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

NucPred

Fetching Q8VI47 from www.uniprot.org...

The NucPred score for your sequence is 0.49 (see score help below)

   1  MDEFCNSTFWNLSLLKSPEADLPLCFEQTVLVWIPLGFLWLLAPWQLYRI    50
  51  YRSRTKRFAITKFYLAKQVFVVCLLILAAIDLSLALTEDTGQATIPPVKY   100
 101  TNPILYLCTWLLVLVIQHCRQCCIQKNSWFLSMFWILSLLCGIFQFQTLI   150
 151  RALLQDSKSNMTYSCLFFVSYGFQIVILILSAFSESSDSTHAPSATASFL   200
 201  SSVTFSWYDSTVLKGYKHPLTIEDVWDIEENLKAKSLTSKFKTIMTKDLQ   250
 251  KARQALQRRLKKSQQSPEGTSHGLTKKQSQSQDVLVLEDSKKKKKKSEAT   300
 301  KDFPKSWLVKALFKTFYVVILKSFILKLAHDILLFLNPQLLKFLIGFVKD   350
 351  PDSYPWVGYIYAILMFSVTLIQSFFLQCYFQFCFVLGMTVRTTIIASVYK   400
 401  KALTLSNLARRQYTIGETVNLMSVDSQKLMDVTNYIHLLWSSVLQIALSI   450
 451  FFLWRELGPSILAGVGLMVLLVPVNGVLATKIRKIQVQNMKNKDKRLKIM   500
 501  NEILSGIKILKYFAWEPSFKEQVNSIRKKELRNLLRFSQLQTILIFILHL   550
 551  TPTLVSVITFSVYVLVDSQNVLNAEKAFTSITLFNILRFPLAMLPMVISS   600
 601  VIQASVSVDRLEQYLGSDDLDLSAIRHVCHFDKAVQFSEASFTWDRDLEA   650
 651  TIQDVNLDIKPGQLVAVVGTVGSGKSSLISAMLGEMENVHGHITIKGSIA   700
 701  YVPQQAWIQNGTIKDNILFGSEYDEKKYQRVIEACALLPDLEMLPGGDMA   750
 751  EIGEKGINLSGGQKHRVSLARATYQDADIYILDDPLSAVDTHVGKHIFNK   800
 801  VVGPNGLLSGKTRILVTHGIHFLPQVDEIVVLGKGTILEKGSYSDLMDKK   850
 851  GVFAKNWKTFMKHSGPEGEATVDNDSEEEDGDCGLIPTVEEIPDDAASLT   900
 901  MRRENSLRRTLSRSSRSGSRRGKSLKSSLKIKSVNALNKKEEVVKGQKLI   950
 951  KKEFVETGKVKFSIYLKYLQAVGWWSLLFIVIFYVLNYVAFIGTNLWLSA  1000
1001  WTSDSEKQNGTDNSPSQRDMRIGVFGALGIAQGIFLLSSSLWSIYACRNA  1050
1051  SKTLHRQLLTNILRAPMSFFDTTPTGRIVNRFAGDISTVDDTLPQTLRSW  1100
1101  LLCFFGIVSTLVMICMATPIFIIIIIPLSILYVSVQVFYVATSRQLRRLD  1150
1151  SVTKSPIYSHFSETVSGLPVIRAFEHQQRFLANSEKQIDTNQKCVFSWIT  1200
1201  SNRWLAIRLELVGNLIVFCSALLLVIYKNSLTGDTVGFVLSNALNITQTL  1250
1251  NWLVRMTSEVETNIVAVERINEYINVDNEAPWVTDKKPPADWPKKGEIQF  1300
1301  NNYQVRYRPELDLVLKGITCNIKSTEKVGVVGRTGAGKSSLTNCLFRILE  1350
1351  SAGGQIIIDGIDIASIGLHDLRGRLTIIPQDPILFSGNLRMNLDPFNKYS  1400
1401  DEEIWRALELAHLKSFVAGLQLGLLHEVTEGGDNLSIGQRQLLCLGRAVL  1450
1451  RKSKILVLDEATAAVDLETDSLIQTTIRNEFSQCTVITIAHRLHTIMDSD  1500
1501  KIMVLDSGKIVEYGSPEELLSNMGPFYLMAKEAGIESVNHTEL         1543

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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