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

NucPred

Fetching Q80VC9 from www.uniprot.org...

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

   1  MVEAAPAGSGPLRRTFLVPEIKSLDQYDFSRAKAAASLAWVLRAAFGGAE    50
  51  HVPPELWEPFYTDQYAQEHVKPPVTRLLLSAELYCRAWRQALPQLEPSPS   100
 101  PSALLALLARRGTVPSLPEHPVREADLKHQPILMGAHLAVIDALMVAFSF   150
 151  EWTKTLPGPLALSSLEHKLLFWVDTTVRRLQEKTEQEAAQRASPAAPLDG   200
 201  ASPAQPSIRYRKDRAIARRAPCFPNVTTLQDLASGAALAATIHCYCPQLL   250
 251  RLEEVCLKDPMSVADSLYNLQLVQDFCASHLPRGCPLSLEDLLYVPPPLK   300
 301  VNLVVLLAEMYMCFEVLKPDFVQAKDLPDGHAVSPRNTETVPSQNNSGSS   350
 351  SPVFNFRHPLLSPGGPQSPLRGSTGSLKSSPSMSHMEALGKAWNRQLSRP   400
 401  LSQAVSFSTPFGLDSDVDVVMGDPVLLRSVSSDSLGPPRPVSTSSRNSAQ   450
 451  PAPESGDLPTIEEALQIIHSAEPRLLPDGAADGSFYLHSPEGLSKPPLSP   500
 501  YPPEGASKPLSDRLNKAPIYISHPENPSKSSPCSTGEILKPPPPSEGSPK   550
 551  AVASSPAANNSEVKMTSFAERKKQLVKAEAESGLGSPTSTPVAPEALSSE   600
 601  MSELGARLEEKRRAIEAQKRRIEAIFAKHRQRLGKSAFLQVQPREAAGEA   650
 651  EEEAELGSVPGGERPAGEGQGEPSLRHKSVTFSPDLGPVPPEGLGDYNRA   700
 701  VSKLSAALSSLQRDMQRLTDQQQRLLAPPEAPGPAPPPAAWVIPGPATGP   750
 751  KAASPSPARRAPAARRSPGPGPSPTPRSPKHARPAELKLAPLTRVLTPPH   800
 801  DVDSLPHLRKFSPSQVPVQTRSSILLSEGTPPEEPTTKPALIEIPLASLG   850
 851  EPAADEEGDGSPPGAEDSLEEEASSEGEPRSGLGFFYKDEDKPEDEMAQK   900
 901  RASLLERQQRRVEEARRRKQWQEAEKEQKREEAARLAQEAPGLAFTTPVV   950
 951  ASAAPVATLAPTTRAMAPAEEEVGPRRGDFTRLEYERRAQLKLMDDLDKV  1000
1001  LRPRASGTGGPGRGGRRATRPRSGCCDDSALARSPARGLLGSRLSKVYSQ  1050
1051  STLSLSTVANEAPNNLGVKRPTSRAPSPSGLMSPSRLPGSRERDWENGSN  1100
1101  ASSPASVPEYTGPRLYKEPSAKSNKFIIHNALSHCCLAGKVNEPQKNRIL  1150
1151  EEIEKSKANHFLILFRDSSCQFRALYTLSGETEELSRLAGYGPRTVTPAM  1200
1201  VEGIYKYNSDRKRFTQIPAKTMSMSVDAFTIQGHLWQSKKPTTPKKGGGT  1250
1251  PK                                                  1252

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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