKHILAYMEICSASTRS   950
 951  IEQHRHTMHACNISRNISHSQTMNIMPMSKELSPELEMPPALPPKNYKQR  1000
1001  KATSMVASPTLQPVIVTTPPPSPKPTLGENGSTGRPDSRMATVCEELNDA  1050
1051  VASEDAMPEPRSPVLDSNENVSAVDDGQTFYCHSHQLPAAEMEMSEDASS  1100
1101  ADNQPITTPQVLEEQEEPTAESRPLVAVHESVKPANVDEDEEAERADMLI  1150
1151  NMLEEVNITRYLILKKREEDGPEVKGGYIDALIVHASRVQKVADNAFCEA  1200
1201  FITTFRTFIQPIDVIEKLTHRYTYFFCQVQDNKQKAAKETFALLVRVVND  1250
1251  LTSTDLTSQLLSLLVEFVYQLVCSGQLYLAKLLRNKFVEKVTLYKEPKVY  1300
1301  GFVGELGGAGSVGGAGIAGSGGCSGTAGGGNQPSLLDLKSLEIAEQMTLL  1350
1351  DAELFTKIEIPEVLLFAKDQCEEKSPNLNKFTEHFNKMSYWARSKILRLQ  1400
1401  DAKEREKHVNKFIKIMKHLRKMNNYNSYLALLSALDSGPIRRLEWQKGIT  1450
1451  EEVRSFCALIDSSSSFRAYRQALAETNPPCIPYIGLILQDLTFVHVGNQD  1500
1501  YLSKGVINFSKRWQQYNIIDNMKRFKKCAYPFRRNERIIRFFDNFKDFMG  1550
1551  EEEMWQISEKIKPRGRRPVNY                               1571

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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