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

NucPred

Fetching Q92817 from www.uniprot.org...

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

   1  MFKGLSKGSQGKGSPKGSPAKGSPKGSPSRHSRAATQELALLISRMQANA    50
  51  DQVERDILETQKRLQQDRLNSEQSQALQHQQETGRSLKEAEVLLKDLFLD   100
 101  VDKARRLKHPQAEEIEKDIKQLHERVTQECAEYRALYEKMVLPPDVGPRV   150
 151  DWARVLEQKQKQVCAGQYGPGMAELEQQIAEHNILQKEIDAYGQQLRSLV   200
 201  GPDAATIRSQYRDLLKAASWRGQSLGSLYTHLQGCTRQLSALAEQQRRIL   250
 251  QQDWSDLMADPAGVRREYEHFKQHELLSQEQSVNQLEDDGERMVELRHPA   300
 301  VGPIQAHQEALKMEWQNFLNLCICQETQLQHVEDYRRFQEEADSVSQTLA   350
 351  KLNSNLDAKYSPAPGGPPGAPTELLQQLEAEEKRLAVTERATGDLQRRSR   400
 401  DVAPLPQRRNPPQQPLHVDSICDWDSGEVQLLQGERYKLVDNTDPHAWVV   450
 451  QGPGGETKRAPAACFCIPAPDPDAVARASRLASELQALKQKLATVQSRLK   500
 501  ASAVESLRPSQQAPSGSDLANPQAQKLLTQMTRLDGDLGQIERQVLAWAR   550
 551  APLSRPTPLEDLEGRIHSHEGTAQRLQSLGTEKETAQKECEAFLSTRPVG   600
 601  PAALQLPVALNSVKNKFSDVQVLCSLYGEKAKAALDLERQIQDADRVIRG   650
 651  FEATLVQEAPIPAEPGALQERVSELQRQRRELLEQQTCVLRLHRALKASE   700
 701  HACAALQNNFQEFCQDLPRQQRQVRALTDRYHAVGDQLDLREKVVQDAAL   750
 751  TYQQFKNCKDNLSSWLEHLPRSQVRPSDGPSQIAYKLQAQKRLTQEIQSR   800
 801  ERDRATASHLSQALQAALQDYELQADTYRCSLEPTLAVSAPKRPRVAPLQ   850
 851  ESIQAQEKNLAKAYTEVAAAQQQLLQQLEFARKMLEKKELSEDIRRTHDA   900
 901  KQGSESPAQAGRESEALKAQLEEERKRVARVQHELEAQRSQLLQLRTQRP   950
 951  LERLEEKEVVEFYRDPQLEGSLSRVKAQVEEEGKRRAGLQADLEVAAQKV  1000
1001  VQLESKRKTMQPHLLTKEVTQVERDPGLDSQAAQLRIQIQQLRGEDAVIS  1050
1051  ARLEGLKKELLALEKREVDVKEKVVVKEVVKVEKNLEMVKAAQALRLQME  1100
1101  EDAARRKQAEEAVAKLQARIEDLERAISSVEPKVIVKEVKKVEQDPGLLQ  1150
1151  ESSRLRSLLEEERTKNATLARELSDLHSKYSVVEKQRPKVQLQERVHEIF  1200
1201  QVDPETEQEITRLKAKLQEMAGKRSGVEKEVEKLLPDLEVLRAQKPTVEY  1250
1251  KEVTQEVVRHERSPEVLREIDRLKAQLNELVNSHGRSQEQLIRLQGERDE  1300
1301  WRRERAKVETKTVSKEVVRHEKDPVLEKEAERLRQEVREAAQKRRAAEDA  1350
1351  VYELQSKRLLLERRKPEEKVVVQEVVVTQKDPKLREEHSRLSGSLDEEVG  1400
1401  RRRQLELEVQQLRAGVEEQEGLLSFQEDRSKKLAVERELRQLTLRIQELE  1450
1451  KRPPTVQEKIIMEEVVKLEKDPDLEKSTEALRWDLDQEKTQVTELNRECK  1500
1501  NLQVQIDVLQKAKSQEKTIYKEVIRVQKDRVLEDERARVWEMLNRERTAR  1550
1551  QAREEEARRLRERIDRAETLGRTWSREESELQRARDQADQECGRLQQELR  1600
1601  ALERQKQQQTLQLQEESKLLSQKTESERQKAAQRGQELSRLEAAILREKD  1650
1651  QIYEKERTLRDLHAKVSREELSQETQTRETNLSTKISILEPETGKDMSPY  1700
1701  EAYKRGIIDRGQYLQLQELECDWEEVTTSGPCGEESVLLDRKSGKQYSIE  1750
1751  AALRCRRISKEEYHLYKDGHLPISEFALLVAGETKPSSSLSIGSIISKSP  1800
1801  LASPAPQSTSFFSPSFSLGLGDDSFPIAGIYDTTTDNKCSIKTAVAKNML  1850
1851  DPITGQKLLEAQAATGGIVDLLSRERYSVHKAMERGLIENTSTQRLLNAQ  1900
1901  KAFTGIEDPVTKKRLSVGEAVQKGWMPRESVLPHLQVQHLTGGLIDPKRT  1950
1951  GRIPIQQALLSGMISEELAQLLQDESSYEKDLTDPISKERLSYKEAMGRC  2000
2001  RKDPLSGLLLLPAALEGYRCYRSASPTVPRSLR                   2033

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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