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

NucPred

Fetching Q8HZK2 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MLCIRPEALVLLGALLTVPLDPVGGQDALSLTWEVQRYDGWFNNLRQHEH    50
  51  GAAGSPLRRLVPANYADGVYQALGEPLLPNPRQLSHTTMRGPAGLRSIRN   100
 101  RTVLGVFFGYHVLSDLVSIEKPGCPAEFLNIHIPPGDPVFDPHKSGDVVL   150
 151  PFQRSRWDPNTGQSPSNPRDLTNEVTGWLDGSAIYGSSHSWSDELRSFSG   200
 201  GQLASGPDPAFPRQAQDPLFMWTPPDPATGQRGPQGLYAFGAEQGNREPF   250
 251  LQALGLLWFRYHNLCAQKLAREHPLWGDEELFQHARKRVIATYQSITMYE   300
 301  WLPSFLQQTPPNYTEYRPFLDPSISPEFLAASEQFFSTMVPPGVYMRNAS   350
 351  CHFQMVLNESYGSFPALRVCNSYWIRENPNLNSAEAVNQLLLGMASQISE   400
 401  LEDWIVVEDLRDYWPGPGKFSRTDYVASSIQRGRDMGLPSYTQALQALGL   450
 451  NTPKNWSDFNPNVDPQVLEATAALYNQDLSRLELFSGGLLESYGDPGPLF   500
 501  STIVLDQFVRLRDGDRYWFENTKNGLFSKEEIAEIRSTTLRDVLVAVTNV   550
 551  SSSALQPNVFIWNEDSPCPQPQQLTTEDLPHCVPLTVIQYFEGSGPGFGI   600
 601  TIVALCCLPLMSLLISGVVAYFRSRERKKLQKRGKESVKKEADKDGVSAM   650
 651  EWPGPKERSYPVSIQLLPDRHLQVLDRHLSVLRTIQLRPRHRVNLILSNN   700
 701  LGRRTLLLKIPKEYDLVLLFNSEDERGAFVQHLQGFCASCALGLDIDEMG   750
 751  ESELFRKAVTKQQRGRILEIFFRHLFAQVLDIDQADAGALPLDSSQKVRE   800
 801  ALTCELSRAEFAESLGLKPQDMFVESMFSLADKDGNGYLSFREFLDVLVV   850
 851  FMKGSPEDKSRLMFTMYDLDGNGFLSKDEFFTMIRSFIEISNNCLSKAQL   900
 901  TEVVESMFREAGFQDKQELTWEDFHFMLRDHDSELRHTQLCVKGGGGGVG   950
 951  VIFKPDISSRVSFIIRTPEERSSPQGVRLPASEASELGGPVLKKRFGKKA  1000
1001  VVPPPRLYTEALQEKKQRGFLAQKLQQYKRFVENYRRHIVCVAIFSAICA  1050
1051  GLFVERAYYYAFVSPPSGIAETTFVGIILSRGTAASVSFMFSYILLTMCR  1100
1101  NLITFLRETFLNHYVPFDAAVDFHRWIAMAALVLAILHSVGHVVNVYIFS  1150
1151  VSPLSLLACVFPSVFVNDGSKLPQKFYWWFFQTIPGMTGVLLLVVLAIMY  1200
1201  VFASPYFRRRSFRGFWLTHHFYILLYVLLIIHGSFALIQLPRFHIFFLVP  1250
1251  ALIYVGDKLVSLSRKKVEISVVKAELLPSGVTHLQFQRPQGFEYKSGQWV  1300
1301  RIACLGLGTNEYHPFTLTSAPHEDTLSLHIRAVGPWTTRLREIYSHPMGD  1350
1351  GYARYPKLYLDGPFGEGHQEWHKFEVSVLVGGGIGVTPFASILKDLVFKS  1400
1401  SLGSQMLCKKIYFIWVTRTQRQFEWLADIIREVEENDHRDLVSVHIYITQ  1450
1451  LAEKFDLRTTMLYICERHFQKVLNRSLFTGLRSITHFGRPPFEPFFNSLQ  1500
1501  EVHPQVRKIGVFSCGPPGMTKNVEKTCQLINRQDQTHFVHHYENF       1545

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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