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

NucPred

Fetching Q924A2 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MKPMKKACPGLAGSASGSKSPPATRAKALRRRGAGEGDKPEEEEEAQPQE    50
  51  QAGPEEAEEGEEEEAERDPGAEGTHPELQPNDPTPGLTEDPKGDGEAGRW   100
 101  EPSLSRKTATFKSRAPKKKYVEEHGTGNVGVVGAPEERERTPEDASALGV   150
 151  PPRPPTSTRSSSTDTASEHSADLEDEPPEACGPGPWPSTGTSEGYDLRQL   200
 201  RSQRVLARRGDGLFLPAVVRQVRRSQDLGVQFPGDRALTFYEGVPGGGVD   250
 251  VVLDVTPPPGALMVGTAVCTCVEPGVAAYREGVVVEVATKPAAYKVRLSP   300
 301  GPSSHAGPPGTLPQAQQTLHREPEEAVWVTRSSLRLLRPPWEPGALLRKH   350
 351  PAGPEEEQAEPGPALPPCPSSVEPKQPEDAEVSNISFGSNLGTRCEEGEE   400
 401  KHPPSLGTPVLLPLPPPQLLSPPPKSPAFGGPGRPSEQPSPCQEGSQGGS   450
 451  RSSSVASLEKGAAPAARARTPLTAAQQKYKKGDVVCTPNGIRKKFNGKQW   500
 501  RRLCSRDGCMKESQRRGYCSRHLSMRTKEMEGLADSGPGGTGRPAGVAAR   550
 551  EGSTEFDWGDETSRDSEASSVAARGDSRPRLVAPADLSRFEFDECEAAVM   600
 601  LVSLGSSRSGTPSFSPVSTQSPFSPAPSPSPSPLFGFRPANFSPINASPV   650
 651  IQRTAVRSRHLSASTPKAGVLTPPDLGPHPPPPAPRERHSSGILPTFQTN   700
 701  LTFTVPISPGRRKTELLPHPGTLGASGAGGGGAAPDFPKSDSLDSGVDSV   750
 751  SHTPTPSTPAGFRAVSPAVPFSRSRQPSPLLLLPPPAGLTSDPGPSVRRV   800
 801  PAVQRDSPVIVRNPDVPLPSKFPGEVGTAGEARAGGPGRSCRETPVPPGV   850
 851  ASGKPGLPPPLPAPVPITVPPAAPTAVAQPMPTLGLASSPFQPVAFHPSP   900
 901  AALLPVLVPSSYPSHPAPKKEVIMGRPGTVWTNVEPRSVAVFPWHSLVPF   950
 951  LAPSQPDPSVQPSEAQQPASHPVASNQSKEPAESAAVAHEQPPGGTGGAD  1000
1001  PGRPPGAVCPESPGPGPPLTLGGVDPGKSLPPTTEEEAPGPPGEPRLDSE  1050
1051  TESDHDDAFLSIMSPEIQLPLPPGKRRTQSLSALPKERDSSSEKDGRSPN  1100
1101  KREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGP  1150
1151  KEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKKSSSEAKPASLGLAGGHK  1200
1201  ETRERSMSETGTAAAPGVSSELLSVAAQTLLSSDTKVPGSGPCGAERLHA  1250
1251  VGAPGSARPRAFSHSGVHSLDGGEVDSQALQELTQMVSGPASYSGPKPSP  1300
1301  QYGAPGSFAAPGEGGTLATSGRPPLLPSRASRSQRAASEDMTSDEERMVI  1350
1351  CEEEGDDDVIADDSFGTTDIDLKCKERVTDSESGDSSGEDPEGNKGFGRK  1400
1401  VFSPVIRSSFTHCRPTLDPEPPGPPDPPAAFSKGYGPTPSSSSSPASTSV  1450
1451  SVSTSFSLGSGTFKTQESGQGSTAVPLRPPPPGAGGPATPSKATRFPPTD  1500
1501  SATFRRKRPESVGSLEAPGPSVIAAPPSGGGNLLQTLVLPPSKEDREGTR  1550
1551  VPSAPAPPLAYGAPAAPLCRPAATMVTNVVRPVSSTPVPIASKPFPTSGR  1600
1601  AEASSNDIAGARTEMGTGSRVPGGSPMGVSLVYSDKKSAAAATSPAPHLV  1650
1651  AGPLLGTVGKAPATVTNLLVGTPGYGAPASPAVQFIAQGAPGSATPAGSG  1700
1701  ASTGSGPNGPVPLGILQPGALGKAGGITQVQYILPTLPQQLQVAPAPAPA  1750
1751  PGTKAAAPSGPAPTTSIRFTLPPGTSTNGKVLAATAPTAGIPILQSVPSA  1800
1801  PPPKAQSVSPVQATPSGGSAQLLPGKVLVPLAAPSMSVRGGGAGQPLPLV  1850
1851  SSPFSVPVQNGAQQPSKIIQLTPVPVSTPSGLVPPLSPATMPGPTSQPQK  1900
1901  VLLPSSTRITYVQSAGGHTLPLGTSSACSQTGTVTSYGPTSSVALGFTSL  1950
1951  GPSGPAFVQPLLSGQAPLLAPGQVGVSPVPSPQLPPACTASGGPVITAFY  2000
2001  PGSPAPTSAPLGPPSQAPPSLVYTVATSTTPPAATILPKGPPASATATPA  2050
2051  PTSPFPSATGSMTYSLVAPKAQRPSPKAPQKVKAAIASIPVGSFESGTTG  2100
2101  RPGSTPRQSSDSGVAREPAAPESELEGQPTPPAPPPPTETWPPTARSSPP  2150
2151  PPLPAEERPGTKGPETASKFPSSSSDWRVPGLGLESRGEPPTPPSPAPAT  2200
2201  GPSGSSSGSSEGSSGRAAGDTPERKEVTSSGKKMKVRPPPLKKTFDSVDK  2250
2251  VLSEVDFEERFAELPEFRPEEVLPSPTLQSLATSPRAILGSYRKKRKNST  2300
2301  DLDSAPEDPTSPKRKMRRRSSCSSEPNTPKSAKCEGDIFTFDRTGTETED  2350
2351  VLGELEYEKVPYSSLRRTLDQRRALVMQLFQDHGFFPSAQATAAFQARYA  2400
2401  DIFPSKVCLQLKIREVRQKIMQAATPTEQPPGAEAPLPGPPPTGMAATPV  2450
2451  PTPSPAGGPDPTSPGSDSGTAQVAPPLPPPPEPGPGQPGWEGAPQPSPPP  2500
2501  SGPSTAATGR                                          2510

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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