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

NucPred

Fetching Q02785 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MSSTDEHIEKDISSRSNHDDDYANSVQSYAASEGQVDNEDLAATSQLSRH    50
  51  LSNILSNEEGIERLESMARVISHKTKKEMDSFEINDLDFDLRSLLHYLRS   100
 101  RQLEQGIEPGDSGIAFKNLTAVGVDASAAYGPSVEEMFRNIASIPAHLIS   150
 151  KFTKKSDVPLRNIIQNCTGVVESGEMLFVVGRPGAGCSTFLKCLSGETSE   200
 201  LVDVQGEFSYDGLDQSEMMSKYKGYVIYCPELDFHFPKITVKETIDFALK   250
 251  CKTPRVRIDKMTRKQYVDNIRDMWCTVFGLRHTYATKVGNDFVRGVSGGE   300
 301  RKRVSLVEAQAMNASIYSWDNATRGLDASTALEFAQAIRTATNMVNNSAI   350
 351  VAIYQAGENIYELFDKTTVLYNGRQIYFGPADKAVGYFQRMGWVKPNRMT   400
 401  SAEFLTSVTVDFENRTLDIKPGYEDKVPKSSSEFEEYWLNSEDYQELLRT   450
 451  YDDYQSRHPVNETRDRLDVAKKQRLQQGQRENSQYVVNYWTQVYYCMIRG   500
 501  FQRVKGDSTYTKVYLSSFLIKALIIGSMFHKIDDKSQSTTAGAYSRGGML   550
 551  FYVLLFASVTSLAEIGNSFSSRPVIVKHKSYSMYHLSAESLQEIITEFPT   600
 601  KFVAIVILCLITYWIPFMKYEAGAFFQYILYLLTVQQCTSFIFKFVATMS   650
 651  KSGVDAHAVGGLWVLMLCVYAGFVLPIGEMHHWIRWLHFINPLTYAFESL   700
 701  VSTEFHHREMLCSALVPSGPGYEGISIANQVCDAAGAVKGNLYVSGDSYI   750
 751  LHQYHFAYKHAWRNWGVNIVWTFGYIVFNVILSEYLKPVEGGGDLLLYKR   800
 801  GHMPELGTENADARTASREEMMEALNGPNVDLEKVIAEKDVFTWNHLDYT   850
 851  IPYDGATRKLLSDVFGYVKPGKMTALMGESGAGKTTLLNVLAQRINMGVI   900
 901  TGDMLVNAKPLPASFNRSCGYVAQADNHMAELSVRESLRFAAELRQQSSV   950
 951  PLEEKYEYVEKIITLLGMQNYAEALVGKTGRGLNVEQRKKLSIGVELVAK  1000
1001  PSLLLFLDEPTSGLDSQSAWSIVQFMRALADSGQSILCTIHQPSATLFEQ  1050
1051  FDRLLLLKKGGKMVYFGDIGPNSETLLKYFERQSGMKCGVSENPAEYILN  1100
1101  CIGAGATASVNSDWHDLWLASPECAAARAEVEELHRTLPGRAVNDDPELA  1150
1151  TRFAASYMTQIKCVLRRTALQFWRSPVYIRAKFFECVACALFVGLSYVGV  1200
1201  NHSVGGAIEAFSSIFMLLLIALAMINQLHVFAYDSRELYEVREAASNTFH  1250
1251  WSVLLLCHAAVENFWSTLCQFMCFICYYWPAQFSGRASHAGFFFFFYVLI  1300
1301  FPLYFVTYGLWILYMSPDVPSASMINSNLFAAMLLFCGILQPREKMPAFW  1350
1351  RRLMYNVSPFTYVVQALVTPLVHNKKVVCNPHEYNIMDPPSGKTCGEFLS  1400
1401  TYMDNNTGYLVNPTATENCQYCPYTVQDQVVAKYNVKWDHRWRNFGFMWA  1450
1451  YICFNIAAMLICYYVVRVKVWSLKSVLNFKKWFNGPRKERHEKDTNIFQT  1500
1501  VPGDENKITKK                                         1511

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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