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

NucPred

Fetching Q9JKC9 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MALRPGAGASGAAGAGTGPGGAGSFMFPVAGGMRPPQGLIPMQQQGFPMV    50
  51  SVMQPNMQGMMGMNYSSQMSQGPIAMQAGIPMGPMPAAGVPFLGQPPFLG   100
 101  MRPAAPQYTPDMQKQFAEEQQKRFEQQQKLLEEERKRRQFEEQKQKLRLL   150
 151  SSVKPKTGEKNRDDALEAIKGNLDGFSRDAKMHPTPASHPKKPDCPTSSH   200
 201  STKTVSPSSAFLGEDEFSGFMQGPVELPTCGPSSTAQPFQSFLPSTPLGQ   250
 251  LHTQKAGAQPLPPGQAPVSFAVHGVHGQIPCLSAASASHSMQKAGPSLEE   300
 301  KLLVSCDISASGQEHIKLSSPEAGHRAVVPGSSKNSPGLMAHNGGAVDGC   350
 351  VSGPTTAVAEKTSDQNLSKEESGVGVFPSQDPVQPRMPPWIYNESLVPDA   400
 401  YKKILETTMTPTGIDTAKLYPILMSSGLPRETLGQIWALANRTTPGKLTK   450
 451  EELYTVLAMVAVTQRGVPAMSPDTLNQFPAAPIPTLSGFPMTLPTPVSQP   500
 501  TAMTSGPAGSIPLSLGQPIMGINLVGPVGGAAAPTSSGFMPAYPSNQVGK   550
 551  TEEDDFQDFQDASKSGSIDDSFTDFQEVPASSKTSNSQHGNSAPSLLIPL   600
 601  PGTKASTDKYAVFKGISAEKPSENPASFGESGDKYSAFRELEPTADSKPL   650
 651  GESFAEFRSTGTDDGFTDFKTADSVSPLEPPTKDSFPSAFASGAAQQTQT   700
 701  QVKTPLNLADLDMFSSVDCSGEKPVPFSAAFSTSKSVSSRPQPAGSAAAP   750
 751  ASLASTKASSLADDFGEFNLFGEYSNPASVGEQDDFADFMAFGNSSIPSE   800
 801  PKADDKYEALREEGSPGALSTSTVEGAHNPPVSSSKYDVFKQLSLEGAGL   850
 851  AIEEFKENTPSTKSDGDFADFHSSKFSSTSSDKSLGEKAVAFRHAKEDSA   900
 901  SVKSLDLPSIGGSSVGKEDSEDALSVQFDMKLADVGGDLKHVMSDSSLDL   950
 951  PTVSGQHPPAAGSALASEDALPETPFPAFASFKDMMPQTTEQKEYESGDF  1000
1001  QDFTRQDMPMVDRSQENTCPSPASSVASHETPKEGADDFGEFQSEKPKIS  1050
1051  KFDFLVANSQSKMKSSEEMIKSELATFDLSVQGSHKRSLSLGDKEISRSS  1100
1101  PSPALEQPFRDRSNTLSERAALPVIRDKYKDLTGEVEENERYAYEWQRCL  1150
1151  GSALDVIKKANDTLNGISSSAVCTEVIQSAQGMEYLLGVVEVYRVTKRVE  1200
1201  LGIKATAVCSEKLQQLLKDIDKVWNNLIGFMSLTTLTPDENSLDFSSCML  1250
1251  RPGIKNAQELACGVCLLNVDSRSRKEETPAEEQPKKAFNSETDSFKLAYG  1300
1301  GHQYHASCANFWINCVEPKPPGLLLPDLL                       1329

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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