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

NucPred

Fetching P26363 from www.uniprot.org...

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

   1  MQKTPLEKASIFSQIFFSWTKPILWKGYRQRLELSDIYQIHPGDSADNLS    50
  51  ERLEREWDREVATSKKNPKLINALKRCFFWKFLFYGILLYLGEVTKAVQP   100
 101  LLLGRIIASYDRDNEHERSIAYYLAIGLCLLFVVRMLLLHPAIFGLHHIG   150
 151  MQMRIAMFSLIYKKTLKLSSKVLDKISTGQLVSLLSNNLNKFDEGLALAH   200
 201  FVWIAPLQVLLLMGLLWDLLQASAFCGLGFLIILSLFQARLGRMMMKYKD   250
 251  KRAGKINERLVITSQIIENIQSVKAYCWENAMEKIIETIRETELKLTRKA   300
 301  AYVRYFNSSAFFFSGFFVVFLSIVPHLLLDGISLRKIFTTISFSIVLRMA   350
 351  VTRQFPWAVQTWYDSLGVINKIQEFLQKEEYKSLEYNLTTTEVAMENVSA   400
 401  SWDEGIGEFFEKAKLEVNGGNISNEDPSAFFSNFSLHVAPVLRNINFKIE   450
 451  KGQLLAIAGSTGAGKTSLLMMIMGELEPSAGKIKHSGRISFSPQVSWIMP   500
 501  GTIKENIVFGVSYDQYRYLSVIKACQLEEDISKFPEKDNTVLGEGGITLS   550
 551  GGQRARISLARAVYKDADLYLLDSPFSYLDLFTEKEIFESCVCKLMANKT   600
 601  RILVTSKVEQLKKADKVLILHEGSCYFYGTFSELEDQRPEFSSHLIGFDH   650
 651  FNAERRNSIITETLRRCSIDSDPSAVRNEVKNKSFKQVADFTEKRKSSII   700
 701  NPRKSSRKFSLMQKSQPQMSGIEEEDMPAEQGERKLSLVPESEQGEASLP   750
 751  RSNFLNTGPTFQGRRRQSVLNLMTRTSISQGSNAFATRNASVRKMSVNSY   800
 801  SNSSFDLDIYNRRLSQDSILEVSEEINEEDLKECFLDDTDSQSPTTTWNT   850
 851  YLRFLTAHKNFIFILVFCLVIFFVEVAASSAWLWIIKRNAPAINMTSNEN   900
 901  VSEVSDTLSVIVTHTSFYYVFYIYVGVADSLLALGIFRGLPLVHSLISVS   950
 951  KVLHKKMLHAILHAPMSTFNTMRAGRILNRFSKDTAILDDILPLSIFDLT  1000
1001  QLVLIVIGAITVVSLLEPYIFLATVPVIVAFILLRSYFLHTSQQLKQLES  1050
1051  KARSPIFAHLITSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLST  1100
1101  LRWFQMTIEMIFVIFFIAVSFISIATSGAGEEKVGIVLTLAMNIMNTLQW  1150
1151  AVNASIDVDSLMRSVSRIFRFIDLPVEELINENKNKEEQLSEVLIYENDY  1200
1201  VKKTQVWPSGGQMTVKNLSANYIDGGNTVLENISFSLSPGQRVGLLGRTG  1250
1251  SGKSTLLSAFLRLLSTQGDIQIDGVSWQTIPLQKWRKAFGVIPQKVFIFS  1300
1301  GSIRKNLDPYGKWSDEELLKVTEEVGLKLIIDQFPGQLDFVLLDGGCVLS  1350
1351  HGHKQLVCLARSVLSKAKILLLDEPSAHLDPITFQIIRKTLKHAFADCTV  1400
1401  ILSEHRLEAMLECQRFLVIEDNTVRQYDSIQKLVNEKSFFKQAISHSDRL  1450
1451  KLFPLHRRNSSKRKSRPQISALQEETEEEVQDTRL                 1485

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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