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

NucPred

Fetching P38800 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MTRDSKKKHHWGTAFLRTIGVKRKHKKDRNFLNNTTGENVSTTASAERFR    50
  51  RVGGNPDIPSLLKPETFTESPAKGSQKAAASSLAHSQGVFNIPIVIDPME   100
 101  TNRLEKTNTNLTAGSLKGRFQDGNSNSNSVPSLSVQALEKEKLQSGKREG   150
 151  SSNQAEEKTPDGHDEHTAFETFLSFAHNAVSHIPKINVQDADNGTISRNE   200
 201  PKDRKKNSSNISGALSENSTNNKNTSSTKESDGPFLKNLDNILAASKSST   250
 251  PSNQQLNTTEAGSKSKPSSLSRLAFGNLKGHIHSNSHSSSNAISGDDTSL   300
 301  DDTRKMTDDMARKVVFEPIRHSHDKPTPGVGNLKLEHFDDSQATLEGLEA   350
 351  MSAESLPEADHLDSRGPVQQSNLERKTVPSKWSVVSSSTTDGVKPRRRAK   400
 401  SMISAMADKQNTSSDVLQDCKKRLSFNSSNGLTNNDPEYEDREPREMSKK   450
 451  FLNRRSFSPGSISMGMKVLPSTALKYSLNKVKNSTDIASTIIPRPSMSNG   500
 501  RPSSGLRRSSSKSFSSTPVNIIEPSEENGRQSSIRIKGVEYASEKKDAEF   550
 551  HAIFKDSGVSPNERLILDHSCALSRDILLQGRMYISDQHIGFYSNILGWV   600
 601  STVFIPFKTIVQIEKRATAGIFPNGIVIDTLHTKYTFASFTSRDATYDLI   650
 651  TEVWNQIILGKRFRSNSNNTNSSSNSISDDENDDYDDDYDDYGDDDDDLY   700
 701  DNSNNISDSTDMTSSVSIGKPEDLPMPLQTDTPYGTGIPPLGPKIHSPTE   750
 751  TVYKPAPNEKLVNESTIHASLGRVVNILFGKDVSYIMAILKAQKNSDISP   800
 801  IPVLVDSPTVSEGKKRDYSYVKTTPGAIGPGKTKCMITETIQHFNLEEYV   850
 851  QVLQTTKTPDVPSGNSFYVRTVYLLSWANNNETKLKLYVSVEWTGKSLIK   900
 901  SPIEKGTFDGVTDATKILVEELGNILTRSATKRKRSSKENTVTVSTLPKM   950
 951  EPSSHAPTEPDIQKDKDDSIIRENENIPAPLGTVVQLLFGSNTEYMQKVI  1000
1001  TRDKNNVNVETIPKFTPSLVEGGSRHYEYTKKLNNSIGPKQTKCLLTESI  1050
1051  EHMDINNYVLVTQTTKTPDVPSGSNFAVESKIFLFWGQHDTTNMTVITKI  1100
1101  NWTSKSFLKGAIEKGSVEGQKVSVDYMLSELRDIISRAKSKKPVKKVMKS  1150
1151  HDKHRPFHSKVEQKSSESRKSDDNKDILTHILDFVQNNFSSEIFMNKLLS  1200
1201  PQKLFLILGLTIMLFWSPRLHVFQEKNNLQIIKPGRLLIDGQEYNYVPSF  1250
1251  GTLYNSYENAISSKKKRENVNYARDKSPIVGRESDIWDWISNRGSAISPR  1300
1301  GRAMLRNDDEHKLQQLSESIKITEMQLNHMKTMLDNIERDANDLS       1345

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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